Bio

Academic Appointments


Administrative Appointments


  • Director, NIH Center of Excellence in Genomic Science at Stanford: The Genomic Basis of Vertebrate Diversity (2007 - 2012)

Honors & Awards


  • Scholar in Biomedical Research, Lucille P. Markey Foundation (1989 to 1996)
  • Researcher, Howard Hughes Medical Institute (1997 to present)
  • Fellow, American Academy of Arts and Sciences (2005)
  • Conklin Medal, Society for Developmental Biology (2009)
  • Member, National Academy of Sciences (2011)

Professional Education


  • Ph.D., MIT, Biology (1986)
  • B.S., Yale, Biology (1981)

Community and International Work


  • Stickleback Genome Project and Summer Training Course, Stanford

    Topic

    see http://cegs.stanford.edu/

    Partnering Organization(s)

    NIH Human Genome Research Institute

    Populations Served

    Worldwide research community in vertebrate genetics

    Location

    International

    Ongoing Project

    Yes

    Opportunities for Student Involvement

    No

Research & Scholarship

Current Research and Scholarly Interests


Naturally occurring species show spectacular differences in morphology, physiology, lifestyle, and behavior. They also differ in disease susceptibility and life span. Although the genomes of many organisms have now been completely sequenced, we still know relatively little about the specific DNA sequence changes that underlie interesting species-specific traits. My laboratory is using a combination of genetic and genomic approaches to identify the detailed molecular mechanisms that control evolutionary change in vertebrates, with a focus on five fundamental questions:

1. Are new evolutionary traits controlled by countless genetic differences of small effect, or by a few genetic changes with large effects?

2. What specific genes have changed to produce interesting evolutionary differences seen in nature?

3. What kinds of mutations have occurred in these genes (e.g., dominant or recessive, coding or regulatory, preexisting or de novo)?

4. How predictable is evolution? If you know how evolution has occurred in one population, is it possible to predict the genes and mutations that also underlie the same trait in different populations?

5. How has evolution produced the unique characteristics of humans?

We study these questions using a variety of methods in  mice, sticklebacks, and people.

Mice are often the best system available for asking detailed mechanistic questions in mammals, or testing the phenotypic effects of particular sequence changes seen in other species. We have used classical genetics in mice to identify fundamental pathways that control formation and patterning of cartilage, bone, and joints. We also make extensive use of mice identifying the regulatory mechanisms that lay out expression of key developmental control genes, with the ultimate aim of identifying how vertebrate morphology itself is encoded in the genome.

Sticklebacks offer an unusually powerful system for studying the molecular basis of evolutionary change in naturally occurring species.  Our lab has pioneered the development of a large number of new  genetic and genomic resources for the fish, and has worked with Hudson Alpha Institute and the Broad Institute to develop a mapped, whole genome sequence assembly for sticklebacks.  Using these new tools, we have now successfully identified both the molecular mechanisms that control repeated evolution of armor plate patterning, pelvic reduction, and skin color changes in nature. Our studies show that big evolutionary changes can be controlled by single chromosome regions.   The big changes are controlled by alterations in major developmental control genes (key signaling molecules and transcription factors).  Although null mutations in these genes are typically deleterious or lethal, sticklebacks have made regulatory alterations in these genes that produce large morphological effects in particular tissues, while preserving overall viability.  Interestingly, the same genes are used repeatedly when similar phenotypes evolve in different populations, revealing a surprising commonality to the molecular mechanisms that control rapid evolutionary change in diverse organisms.

Although many of our studies have begun in mice or sticklebacks,  the genes and mechanisms that we  have   also turn out to control major differences in human morphology, human arthritis and cancer incidence, and differences in skin color in billions of people around the world.  Building on this work, we  have now  begun a variety of projects to identify other mechanisms responsible for interesting evolutionary traits in humans.  Although we are still far from knowing the detailed molecular basis of most human traits, we are optimistic that many aspects of this  problem can now be studied both computationally and experimentally, and will provide new insights into how humans have evolved and adapted to many environments around the world.

Teaching

2016-17 Courses


Stanford Advisees


Publications

All Publications


  • Evolving New Skeletal Traits by cis-Regulatory Changes in Bone Morphogenetic Proteins CELL Indjeian, V. B., Kingman, G. A., Jones, F. C., Guenther, C. A., Grimwood, J., Schmutz, J., Myers, R. M., Kingsley, D. M. 2016; 164 (1-2): 45-56

    Abstract

    Changes in bone size and shape are defining features of many vertebrates. Here we use genetic crosses and comparative genomics to identify specific regulatory DNA alterations controlling skeletal evolution. Armor bone-size differences in sticklebacks map to a major effect locus overlapping BMP family member GDF6. Freshwater fish express more GDF6 due in part to a transposon insertion, and transgenic overexpression of GDF6 phenocopies evolutionary changes in armor-plate size. The human GDF6 locus also has undergone distinctive regulatory evolution, including complete loss of an enhancer that is otherwise highly conserved between chimps and other mammals. Functional tests show that the ancestral enhancer drives expression in hindlimbs but not forelimbs, in locations that have been specifically modified during the human transition to bipedalism. Both gain and loss of regulatory elements can localize BMP changes to specific anatomical locations, providing a flexible regulatory basis for evolving species-specific changes in skeletal form.

    View details for DOI 10.1016/j.cell.2015.12.007

    View details for Web of Science ID 000368339300008

    View details for PubMedID 26774823

  • A molecular basis for classic blond hair color in Europeans. Nature genetics Guenther, C. A., Tasic, B., Luo, L., Bedell, M. A., Kingsley, D. M. 2014; 46 (7): 748-752

    Abstract

    Hair color differences are among the most obvious examples of phenotypic variation in humans. Although genome-wide association studies (GWAS) have implicated multiple loci in human pigment variation, the causative base-pair changes are still largely unknown. Here we dissect a regulatory region of the KITLG gene (encoding KIT ligand) that is significantly associated with common blond hair color in northern Europeans. Functional tests demonstrate that the region contains a regulatory enhancer that drives expression in developing hair follicles. This enhancer contains a common SNP (rs12821256) that alters a binding site for the lymphoid enhancer-binding factor 1 (LEF1) transcription factor, reducing LEF1 responsiveness and enhancer activity in cultured human keratinocytes. Mice carrying ancestral or derived variants of the human KITLG enhancer exhibit significant differences in hair pigmentation, confirming that altered regulation of an essential growth factor contributes to the classic blond hair phenotype found in northern Europeans.

    View details for DOI 10.1038/ng.2991

    View details for PubMedID 24880339

  • The genomic basis of adaptive evolution in threespine sticklebacks. Nature Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., Swofford, R., Pirun, M., Zody, M. C., White, S., Birney, E., Searle, S., Schmutz, J., Grimwood, J., Dickson, M. C., Myers, R. M., Miller, C. T., Summers, B. R., Knecht, A. K., Brady, S. D., Zhang, H., Pollen, A. A., Howes, T., Amemiya, C., Baldwin, J., Bloom, T., Jaffe, D. B., Nicol, R., Wilkinson, J., Lander, E. S., Di Palma, F., Lindblad-Toh, K., Kingsley, D. M. 2012; 484 (7392): 55-61

    Abstract

    Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.

    View details for DOI 10.1038/nature10944

    View details for PubMedID 22481358

  • Human-specific loss of regulatory DNA and the evolution of human-specific traits NATURE McLean, C. Y., Reno, P. L., Pollen, A. A., Bassan, A. I., Capellini, T. D., Guenther, C., Indjeian, V. B., Lim, X., Menke, D. B., Schaar, B. T., Wenger, A. M., Bejerano, G., Kingsley, D. M. 2011; 471 (7337): 216-219

    Abstract

    Humans differ from other animals in many aspects of anatomy, physiology, and behaviour; however, the genotypic basis of most human-specific traits remains unknown. Recent whole-genome comparisons have made it possible to identify genes with elevated rates of amino acid change or divergent expression in humans, and non-coding sequences with accelerated base pair changes. Regulatory alterations may be particularly likely to produce phenotypic effects while preserving viability, and are known to underlie interesting evolutionary differences in other species. Here we identify molecular events particularly likely to produce significant regulatory changes in humans: complete deletion of sequences otherwise highly conserved between chimpanzees and other mammals. We confirm 510 such deletions in humans, which fall almost exclusively in non-coding regions and are enriched near genes involved in steroid hormone signalling and neural function. One deletion removes a sensory vibrissae and penile spine enhancer from the human androgen receptor (AR) gene, a molecular change correlated with anatomical loss of androgen-dependent sensory vibrissae and penile spines in the human lineage. Another deletion removes a forebrain subventricular zone enhancer near the tumour suppressor gene growth arrest and DNA-damage-inducible, gamma (GADD45G), a loss correlated with expansion of specific brain regions in humans. Deletions of tissue-specific enhancers may thus accompany both loss and gain traits in the human lineage, and provide specific examples of the kinds of regulatory alterations and inactivation events long proposed to have an important role in human evolutionary divergence.

    View details for DOI 10.1038/nature09774

    View details for Web of Science ID 000288170200037

    View details for PubMedID 21390129

  • Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer SCIENCE Chan, Y. F., Marks, M. E., Jones, F. C., Villarreal, G., Shapiro, M. D., Brady, S. D., Southwick, A. M., Absher, D. M., Grimwood, J., Schmutz, J., Myers, R. M., Petrov, D., Jonsson, B., Schluter, D., Bell, M. A., Kingsley, D. M. 2010; 327 (5963): 302-305

    Abstract

    The molecular mechanisms underlying major phenotypic changes that have evolved repeatedly in nature are generally unknown. Pelvic loss in different natural populations of threespine stickleback fish has occurred through regulatory mutations deleting a tissue-specific enhancer of the Pituitary homeobox transcription factor 1 (Pitx1) gene. The high prevalence of deletion mutations at Pitx1 may be influenced by inherent structural features of the locus. Although Pitx1 null mutations are lethal in laboratory animals, Pitx1 regulatory mutations show molecular signatures of positive selection in pelvic-reduced populations. These studies illustrate how major expression and morphological changes can arise from single mutational leaps in natural populations, producing new adaptive alleles via recurrent regulatory alterations in a key developmental control gene.

    View details for DOI 10.1126/science.1182213

    View details for Web of Science ID 000273629700034

    View details for PubMedID 20007865

  • Shaping Skeletal Growth by Modular Regulatory Elements in the Bmp5 Gene PLOS GENETICS Guenther, C., Pantalena-Filho, L., Kingsley, D. M. 2008; 4 (12)

    Abstract

    Cartilage and bone are formed into a remarkable range of shapes and sizes that underlie many anatomical adaptations to different lifestyles in vertebrates. Although the morphological blueprints for individual cartilage and bony structures must somehow be encoded in the genome, we currently know little about the detailed genomic mechanisms that direct precise growth patterns for particular bones. We have carried out large-scale enhancer surveys to identify the regulatory architecture controlling developmental expression of the mouse Bmp5 gene, which encodes a secreted signaling molecule required for normal morphology of specific skeletal features. Although Bmp5 is expressed in many skeletal precursors, different enhancers control expression in individual bones. Remarkably, we show here that different enhancers also exist for highly restricted spatial subdomains along the surface of individual skeletal structures, including ribs and nasal cartilages. Transgenic, null, and regulatory mutations confirm that these anatomy-specific sequences are sufficient to trigger local changes in skeletal morphology and are required for establishing normal growth rates on separate bone surfaces. Our findings suggest that individual bones are composite structures whose detailed growth patterns are built from many smaller lineage and gene expression domains. Individual enhancers in BMP genes provide a genomic mechanism for controlling precise growth domains in particular cartilages and bones, making it possible to separately regulate skeletal anatomy at highly specific locations in the body.

    View details for DOI 10.1371/journal.pgen.1000308

    View details for Web of Science ID 000263667900023

    View details for PubMedID 19096511

  • Role of the mouse ank gene in control of tissue calcification and arthritis SCIENCE Ho, A. M., Johnson, M. D., Kingsley, D. M. 2000; 289 (5477): 265-270

    Abstract

    Mutation at the mouse progressive ankylosis (ank) locus causes a generalized, progressive form of arthritis accompanied by mineral deposition, formation of bony outgrowths, and joint destruction. Here, we show that the ank locus encodes a multipass transmembrane protein (ANK) that is expressed in joints and other tissues and controls pyrophosphate levels in cultured cells. A highly conserved gene is present in humans and other vertebrates. These results identify ANK-mediated control of pyrophosphate levels as a possible mechanism regulating tissue calcification and susceptibility to arthritis in higher animals.

    View details for Web of Science ID 000088169400033

    View details for PubMedID 10894769

  • A distinct regulatory region of the Bmp5 locus activates gene expression following adult bone fracture or soft tissue injury. Bone Guenther, C. A., Wang, Z., Li, E., Tran, M. C., Logan, C. Y., Nusse, R., Pantalena-Filho, L., Yang, G. P., Kingsley, D. M. 2015; 77: 31-41

    Abstract

    Bone morphogenetic proteins (BMPs) are key signaling molecules required for normal development of bones and other tissues. Previous studies have shown that null mutations in the mouse Bmp5 gene alter the size, shape and number of multiple bone and cartilage structures during development. Bmp5 mutations also delay healing of rib fractures in adult mutants, suggesting that the same signals used to pattern embryonic bone and cartilage are also reused during skeletal regeneration and repair. Despite intense interest in BMPs as agents for stimulating bone formation in clinical applications, little is known about the regulatory elements that control developmental or injury-induced BMP expression. To compare the DNA sequences that activate gene expression during embryonic bone formation and following acute injuries in adult animals, we assayed regions surrounding the Bmp5 gene for their ability to stimulate lacZ reporter gene expression in transgenic mice. Multiple genomic fragments, distributed across the Bmp5 locus, collectively coordinate expression in discrete anatomic domains during normal development, including in embryonic ribs. In contrast, a distinct regulatory region activated expression following rib fracture in adult animals. The same injury control region triggered gene expression in mesenchymal cells following tibia fracture, in migrating keratinocytes following dorsal skin wounding, and in regenerating epithelial cells following lung injury. The Bmp5 gene thus contains an "injury response" control region that is distinct from embryonic enhancers, and that is activated by multiple types of injury in adult animals.

    View details for DOI 10.1016/j.bone.2015.04.010

    View details for PubMedID 25886903

  • A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA ELIFE O'Brown, N. M., Summers, B. R., Jones, F. C., Brady, S. D., Kingsley, D. M. 2015; 4
  • Mesenchymal cells. Defining a mesenchymal progenitor niche at single-cell resolution. Science Kumar, M. E., Bogard, P. E., Espinoza, F. H., Menke, D. B., Kingsley, D. M., Krasnow, M. A. 2014; 346 (6211)

    Abstract

    Most vertebrate organs are composed of epithelium surrounded by support and stromal tissues formed from mesenchyme cells, which are not generally thought to form organized progenitor pools. Here, we use clonal cell labeling with multicolor reporters to characterize individual mesenchymal progenitors in the developing mouse lung. We observe a diversity of mesenchymal progenitor populations with different locations, movements, and lineage boundaries. Airway smooth muscle (ASM) progenitors map exclusively to mesenchyme ahead of budding airways. Progenitors recruited from these tip pools differentiate into ASM around airway stalks; flanking stalk mesenchyme can be induced to form an ASM niche by a lateral bud or by an airway tip plus focal Wnt signal. Thus, mesenchymal progenitors can be organized into localized and carefully controlled domains that rival epithelial progenitor niches in regulatory sophistication.

    View details for DOI 10.1126/science.1258810

    View details for PubMedID 25395543

  • The phosphate exporter xpr1b is required for differentiation of tissue-resident macrophages. Cell reports Meireles, A. M., Shiau, C. E., Guenther, C. A., Sidik, H., Kingsley, D. M., Talbot, W. S. 2014; 8 (6): 1659-1667

    Abstract

    Phosphate concentration is tightly regulated at the cellular and organismal levels. The first metazoan phosphate exporter, XPR1, was recently identified, but its in vivo function remains unknown. In a genetic screen, we identified a mutation in a zebrafish ortholog of human XPR1, xpr1b. xpr1b mutants lack microglia, the specialized macrophages that reside in the brain, and also displayed an osteopetrotic phenotype characteristic of defects in osteoclast function. Transgenic expression studies indicated that xpr1b acts autonomously in developing macrophages. xpr1b mutants display no gross developmental defects that may arise from phosphate imbalance. We constructed a targeted mutation of xpr1a, a duplicate of xpr1b in the zebrafish genome, to determine whether Xpr1a and Xpr1b have redundant functions. Single mutants for xpr1a were viable, and double mutants for xpr1b;xpr1a were similar to xpr1b single mutants. Our genetic analysis reveals a specific role for the phosphate exporter Xpr1 in the differentiation of tissue macrophages.

    View details for DOI 10.1016/j.celrep.2014.08.018

    View details for PubMedID 25220463

  • Evolved tooth gain in sticklebacks is associated with a cis-regulatory allele of Bmp6. Proceedings of the National Academy of Sciences of the United States of America Cleves, P. A., Ellis, N. A., Jimenez, M. T., Nunez, S. M., Schluter, D., Kingsley, D. M., Miller, C. T. 2014; 111 (38): 13912-13917

    Abstract

    Developmental genetic studies of evolved differences in morphology have led to the hypothesis that cis-regulatory changes often underlie morphological evolution. However, because most of these studies focus on evolved loss of traits, the genetic architecture and possible association with cis-regulatory changes of gain traits are less understood. Here we show that a derived benthic freshwater stickleback population has evolved an approximate twofold gain in ventral pharyngeal tooth number compared with their ancestral marine counterparts. Comparing laboratory-reared developmental time courses of a low-toothed marine population and this high-toothed benthic population reveals that increases in tooth number and tooth plate area and decreases in tooth spacing arise at late juvenile stages. Genome-wide linkage mapping identifies largely separate sets of quantitative trait loci affecting different aspects of dental patterning. One large-effect quantitative trait locus controlling tooth number fine-maps to a genomic region containing an excellent candidate gene, Bone morphogenetic protein 6 (Bmp6). Stickleback Bmp6 is expressed in developing teeth, and no coding changes are found between the high- and low-toothed populations. However, quantitative allele-specific expression assays of Bmp6 in developing teeth in F1 hybrids show that cis-regulatory changes have elevated the relative expression level of the freshwater benthic Bmp6 allele at late, but not early, stages of stickleback development. Collectively, our data support a model where a late-acting cis-regulatory up-regulation of Bmp6 expression underlies a significant increase in tooth number in derived benthic sticklebacks.

    View details for DOI 10.1073/pnas.1407567111

    View details for PubMedID 25205810

  • Genetics of ecological divergence during speciation NATURE Arnegard, M. E., Mcgee, M. D., Matthews, B., Marchinko, K. B., Conte, G. L., Kabir, S., Bedford, N., Bergek, S., Chan, Y. F., Jones, F. C., Kingsley, D. M., Peichel, C. L., Schluter, D. 2014; 511 (7509): 307-?

    Abstract

    Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Although this process is a major generator of biodiversity, its genetic basis is still poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces the growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but depend on the ecological context.

    View details for DOI 10.1038/nature13301

    View details for Web of Science ID 000338992200027

    View details for PubMedID 24909991

  • Efficient Imputation of Missing Markers in Low-Coverage Genotyping-by-Sequencing Data from Multiparental Crosses GENETICS Miller, C. T., Glazer, A. M., Summers, B. R., Blackman, B. K., Norman, A. R., Shapiro, M. D., Cole, B. L., Peichel, C. L., Schluter, D., Kingsley, D. M. 2014; 197 (1): 405-?
  • A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA. eLife O'Brown, N. M., Summers, B. R., Jones, F. C., Brady, S. D., Kingsley, D. M. 2014; 4

    Abstract

    Armor plate changes in sticklebacks are a classic example of repeated adaptive evolution. Previous studies identified ectodysplasin (EDA) gene as the major locus controlling recurrent plate loss in freshwater fish, though the causative DNA alterations were not known. Here we show that freshwater EDA alleles have cis-acting regulatory changes that reduce expression in developing plates and spines. An identical T → G base pair change is found in EDA enhancers of divergent low-plated fish. Recreation of the T → G change in a marine enhancer strongly reduces expression in posterior armor plates. Bead implantation and cell culture experiments show that Wnt signaling strongly activates the marine EDA enhancer, and the freshwater T → G change reduces Wnt responsiveness. Thus parallel evolution of low-plated sticklebacks has occurred through a shared DNA regulatory change, which reduces the sensitivity of an EDA enhancer to Wnt signaling, and alters expression in developing armor plates while preserving expression in other tissues.

    View details for DOI 10.7554/eLife.05290

    View details for PubMedID 25629660

  • Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide single nucleotide polymorphism genotyping MOLECULAR ECOLOGY Deagle, B. E., Jones, F. C., Absher, D. M., Kingsley, D. M., Reimchen, T. E. 2013; 22 (7): 1917-1932

    Abstract

    Threespine stickleback populations are model systems for studying adaptive evolution and the underlying genetics. In lakes on the Haida Gwaii archipelago (off western Canada), stickleback have undergone a remarkable local radiation and show phenotypic diversity matching that seen throughout the species distribution. To provide a historical context for this radiation, we surveyed genetic variation at >1000 single nucleotide polymorphism (SNP) loci in stickleback from over 100 populations. SNPs included markers evenly distributed throughout genome and candidate SNPs tagging adaptive genomic regions. Based on evenly distributed SNPs, the phylogeographic pattern differs substantially from the disjunct pattern previously observed between two highly divergent mtDNA lineages. The SNP tree instead shows extensive within watershed population clustering and different watersheds separated by short branches deep in the tree. These data are consistent with separate colonizations of most watersheds, despite underlying genetic connections between some independent drainages. This supports previous suppositions that morphological diversity observed between watersheds has been shaped independently, with populations exhibiting complete loss of lateral plates and giant size each occurring in several distinct clades. Throughout the archipelago, we see repeated selection of SNPs tagging candidate freshwater adaptive variants at several genomic regions differentiated between marine-freshwater populations on a global scale (e.g. EDA, Na/K ATPase). In estuarine sites, both marine and freshwater allelic variants were commonly detected. We also found typically marine alleles present in a few freshwater lakes, especially those with completely plated morphology. These results provide a general model for postglacial colonization of freshwater habitat by sticklebacks and illustrate the tremendous potential of genome-wide SNP data sets hold for resolving patterns and processes underlying recent adaptive divergences.

    View details for DOI 10.1111/mec.12215

    View details for Web of Science ID 000316575800012

    View details for PubMedID 23452150

  • Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements DEVELOPMENTAL BIOLOGY Infante, C. R., Park, S., Mihala, A. G., Kingsley, D. M., Menke, D. B. 2013; 374 (1): 234-244

    Abstract

    Extensive functional analyses have demonstrated that the pituitary homeodomain transcription factor Pitx1 plays a critical role in specifying hindlimb morphology in vertebrates. However, much less is known regarding the target genes and cis-regulatory elements through which Pitx1 acts. Earlier studies suggested that the hindlimb transcription factors Tbx4, HoxC10, and HoxC11 might be transcriptional targets of Pitx1, but definitive evidence for direct regulatory interactions has been lacking. Using ChIP-Seq on embryonic mouse hindlimbs, we have pinpointed the genome-wide location of Pitx1 binding sites during mouse hindlimb development and identified potential gene targets for Pitx1. We determined that Pitx1 binding is significantly enriched near genes involved in limb morphogenesis, including Tbx4, HoxC10, and HoxC11. Notably, Pitx1 is bound to the previously identified HLEA and HLEB hindlimb enhancers of the Tbx4 gene and to a newly identified Tbx2 hindlimb enhancer. Moreover, Pitx1 binding is significantly enriched on hindlimb relative to forelimb-specific cis-regulatory features that are differentially marked by H3K27ac. However, our analysis revealed that Pitx1 also strongly associates with many functionally verified limb enhancers that exhibit similar levels of activity in the embryonic mesenchyme of forelimbs and hindlimbs. We speculate that Pitx1 influences hindlimb morphology both through the activation of hindlimb-specific enhancers as well as through the hindlimb-specific modulation of enhancers that are active in both sets of limbs.

    View details for DOI 10.1016/j.ydbio.2012.11.017

    View details for Web of Science ID 000314145300021

    View details for PubMedID 23201014

  • A penile spine/vibrissa enhancer sequence is missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae. PloS one Reno, P. L., McLean, C. Y., Hines, J. E., Capellini, T. D., Bejerano, G., Kingsley, D. M. 2013; 8 (12)

    Abstract

    Previous studies show that humans have a large genomic deletion downstream of the Androgen Receptor gene that eliminates an ancestral mammalian regulatory enhancer that drives expression in developing penile spines and sensory vibrissae. Here we use a combination of large-scale sequence analysis and PCR amplification to demonstrate that the penile spine/vibrissa enhancer is missing in all humans surveyed and in the Neandertal and Denisovan genomes, but is present in DNA samples of chimpanzees and bonobos, as well as in multiple other great apes and primates that maintain some form of penile integumentary appendage and facial vibrissae. These results further strengthen the association between the presence of the penile spine/vibrissa enhancer and the presence of penile spines and macro- or micro- vibrissae in non-human primates as well as show that loss of the enhancer is both a distinctive and characteristic feature of the human lineage.

    View details for DOI 10.1371/journal.pone.0084258

    View details for PubMedID 24367647

  • A "Forward Genomics'' Approach Links Genotype to Phenotype using Independent Phenotypic Losses among Related Species CELL REPORTS Hiller, M., Schaar, B. T., Indjeian, V. B., Kingsley, D. M., Hagey, L. R., Bejerano, G. 2012; 2 (4): 817-823

    Abstract

    Genotype-phenotype mapping is hampered by countless genomic changes between species. We introduce a computational "forward genomics" strategy that-given only an independently lost phenotype and whole genomes-matches genomic and phenotypic loss patterns to associate specific genomic regions with this phenotype. We conducted genome-wide screens for two metabolic phenotypes. First, our approach correctly matches the inactivated Gulo gene exactly with the species that lost the ability to synthesize vitamin C. Second, we attribute naturally low biliary phospholipid levels in guinea pigs and horses to the inactivated phospholipid transporter Abcb4. Human ABCB4 mutations also result in low phospholipid levels but lead to severe liver disease, suggesting compensatory mechanisms in guinea pig and horse. Our simulation studies, counts of independent changes in existing phenotype surveys, and the forthcoming availability of many new genomes all suggest that forward genomics can be applied to many phenotypes, including those relevant for human evolution and disease.

    View details for DOI 10.1016/j.celrep.2012.08.032

    View details for Web of Science ID 000314455600014

    View details for PubMedID 23022484

  • Genetic Architecture of Variation in the Lateral Line Sensory System of Threespine Sticklebacks G3-GENES GENOMES GENETICS Wark, A. R., Mills, M. G., Dang, L., Chan, Y. F., Jones, F. C., Brady, S. D., Absher, D. M., Grimwood, J., Schmutz, J., Myers, R. M., Kingsley, D. M., Peichel, C. L. 2012; 2 (9): 1047-1056

    Abstract

    Vertebrate sensory systems have evolved remarkable diversity, but little is known about the underlying genetic mechanisms. The lateral line sensory system of aquatic vertebrates is a promising model for genetic investigations of sensory evolution because there is extensive variation within and between species, and this variation is easily quantified. In the present study, we compare the lateral line sensory system of threespine sticklebacks (Gasterosteus aculeatus) from an ancestral marine and a derived benthic lake population. We show that lab-raised individuals from these populations display differences in sensory neuromast number, neuromast patterning, and groove morphology. Using genetic linkage mapping, we identify regions of the genome that influence different aspects of lateral line morphology. Distinct loci independently affect neuromast number on different body regions, suggesting that a modular genetic structure underlies the evolution of peripheral receptor number in this sensory system. Pleiotropy and/or tight linkage are also important, as we identify a region on linkage group 21 that affects multiple aspects of lateral line morphology. Finally, we detect epistasis between a locus on linkage group 4 and a locus on linkage group 21; interactions between these loci contribute to variation in neuromast pattern. Our results reveal a complex genetic architecture underlying the evolution of the stickleback lateral line sensory system. This study further uncovers a genetic relationship between sensory morphology and non-neural traits (bony lateral plates), creating an opportunity to investigate morphological constraints on sensory evolution in a vertebrate model system.

    View details for DOI 10.1534/g3.112.003079

    View details for Web of Science ID 000312456100008

    View details for PubMedID 22973542

  • GENETIC SIGNATURE OF ADAPTIVE PEAK SHIFT IN THREESPINE STICKLEBACK EVOLUTION Rogers, S. M., Tamkee, P., Summers, B., Balabahadra, S., Marks, M., Kingsley, D. M., Schluter, D. 2012; 66 (8): 2439-2450

    Abstract

    Transition of an evolving population to a new adaptive optimum is predicted to leave a signature in the distribution of effect sizes of fixed mutations. If they affect many traits (are pleiotropic), large effect mutations should contribute more when a population evolves to a farther adaptive peak than to a nearer peak. We tested this prediction in wild threespine stickleback fish (Gasterosteus aculeatus) by comparing the estimated frequency of large effect genetic changes underlying evolution as the same ancestor adapted to two lake types since the end of the ice age. A higher frequency of large effect genetic changes (quantitative trait loci) contributed to adaptive evolution in populations that adapted to lakes representing a more distant optimum than to lakes in which the optimum phenotype was nearer to the ancestral state. Our results also indicate that pleiotropy, not just optimum overshoot, contributes to this difference. These results suggest that a series of adaptive improvements to a new environment leaves a detectable mark in the genome of wild populations. Although not all assumptions of the theory are likely met in natural systems, the prediction may be robust enough to the complexities of natural environments to be useful when forecasting adaptive responses to large environmental changes.

    View details for DOI 10.1111/j.1558-5646.2012.01622.x

    View details for Web of Science ID 000306804100008

    View details for PubMedID 22834743

  • Population genomics of parallel phenotypic evolution in stickleback across stream-lake ecological transitions PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Deagle, B. E., Jones, F. C., Chan, Y. F., Absher, D. M., Kingsley, D. M., Reimchen, T. E. 2012; 279 (1732): 1277-1286

    Abstract

    Understanding the genetics of adaptation is a central focus in evolutionary biology. Here, we use a population genomics approach to examine striking parallel morphological divergences of parapatric stream-lake ecotypes of threespine stickleback fish in three watersheds on the Haida Gwaii archipelago, western Canada. Genome-wide variation at greater than 1000 single nucleotide polymorphism loci indicate separate origin of giant lake and small-bodied stream fish within each watershed (mean F(ST) between watersheds = 0.244 and within = 0.114). Genome scans within watersheds identified a total of 21 genomic regions that are highly differentiated between ecotypes and are probably subject to directional selection. Most outliers were watershed-specific, but genomic regions undergoing parallel genetic changes in multiple watersheds were also identified. Interestingly, several of the stream-lake outlier regions match those previously identified in marine-freshwater and benthic-limnetic genome scans, indicating reuse of the same genetic loci in different adaptive scenarios. We also identified multiple new outlier loci, which may contribute to unique aspects of differentiation in stream-lake environments. Overall, our data emphasize the important role of ecological boundaries in driving both local and broadly occurring parallel genetic changes during adaptation.

    View details for DOI 10.1098/rspb.2011.1552

    View details for Web of Science ID 000300822400004

    View details for PubMedID 21976692

  • A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks CURRENT BIOLOGY Jones, F. C., Chan, Y. F., Schmutz, J., Grimwood, J., Brady, S. D., Southwick, A. M., Absher, D. M., Myers, R. M., Reimchen, T. E., Deagle, B. E., Schluter, D., Kingsley, D. M. 2012; 22 (1): 83-90

    Abstract

    Genes underlying repeated adaptive evolution in natural populations are still largely unknown. Stickleback fish (Gasterosteus aculeatus) have undergone a recent dramatic evolutionary radiation, generating numerous examples of marine-freshwater species pairs and a small number of benthic-limnetic species pairs found within single lakes [1]. We have developed a new genome-wide SNP genotyping array to study patterns of genetic variation in sticklebacks over a wide geographic range, and to scan the genome for regions that contribute to repeated evolution of marine-freshwater or benthic-limnetic species pairs. Surveying 34 global populations with 1,159 informative markers revealed substantial genetic variation, with predominant patterns reflecting demographic history and geographic structure. After correcting for geographic structure and filtering for neutral markers, we detected large repeated shifts in allele frequency at some loci, identifying both known and novel loci likely contributing to marine-freshwater and benthic-limnetic divergence. Several novel loci fall close to genes implicated in epithelial barrier or immune functions, which have likely changed as sticklebacks adapt to contrasting environments. Specific alleles differentiating sympatric benthic-limnetic species pairs are shared in nearby solitary populations, suggesting an allopatric origin for adaptive variants and selection pressures unrelated to sympatry in the initial formation of these classic vertebrate species pairs.

    View details for DOI 10.1016/j.cub.2011.11.045

    View details for Web of Science ID 000299144200027

    View details for PubMedID 22197244

  • Three Periods of Regulatory Innovation During Vertebrate Evolution SCIENCE Lowe, C. B., Kellis, M., Siepel, A., Raney, B. J., Clamp, M., Salama, S. R., Kingsley, D. M., Lindblad-Toh, K., Haussler, D. 2011; 333 (6045): 1019-1024

    Abstract

    The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.

    View details for DOI 10.1126/science.1202702

    View details for Web of Science ID 000294000400056

    View details for PubMedID 21852499

  • The genetic basis of divergent pigment patterns in juvenile threespine sticklebacks HEREDITY Greenwood, A. K., Jones, F. C., Chan, Y. F., Brady, S. D., Absher, D. M., Grimwood, J., Schmutz, J., Myers, R. M., KINGSLEY, D. M., Peichel, C. L. 2011; 107 (2): 155-166

    Abstract

    Animal pigment patterns are important for a range of functions, including camouflage and communication. Repeating pigment patterns, such as stripes, bars and spots have been of particular interest to developmental and theoretical biologists, but the genetic basis of natural variation in such patterns is largely unexplored. In this study, we identify a difference in a periodic pigment pattern among juvenile threespine sticklebacks (Gasterosteus aculeatus) from different environments. Freshwater sticklebacks exhibit prominent vertical bars that visually break up the body shape, but sticklebacks from marine populations do not. We hypothesize that these distinct pigment patterns are tuned to provide crypsis in different habitats. This phenotypic difference is widespread and appears in most of the freshwater populations that we sampled. We used quantitative trait locus (QTL) mapping in freshwater-marine F2 hybrids to elucidate the genetic architecture underlying divergence in this pigmentation pattern. We identified two QTL that were significantly associated with variation in barring. Interestingly, these QTL were associated with two distinct aspects of the pigment pattern: melanophore number and overall pigment level. We compared the QTL locations with positions of known pigment candidate genes in the stickleback genome. We also identified two major QTL for juvenile body size, providing new insights into the genetic basis of juvenile growth rates in natural populations. In summary, although there is a growing literature describing simple genetic bases for adaptive coloration differences, this study emphasizes that pigment patterns can also possess a more complex genetic architecture.

    View details for DOI 10.1038/hdy.2011.1

    View details for Web of Science ID 000292911500007

    View details for PubMedID 21304547

  • The Progressive Ankylosis Protein Regulates Cementum Apposition and Extracellular Matrix Composition CELLS TISSUES ORGANS Foster, B. L., Nagatomo, K. J., Bamashmous, S. O., Tompkins, K. A., Fong, H., Dunn, D., Chu, E. Y., Guenther, C., KINGSLEY, D. M., Rutherford, R. B., Somerman, M. J. 2011; 194 (5): 382-405

    Abstract

    Tooth root cementum is sensitive to modulation of inorganic pyrophosphate (PP(i)), an inhibitor of hydroxyapatite precipitation. Factors increasing PP(i) include progressive ankylosis protein (ANK) and ectonucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) while tissue nonspecific alkaline phosphatase hydrolyzes PP(i). Studies here aimed to define the role of ANK in root and cementum by analyzing tooth development in Ank knock-out (KO) mice versus wild type.Periodontal development in KO versus control mice was analyzed by histology, histomorphometry, immunohistochemistry, in situ hybridization, electron microscopy, and nanoindentation. Cementoblast cultures were used in vitro to provide mechanistic underpinnings for PP(i) modulation of cell function.Over the course of root development, Ank KO cervical cementum became 8- to 12-fold thicker than control cervical cementum. Periodontal ligament width was maintained and other dentoalveolar tissues, including apical cementum, were unaltered. Cervical cementum uncharacteristically included numerous cells, from rapid cementogenesis. Ank KO increased osteopontin and dentin matrix protein 1 gene and protein expression, and markedly increased NPP1 protein expression in cementoblasts but not in other cell types. Conditional ablation of Ank in joints and periodontia confirmed a local role for ANK in cementogenesis. In vitro studies employing cementoblasts indicated that Ank and Enpp1 mRNA levels increased in step with mineral nodule formation, supporting a role for these factors in regulation of cementum matrix mineralization.ANK, by modulating local PP(i), controls cervical cementum apposition and extracellular matrix. Loss of ANK created a local environment conducive to rapid cementogenesis; therefore, approaches modulating PP(i) in periodontal tissues have potential to promote cementum regeneration.

    View details for DOI 10.1159/000323457

    View details for Web of Science ID 000296044900004

    View details for PubMedID 21389671

  • Human-specific loss of an androgen receptor enhancer is associated with the loss of vibrissae and penile spines Reno, P. L., McLean, C. Y., Pollen, A. A., Bejerano, G., Kingsley, D. M. WILEY-BLACKWELL. 2011: 252-252
  • Synovial joint morphogenesis requires the chondrogenic action of Sox5 and Sox6 in growth plate and articular cartilage DEVELOPMENTAL BIOLOGY Dy, P., Smits, P., Silvester, A., Penzo-Mendez, A., Dumitriu, B., Han, Y., de la Motte, C. A., Kingsley, D. M., Lefebvre, V. 2010; 341 (2): 346-359

    Abstract

    The mechanisms underlying synovial joint development remain poorly understood. Here we use complete and cell-specific gene inactivation to identify the roles of the redundant chondrogenic transcription factors Sox5 and Sox6 in this process. We show that joint development aborts early in complete mutants (Sox5(-/-)6(-/-)). Gdf5 and Wnt9a expression is punctual in articular progenitor cells, but Sox9 downregulation and cell condensation in joint interzones are late. Joint cell differentiation is unsuccessful, regardless of lineage, and cavitation fails. Sox5 and Sox6 restricted expression to chondrocytes in wild-type embryos and continued Erg expression and weak Ihh expression in Sox5(-/-)6(-/-) growth plates suggest that growth plate failure contribute to this Sox5(-/-)6(-/-) joint morphogenesis block. Sox5/6 inactivation in specified joint cells and chondrocytes (Sox5(fl/fl)6(fl/fl)Col2Cre) also results in a joint morphogenesis block, whereas Sox5/6 inactivation in specified joint cells only (Sox5(fl/fl)6(fl/fl)Gdf5Cre) results in milder joint defects and normal growth plates. Sox5(fl/fl)6(fl/fl)Gdf5Cre articular chondrocytes remain undifferentiated, as shown by continued Gdf5 expression and pancartilaginous gene downregulation. Along with Prg4 downregulation, these defects likely account for joint tissue overgrowth and incomplete cavitation in adult mice. Together, these data suggest that synovial joint morphogenesis relies on essential roles for Sox5/6 in promoting both growth plate and articular chondrocyte differentiation.

    View details for DOI 10.1016/j.ydbio.2010.02.024

    View details for Web of Science ID 000277404300002

    View details for PubMedID 20206616

  • Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species JOURNAL OF HEREDITY Haussler, D., O'Brien, S. J., Ryder, O. A., Barker, F. K., Clamp, M., Crawford, A. J., Hanner, R., Hanotte, O., Johnson, W. E., McGuire, J. A., Miller, W., Murphy, R. W., Murphy, W. J., Sheldon, F. H., Sinervo, B., Venkatesh, B., Wiley, E. O., Allendorf, F. W., Amato, G., Baker, C. S., Bauer, A., Beja-Pereira, A., Bermingham, E., Bernardi, G., Bonvicino, C. R., Brenner, S., Burke, T., Cracraft, J., Diekhans, M., Edwards, S., Ericson, P. G., Estes, J., Fjelsda, J., Flesness, N., Gamble, T., Gaubert, P., Graphodatsky, A. S., Graves, J. A., Green, E. D., Green, R. E., Hackett, S., Hebert, P., Helgen, K. M., Joseph, L., Kessing, B., Kingsley, D. M., Lewin, H. A., Luikart, G., Martelli, P., Moreira, M. A., Nguyen, N., Orti, G., Pike, B. L., Rawson, D. M., Schuster, S. C., Seuanez, H. N., Shaffer, H. B., Springer, M. S., Stuart, J. M., Sumner, J., Teeling, E., Vrijenhoek, R. C., Ward, R. D., Warren, W. C., Wayne, R., Williams, T. M., Wolfe, N. D., Zhang, Y., Graph-Odatsky, A., Johnson, W. E., Felsenfeld, A., Turner, S. 2009; 100 (6): 659-674

    Abstract

    The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16,203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60,000 living species). In this proposal, we present precise counts for these 16,203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

    View details for DOI 10.1093/jhered/esp086

    View details for Web of Science ID 000271817600001

    View details for PubMedID 19892720

  • A role for a neo-sex chromosome in stickleback speciation NATURE Kitano, J., Ross, J. A., Mori, S., Kume, M., Jones, F. C., Chan, Y. F., Absher, D. M., Grimwood, J., Schmutz, J., Myers, R. M., Kingsley, D. M., Peichel, C. L. 2009; 461 (7267): 1079-1083

    Abstract

    Sexual antagonism, or conflict between the sexes, has been proposed as a driving force in both sex-chromosome turnover and speciation. Although closely related species often have different sex-chromosome systems, it is unknown whether sex-chromosome turnover contributes to the evolution of reproductive isolation between species. Here we show that a newly evolved sex chromosome contains genes that contribute to speciation in threespine stickleback fish (Gasterosteus aculeatus). We first identified a neo-sex chromosome system found only in one member of a sympatric species pair in Japan. We then performed genetic linkage mapping of male-specific traits important for reproductive isolation between the Japanese species pair. The neo-X chromosome contains loci for male courtship display traits that contribute to behavioural isolation, whereas the ancestral X chromosome contains loci for both behavioural isolation and hybrid male sterility. Our work not only provides strong evidence for a large X-effect on reproductive isolation in a vertebrate system, but also provides direct evidence that a young neo-X chromosome contributes to reproductive isolation between closely related species. Our data indicate that sex-chromosome turnover might have a greater role in speciation than was previously appreciated.

    View details for DOI 10.1038/nature08441

    View details for Web of Science ID 000270987600035

    View details for PubMedID 19783981

  • The Genetic Architecture of Skeletal Convergence and Sex Determination in Ninespine Sticklebacks CURRENT BIOLOGY Shapiro, M. D., Summers, B. R., Balabhadra, S., Aldenhoven, J. T., Miller, A. L., Cunningham, C. B., Bell, M. A., Kingsley, D. M. 2009; 19 (13): 1140-1145

    Abstract

    The history of life offers plentiful examples of convergent evolution, the independent derivation of similar phenotypes in distinct lineages. The emergence of convergent phenotypes among closely related lineages (frequently termed "parallel" evolution) is often assumed to result from changes in similar genes or developmental pathways, but the genetic origins of convergence remains poorly understood. Ninespine (Pungitius pungitius) and threespine (Gasterosteus aculeatus) stickleback fish provide many examples of convergent evolution of adaptive phenotypes, both within and between genera. The genetic architecture of several important traits is now known for threespine sticklebacks; thus, ninespine sticklebacks provide a unique opportunity to critically test whether similar or different chromosome regions control similar phenotypes in these lineages. We have generated the first genome-wide linkage map for ninespine sticklebacks and used quantitative trait locus mapping to identify chromosome regions controlling several skeletal traits and sex determination. In ninespine sticklebacks, these traits mapped to chromosome regions not previously known to control the corresponding traits in threespine sticklebacks. Therefore, convergent morphological evolution in these related, but independent, vertebrate lineages might have different genetic origins. Comparative genetics in sticklebacks provides an exciting opportunity to study the mechanisms controlling similar phenotypic changes in different animal groups.

    View details for DOI 10.1016/j.cub.2009.05.029

    View details for Web of Science ID 000268059200026

    View details for PubMedID 19500990

  • Muscle Contraction Is Necessary to Maintain Joint Progenitor Cell Fate DEVELOPMENTAL CELL Kahn, J., Shwartz, Y., Blitz, E., Krief, S., Sharir, A., Breitel, D. A., Rattenbach, R., Relaix, F., Maire, P., Rountree, R. B., Kingsley, D. M., Zelzer, E. 2009; 16 (5): 734-743

    Abstract

    During embryogenesis, organ development is dependent upon maintaining appropriate progenitor cell commitment. Synovial joints develop from a pool of progenitor cells that differentiate into various cell types constituting the mature joint. The involvement of the musculature in joint formation has long been recognized. However, the mechanism by which the musculature regulates joint formation has remained elusive. In this study, we demonstrate, utilizing various murine models devoid of limb musculature or its contraction, that the contracting musculature is fundamental in maintaining joint progenitors committed to their fate, a requirement for correct joint cavitation and morphogenesis. Furthermore, contraction-dependent activation of beta-catenin, a key modulator of joint formation, provides a molecular mechanism for this regulation. In conclusion, our findings provide the missing link between progenitor cell fate determination and embryonic movement, two processes shown to be essential for correct organogenesis.

    View details for DOI 10.1016/j.devcel.2009.04.013

    View details for Web of Science ID 000266347100015

    View details for PubMedID 19460349

  • From Atoms to Traits SCIENTIFIC AMERICAN Kingsley, D. M. 2009; 300 (1): 52-59

    View details for Web of Science ID 000261816200029

    View details for PubMedID 19186749

  • Dual hindlimb control elements in the Tbx4 gene and region-specific control of bone size in vertebrate limbs DEVELOPMENT Menke, D. B., Guenther, C., Kingsley, D. M. 2008; 135 (15): 2543-2553

    Abstract

    The Tbx4 transcription factor is crucial for normal hindlimb and vascular development, yet little is known about how its highly conserved expression patterns are generated. We have used comparative genomics and functional scanning in transgenic mice to identify a dispersed group of enhancers controlling Tbx4 expression in different tissues. Two independent enhancers control hindlimb expression, one located upstream and one downstream of the Tbx4 coding exons. These two enhancers, hindlimb enhancer A and hindlimb enhancer B (HLEA and HLEB), differ in their primary sequence, in their precise patterns of activity within the hindlimb, and in their degree of sequence conservation across animals. HLEB is highly conserved from fish to mammals. Although Tbx4 expression and hindlimb development occur at different axial levels in fish and mammals, HLEB cloned from either fish or mouse is capable of driving expression at the appropriate position of hindlimb development in mouse embryos. HLEA is highly conserved only in mammals. Deletion of HLEA from the endogenous mouse locus reduces expression of Tbx4 in the hindlimb during embryogenesis, bypasses the embryonic lethality of Tbx4-null mutations, and produces viable, fertile mice with characteristic changes in the size of bones in the hindlimb but not the forelimb. We speculate that dual hindlimb enhancers provide a flexible genomic mechanism for altering the strength and location of Tbx4 expression during normal development, making it possible to separately modify the size of forelimb and hindlimb bones during vertebrate evolution.

    View details for DOI 10.1242/dev.017384

    View details for Web of Science ID 000257557200006

    View details for PubMedID 18579682

  • Dominant negative Bmp5 mutation reveals key role of BMPs in skeletal response to mechanical stimulation BMC DEVELOPMENTAL BIOLOGY Ho, A. M., Marker, P. C., Peng, H., Quintero, A. J., Kingsley, D. M., Huard, J. 2008; 8

    Abstract

    Over a hundred years ago, Wolff originally observed that bone growth and remodeling are exquisitely sensitive to mechanical forces acting on the skeleton. Clinical studies have noted that the size and the strength of bone increase with weight bearing and muscular activity and decrease with bed rest and disuse. Although the processes of mechanotransduction and functional response of bone to mechanical strain have been extensively studied, the molecular signaling mechanisms that mediate the response of bone cells to mechanical stimulation remain unclear.Here, we identify a novel germline mutation at the mouse Bone morphogenetic protein 5 (Bmp5) locus. Genetic analysis shows that the mutation occurs at a site encoding the proteolytic processing sequence of the BMP5 protein and blocks proper processing of BMP5. Anatomic studies reveal that this mutation affects the formation of multiple skeletal features including several muscle-induced skeletal sites in vivo. Biomechanical studies of osteoblasts from these anatomic sites show that the mutation inhibits the proper response of bone cells to mechanical stimulation.The results from these genetic, biochemical, and biomechanical studies suggest that BMPs are required not only for skeletal patterning during embryonic development, but also for bone response and remodeling to mechanical stimulation at specific anatomic sites in the skeleton.

    View details for DOI 10.1186/1471-213X-8-35

    View details for Web of Science ID 000255931900001

    View details for PubMedID 18380899

  • A distinct cohort of progenitor cells participates in synovial Joint and articular cartilage formation during mouse limb skeletogenesis DEVELOPMENTAL BIOLOGY Koyama, E., Shibukawa, Y., Nagayama, M., Sugito, H., Young, B., Yuasa, T., Okabe, T., Ochiai, T., Kamiya, N., Rountree, R. B., Kingsley, D. M., Iwamoto, M., Enomoto-Iwamoto, M., Pacifici, M. 2008; 316 (1): 62-73

    Abstract

    The origin, roles and fate of progenitor cells forming synovial joints during limb skeletogenesis remain largely unclear. Here we produced prenatal and postnatal genetic cell fate-maps by mating ROSA-LacZ-reporter mice with mice expressing Cre-recombinase at prospective joint sites under the control of Gdf5 regulatory sequences (Gdf5-Cre). Reporter-expressing cells initially constituted the interzone, a compact mesenchymal structure representing the first overt sign of joint formation, and displayed a gradient-like distribution along the ventral-to-dorsal axis. The cells expressed genes such as Wnt9a, Erg and collagen IIA, remained predominant in the joint-forming sites over time, gave rise to articular cartilage, synovial lining and other joint tissues, but contributed little if any to underlying growth plate cartilage and shaft. To study their developmental properties more directly, we isolated the joint-forming cells from prospective autopod joint sites using a novel microsurgical procedure and tested them in vitro. The cells displayed a propensity to undergo chondrogenesis that was enhanced by treatment with exogenous rGdf5 but blocked by Wnt9a over-expression. To test roles for such Wnt-mediated anti-chondrogenic capacity in vivo, we created conditional mutants deficient in Wnt/beta-catenin signaling using Col2-Cre or Gdf5-Cre. Synovial joints did form in both mutants; however, the joints displayed a defective flat cell layer normally abutting the synovial cavity and expressed markedly reduced levels of lubricin. In sum, our data indicate that cells present at prospective joint sites and expressing Gdf5 constitute a distinct cohort of progenitor cells responsible for limb joint formation. The cells appear to be patterned along specific limb symmetry axes and rely on local signaling tools to make distinct contributions to joint formation.

    View details for DOI 10.1016/j.ydbio.2008.01.012

    View details for Web of Science ID 000254845200006

    View details for PubMedID 18295755

  • The genetics of adaptive shape shift in stickleback: Pleiotropy and effect size EVOLUTION Albert, A. Y., Sawaya, S., Vines, T. H., Knecht, A. K., Miller, C. T., Summers, B. R., Balabhadra, S., Kingsley, D. M., Schluter, D. 2008; 62 (1): 76-85

    Abstract

    The distribution of effect sizes of genes underlying adaptation is unknown (Orr 2005). Are suites of traits that diverged under natural selection controlled by a few pleiotropic genes of large effect (major genes model), by many independently acting genes of small effect (infinitesimal model), or by a combination, with frequency inversely related to effect size (geometric model)? To address this we carried out a quantitative trait loci (QTL) study of a suite of 54 position traits describing body shapes of two threespine stickleback species: an ancestral Pacific marine form and a highly derived benthic species inhabiting a geologically young lake. About half of the 26 detected QTL affected just one coordinate and had small net effects, but several genomic regions affected multiple aspects of shape and had large net effects. The distribution of effect sizes followed the gamma distribution, as predicted by the geometric model of adaptation when detection limits are taken into account. The sex-determining chromosome region had the largest effect of any QTL. Ancestral sexual dimorphism was similar to the direction of divergence, and was largely eliminated during freshwater adaptation, suggesting that sex differences may provide variation upon which selection can act. Several shape QTL are linked to Eda, a major gene responsible for reduction of lateral body armor in freshwater. Our results are consistent with predictions of the geometric model of adaptation. Shape evolution in stickleback results from a few genes with large and possibly widespread effects and multiple genes of smaller effect.

    View details for DOI 10.1111/j.1558-5646.2007.00259.x

    View details for Web of Science ID 000252108700007

    View details for PubMedID 18005154

  • cis-regulatory changes in kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans CELL Miller, C. T., Beleza, S., Pollen, A. A., Schluter, D., Kittles, R. A., Shriver, M. D., Kingsley, D. M. 2007; 131 (6): 1179-1189

    Abstract

    Dramatic pigmentation changes have evolved within most vertebrate groups, including fish and humans. Here we use genetic crosses in sticklebacks to investigate the parallel origin of pigmentation changes in natural populations. High-resolution mapping and expression experiments show that light gills and light ventrums map to a divergent regulatory allele of the Kit ligand (Kitlg) gene. The divergent allele reduces expression in gill and skin tissue and is shared by multiple derived freshwater populations with reduced pigmentation. In humans, Europeans and East Asians also share derived alleles at the KITLG locus. Strong signatures of selection map to regulatory regions surrounding the gene, and admixture mapping shows that the KITLG genomic region has a significant effect on human skin color. These experiments suggest that regulatory changes in Kitlg contribute to natural variation in vertebrate pigmentation, and that similar genetic mechanisms may underlie rapid evolutionary change in fish and humans.

    View details for DOI 10.1016/j.cell.2007.10.055

    View details for Web of Science ID 000252217100024

    View details for PubMedID 18083106

  • Over-expression of BMP4 and BMP5 in a child with axial skeletal malformations and heterotopic ossification: A new syndrome AMERICAN JOURNAL OF MEDICAL GENETICS PART A Feldman, G. J., Billings, P. C., Patel, R. V., Caron, R. J., Guenther, C., Kingsley, D. M., Kaplan, F. S., Shore, E. M. 2007; 143A (7): 699-706
  • Constraints on utilization of the EDA-signaling pathway in threespine stickleback evolution EVOLUTION & DEVELOPMENT Knecht, A. K., Hosemann, K. E., Kingsley, D. M. 2007; 9 (2): 141-154

    Abstract

    Many traits evolve in parallel in widely separated populations. The evolutionary radiation of threespine sticklebacks provides a powerful model for testing the molecular basis of parallel evolution in vertebrates. Although marine sticklebacks are completely covered with bony armor plates, most freshwater populations have dramatic reductions in plates. Recent genetic studies have shown that major changes in armor patterning are likely due to regulatory alterations in the gene encoding the secreted signaling molecule ectodysplasin (EDA). In mammals, mutations in many different components of the EDA-signaling pathway produce similar changes in hair, teeth, sweat glands, and dermal bones. To test whether other genes in the EDA pathway also control natural variation in armor plates, we identified and mapped stickleback EDA Receptor (EDAR), the EDAR-Associated Death Domain adaptor, Tumor Necrosis Factor Receptor (TNFR) SuperFamily member 19, its adaptor TNFR-Associated Factor 6, and the downstream regulator nuclear factor kappa B Essential Modulator (NEMO). In contrast to the diversity of genes underlying ectodermal dysplasia disease phenotypes in humans, none of these EDA pathway components map to chromosomes previously shown to modify armor plates in natural populations, though EDAR showed a small but significant effect on plate number. We further investigated whether these genes exhibit differences in copy number, target size, or genomic organization that might make them less suitable targets for evolutionary change. In comparison with EDA, all these genes have smaller surrounding noncoding (putative regulatory) regions, with fewer evolutionarily conserved regions. We suggest that the presence of highly modular cis-acting control sequences may be a key factor influencing the likelihood that particular genes will serve as the basis of major phenotypic changes in nature.

    View details for Web of Science ID 000244942700004

    View details for PubMedID 17371397

  • Synovial joint formation during mouse limb skeletogenesis - Roles of Indian hedgehog signaling SKELETAL BIOLOGY AND MEDICINE, PT A Koyama, E., Ochiai, T., Rountree, R. B., Kingsley, D. M., Enomoto-Iwamoto, M., Iwamoto, M., Pacifici, M. 2007; 1116: 100-112

    Abstract

    Indian hedgehog (Ihh) has been previously found to regulate synovial joint formation. To analyze mechanisms, we carried out morphological, molecular, and cell fate map analyses of interzone and joint development in wild-type and Ihh(-/-) mouse embryo long bones. We found that Ihh(-/-) cartilaginous digit anlagen remained fused and lacked interzones or mature joints, whereas wrist skeletal elements were not fused but their joints were morphologically abnormal. E14.5 and E17.5 wild-type digit and ankle prospective joints expressed hedgehog target genes including Gli1 and Gli2 and interzone-associated genes including Gdf5, Erg, and tenascin-C, but expression of all these genes was barely detectable in mutant joints. For cell fate map analysis of joint progenitor cells, we mated Gdf5-Cre(+/-)/Rosa R26R(+/-) double transgenic mice with heterozygous Ihh(+/-) mice and monitored reporter beta-galactosidase activity and gene expression in triple-transgenic progeny. In control Gdf5-Cre(+/-)/R26R(+/-)/Ihh(+/-) limbs, reporter-positive cells were present in developing interzones, articulating layers, and synovial lining tissue and absent from underlying growth plates. In mutant Gdf5-Cre(+/-)/R26R(+/-)/Ihh(-/-) specimens, reporter-positive cells were present also. However, the cells were mostly located around the prospective and uninterrupted digit joint sites and, interestingly, still expressed Erg, tenascin-C, and Gdf5. Topographical analysis revealed that interzone and associated cells were not uniformly distributed, but were much more numerous ventrally. A similar topographical bias was seen for cavitation process and capsule primordia formation. In sum, Ihh is a critical and possibly direct regulator of joint development. In its absence, distribution and function of Gdf5-expressing interzone-associated cells are abnormal, but their patterning at prospective joint sites still occurs. The joint-forming functions of the cells appear to normally involve a previously unsuspected asymmetric distribution along the ventral-to-dorsal plane of the developing joint.

    View details for DOI 10.1196/annals.1402.063

    View details for Web of Science ID 000251898900007

    View details for PubMedID 18083924

  • Biochemical and genetic analysis of ANK in arthritis and bone disease AMERICAN JOURNAL OF HUMAN GENETICS Gurley, K. A., Reimer, R. J., Kingsley, D. M. 2006; 79 (6): 1017-1029

    Abstract

    Mutations in the progressive ankylosis gene (Ank/ANKH) cause surprisingly different skeletal phenotypes in mice and humans. In mice, recessive loss-of-function mutations cause arthritis, ectopic crystal formation, and joint fusion throughout the body. In humans, some dominant mutations cause chondrocalcinosis, an adult-onset disease characterized by the deposition of ectopic joint crystals. Other dominant mutations cause craniometaphyseal dysplasia, a childhood disease characterized by sclerosis of the skull and abnormal modeling of the long bones, with little or no joint pathology. Ank encodes a multiple-pass transmembrane protein that regulates pyrophosphate levels inside and outside tissue culture cells in vitro, but its mechanism of action is not yet clear, and conflicting models have been proposed to explain the effects of the human mutations. Here, we test wild-type and mutant forms of ANK for radiolabeled pyrophosphate-transport activity in frog oocytes. We also reconstruct two human mutations in a bacterial artificial chromosome and test them in transgenic mice for rescue of the Ank null phenotype and for induction of new skeletal phenotypes. Wild-type ANK stimulates saturable transport of pyrophosphate ions across the plasma membrane, with half maximal rates attained at physiological levels of pyrophosphate. Chondrocalcinosis mutations retain apparently wild-type transport activity and can rescue the joint-fusion phenotype of Ank null mice. Craniometaphyseal dysplasia mutations do not transport pyrophosphate and cannot rescue the defects of Ank null mice. Furthermore, microcomputed tomography revealed previously unappreciated phenotypes in Ank null mice that are reminiscent of craniometaphyseal dysplasia. The combination of biochemical and genetic analyses presented here provides insight into how mutations in ANKH cause human skeletal disease.

    View details for Web of Science ID 000242131600003

    View details for PubMedID 17186460

  • Parallel genetic origins of pelvic reduction in vertebrates PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Shapiro, M. D., Bell, M. A., Kingsley, D. M. 2006; 103 (37): 13753-13758

    Abstract

    Despite longstanding interest in parallel evolution, little is known about the genes that control similar traits in different lineages of vertebrates. Pelvic reduction in stickleback fish (family Gasterosteidae) provides a striking example of parallel evolution in a genetically tractable system. Previous studies suggest that cis-acting regulatory changes at the Pitx1 locus control pelvic reduction in a population of threespine sticklebacks (Gasterosteus aculeatus). In this study, progeny from intergeneric crosses between pelvic-reduced threespine and ninespine (Pungitius pungitius) sticklebacks also showed severe pelvic reduction, implicating a similar genetic origin for this trait in both genera. Comparative sequencing studies in complete and pelvic-reduced Pungitius revealed no differences in the Pitx1 coding sequences, but Pitx1 expression was absent from the prospective pelvic region of larvae from pelvic-reduced parents. A much more phylogenetically distant example of pelvic reduction, loss of hindlimbs in manatees, shows a similar left-right size bias that is a morphological signature of Pitx1-mediated pelvic reduction in both sticklebacks and mice. These multiple lines of evidence suggest that changes in Pitx1 may represent a key mechanism of morphological evolution in multiple populations, species, and genera of sticklebacks, as well as in distantly related vertebrate lineages.

    View details for DOI 10.1073/pnas.0604706103

    View details for Web of Science ID 000240648300038

    View details for PubMedID 16945911

  • Mineral formation in joints caused by complete or joint-specific loss of ANK function JOURNAL OF BONE AND MINERAL RESEARCH Gurley, K. A., Chen, H., Guenther, C., Nguyen, E. T., Rountree, R. B., Schoor, M., Kingsley, D. M. 2006; 21 (8): 1238-1247

    Abstract

    To reveal the ANK complete loss of function phenotype in mice, we generated conditional and null alleles. Mice homozygous for the null allele exhibited widespread joint mineralization, similar in severity to animals harboring the original ank allele. A delayed yet similar phenotype was observed in mice with joint-specific loss of ANK function.The ANK pyrophosphate regulator was originally identified and proposed to play a key role in articular cartilage maintenance based on a single spontaneous mouse mutation (ank) that causes severe generalized arthritis. A number of human mutations have subsequently been reported in the human ortholog (ANKH), some of which produce skull and long bone defects with no apparent defects in joints or articular cartilage. None of the currently known mouse or human mutations clearly eliminate the function of the endogenous gene.Two new Ank alleles were generated using homologous recombination in mouse embryonic stem (ES) cells. Joint range of motion assays and muCT studies were used to quantitatively assess phenotypic severity in wildtype, heterozygous, and homozygous mice carrying either the null (Anknull) or original (Ankank) allele. A Gdf5-Cre expressing line was crossed to mice harboring the conditional (Ankfloxp) allele to eliminate ANK function specifically in the joints. Histological stains and beta-galactosidase (LACZ) activity were used to determine the correlation between local loss of ANK function and defective joint phenotypes.Anknull/Anknull mice develop severe ectopic postnatal crystal deposition in almost every joint of the body, leading to eventual joint fusion and loss of mobility. The severity of phenotype in these mice is indistinguishable from that of Ankank/Ankank mice. In addition, despite the widespread expression of Ank in many tissues, the specific deletion of Ank in joints also produces joint mineralization and ankylosis.These studies show that ANK function is required locally in joints to inhibit mineral formation and that the Ank gene plays a key role in postnatal maintenance of joint mobility and function.

    View details for DOI 10.1359/JBMR.060515

    View details for Web of Science ID 000239299400008

    View details for PubMedID 16869722

  • Detection of potential GDF6 regulatory elements by multispecies sequence comparisons and identification of a skeletal joint enhancer GENOMICS Portnoy, M. E., McDermott, K. J., Antonellis, A., Margulies, E. H., Prasad, A. B., KINGSLEY, D. M., Green, E. D., Mortlock, D. P. 2005; 86 (3): 295-305

    Abstract

    The identification of noncoding functional elements within vertebrate genomes, such as those that regulate gene expression, is a major challenge. Comparisons of orthologous sequences from multiple species are effective at detecting highly conserved regions and can reveal potential regulatory sequences. The GDF6 gene controls developmental patterning of skeletal joints and is associated with numerous, distant cis-acting regulatory elements. Using sequence data from 14 vertebrate species, we performed novel multispecies comparative analyses to detect highly conserved sequences flanking GDF6. The complementary tools WebMCS and ExactPlus identified a series of multispecies conserved sequences (MCSs). Of particular interest are MCSs within noncoding regions previously shown to contain GDF6 regulatory elements. A previously reported conserved sequence at -64 kb was also detected by both WebMCS and ExactPlus. Analysis of LacZ-reporter transgenic mice revealed that a 440-bp segment from this region contains an enhancer for Gdf6 expression in developing proximal limb joints. Several other MCSs represent candidate GDF6 regulatory elements; many of these are not conserved in fish or frog, but are strongly conserved in mammals.

    View details for DOI 10.1016/ygeno.2005.05.003

    View details for Web of Science ID 000231350300005

    View details for PubMedID 15979840

  • Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles SCIENCE Colosimo, P. F., Hosemann, K. E., Balabhadra, S., Villarreal, G., Dickson, M., Grimwood, J., Schmutz, J., Myers, R. M., Schluter, D., KINGSLEY, D. M. 2005; 307 (5717): 1928-1933

    Abstract

    Major phenotypic changes evolve in parallel in nature by molecular mechanisms that are largely unknown. Here, we use positional cloning methods to identify the major chromosome locus controlling armor plate patterning in wild threespine sticklebacks. Mapping, sequencing, and transgenic studies show that the Ectodysplasin (EDA) signaling pathway plays a key role in evolutionary change in natural populations and that parallel evolution of stickleback low-plated phenotypes at most freshwater locations around the world has occurred by repeated selection of Eda alleles derived from an ancestral low-plated haplotype that first appeared more than two million years ago. Members of this clade of low-plated alleles are present at low frequencies in marine fish, which suggests that standing genetic variation can provide a molecular basis for rapid, parallel evolution of dramatic phenotypic change in nature.

    View details for DOI 10.1126/science.1107239

    View details for Web of Science ID 000227957300048

    View details for PubMedID 15790847

  • A simple and efficient microinjection protocol for making transgenic sticklebacks BEHAVIOUR Hosemann, K. E., Colosimo, P. E., Summers, B. R., Kingsley, D. M. 2004; 141: 1345-1355
  • New genomic tools for molecular studies of evolutionary change in threespine sticklebacks BEHAVIOUR Kingsley, D. M., Zhu, B. L., Osoegawa, K., de Jong, P. J., Schein, J., Marra, M., Peichel, C., Amamiya, C., Schluter, D., Balabhadra, S., Friedlander, B., Cha, Y. M., Dickson, M., Grimwood, J., Schmutz, J., Talbot, W. S., Myers, R. 2004; 141: 1331-1344
  • BMP receptor signaling is required for postnatal maintenance of articular cartilage PLOS BIOLOGY Rountree, R. B., Schoor, M., Chen, H., Marks, M. E., Harley, V., Mishina, Y., Kingsley, D. M. 2004; 2 (11): 1815-1827

    Abstract

    Articular cartilage plays an essential role in health and mobility, but is frequently damaged or lost in millions of people that develop arthritis. The molecular mechanisms that create and maintain this thin layer of cartilage that covers the surface of bones in joint regions are poorly understood, in part because tools to manipulate gene expression specifically in this tissue have not been available. Here we use regulatory information from the mouse Gdf5 gene (a bone morphogenetic protein [BMP] family member) to develop new mouse lines that can be used to either activate or inactivate genes specifically in developing joints. Expression of Cre recombinase from Gdf5 bacterial artificial chromosome clones leads to specific activation or inactivation of floxed target genes in developing joints, including early joint interzones, adult articular cartilage, and the joint capsule. We have used this system to test the role of BMP receptor signaling in joint development. Mice with null mutations in Bmpr1a are known to die early in embryogenesis with multiple defects. However, combining a floxed Bmpr1a allele with the Gdf5-Cre driver bypasses this embryonic lethality, and leads to birth and postnatal development of mice missing the Bmpr1a gene in articular regions. Most joints in the body form normally in the absence of Bmpr1a receptor function. However, articular cartilage within the joints gradually wears away in receptor-deficient mice after birth in a process resembling human osteoarthritis. Gdf5-Cre mice provide a general system that can be used to test the role of genes in articular regions. BMP receptor signaling is required not only for early development and creation of multiple tissues, but also for ongoing maintenance of articular cartilage after birth. Genetic variation in the strength of BMP receptor signaling may be an important risk factor in human osteoarthritis, and treatments that mimic or augment BMP receptor signaling should be investigated as a possible therapeutic strategy for maintaining the health of joint linings.

    View details for DOI 10.1371/journal.pbio.0020355

    View details for Web of Science ID 000225160300013

    View details for PubMedID 15492776

  • The master sex-determination locus in threespine sticklebacks is on a nascent Y chromosome CURRENT BIOLOGY Peichel, C. L., Ross, J. A., Matson, C. K., Dickson, M., Grimwood, J., Schmutz, J., Myers, R. M., Mori, S., Schluter, D., KINGSLEY, D. M. 2004; 14 (16): 1416-1424

    Abstract

    Many different environmental and genetic sex-determination mechanisms are found in nature. Closely related species can use different master sex-determination switches, suggesting that these developmental pathways can evolve very rapidly. Previous cytological studies suggest that recently diverged species of stickleback fish have different sex chromosome complements. Here, we investigate the genetic and chromosomal mechanisms that underlie sex determination in the threespine stickleback (Gasterosteus aculeatus).Genome-wide linkage mapping identifies a single chromosome region at the distal end of linkage group (LG) 19, which controls male or female sexual development in threespine sticklebacks. Although sex chromosomes are not cytogenetically visible in this species, several lines of evidence suggest that LG 19 is an evolving sex chromosome system, similar to the XX female/XY male system in many other species: (1) males are consistently heterozygous for unique alleles in this region; (2) recombination between loci linked to the sex-determination region is reduced in male meiosis relative to female meiosis; (3) sequence analysis of X- and Y-specific bacterial artificial chromosome (BAC) clones from the sex-determination region reveals many sequence differences between the X- and Y-specific clones; and (4) the Y chromosome has accumulated transposable elements and local duplications.Taken together, our data suggest that threespine sticklebacks have a simple chromosomal mechanism for sex determination based on a nascent Y chromosome that is less than 10 million years old. Further analysis of the stickleback system will provide an exciting window into the evolution of sex-determination pathways and sex chromosomes in vertebrates.

    View details for Web of Science ID 000223586900019

    View details for PubMedID 15324658

  • Evidence for ecology's role in speciation NATURE McKinnon, J. S., Mori, S., Blackman, B. K., David, L., KINGSLEY, D. M., Jamieson, L., Chou, J., Schluter, D. 2004; 429 (6989): 294-298

    Abstract

    A principal challenge in testing the role of natural selection in speciation is to connect the build-up of reproductive isolation between populations to divergence of ecologically important traits. Demonstrations of 'parallel speciation', or assortative mating by selective environment, link ecology and isolation, but the phenotypic traits mediating isolation have not been confirmed. Here we show that the parallel build-up of mating incompatibilities between stickleback populations can be largely accounted for by assortative mating based on one trait, body size, which evolves predictably according to environment. In addition to documenting the influence of body size on reproductive isolation for stickleback populations spread across the Northern Hemisphere, we have confirmed its importance through a new experimental manipulation. Together, these results suggest that speciation may arise largely as a by-product of ecological differences and divergent selection on a small number of phenotypic traits.

    View details for DOI 10.1038/nature02556

    View details for Web of Science ID 000221505900042

    View details for PubMedID 15152252

  • The genetic architecture of parallel armor plate reduction in threespine sticklebacks PLOS BIOLOGY Colosimo, P. F., Peichel, C. L., Nereng, K., Blackman, B. K., Shapiro, M. D., Schluter, D., Kingsley, D. M. 2004; 2 (5): 635-641
  • The genetic architecture of parallel armor plate reduction in threespine sticklebacks. PLoS biology Colosimo, P. F., Peichel, C. L., Nereng, K., Blackman, B. K., Shapiro, M. D., Schluter, D., Kingsley, D. M. 2004; 2 (5): E109-?

    Abstract

    How many genetic changes control the evolution of new traits in natural populations? Are the same genetic changes seen in cases of parallel evolution? Despite long-standing interest in these questions, they have been difficult to address, particularly in vertebrates. We have analyzed the genetic basis of natural variation in three different aspects of the skeletal armor of threespine sticklebacks (Gasterosteus aculeatus): the pattern, number, and size of the bony lateral plates. A few chromosomal regions can account for variation in all three aspects of the lateral plates, with one major locus contributing to most of the variation in lateral plate pattern and number. Genetic mapping and allelic complementation experiments show that the same major locus is responsible for the parallel evolution of armor plate reduction in two widely separated populations. These results suggest that a small number of genetic changes can produce major skeletal alterations in natural populations and that the same major locus is used repeatedly when similar traits evolve in different locations.

    View details for PubMedID 15069472

  • Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks NATURE Shapiro, M. D., Marks, M. E., Peichel, C. L., Blackman, B. K., Nereng, K. S., Jonsson, B., Schluter, D., Kingsley, D. M. 2004; 428 (6984): 717-723

    Abstract

    Hindlimb loss has evolved repeatedly in many different animals by means of molecular mechanisms that are still unknown. To determine the number and type of genetic changes underlying pelvic reduction in natural populations, we carried out genetic crosses between threespine stickleback fish with complete or missing pelvic structures. Genome-wide linkage mapping shows that pelvic reduction is controlled by one major and four minor chromosome regions. Pitx1 maps to the major chromosome region controlling most of the variation in pelvic size. Pelvic-reduced fish show the same left-right asymmetry seen in Pitx1 knockout mice, but do not show changes in Pitx1 protein sequence. Instead, pelvic-reduced sticklebacks show site-specific regulatory changes in Pitx1 expression, with reduced or absent expression in pelvic and caudal fin precursors. Regulatory mutations in major developmental control genes may provide a mechanism for generating rapid skeletal changes in natural populations, while preserving the essential roles of these genes in other processes.

    View details for DOI 10.1038/nature02415

    View details for Web of Science ID 000220823800030

    View details for PubMedID 15085123

  • A general approach for identifying distant regulatory elements applied to the Gdf6 gene GENOME RESEARCH Mortlock, D. P., Guenther, C., Kingsley, D. M. 2003; 13 (9): 2069-2081

    Abstract

    Regulatory sequences in higher genomes can map large distances from gene coding regions, and cannot yet be identified by simple inspection of primary DNA sequence information. Here we describe an efficient method of surveying large genomic regions for gene regulatory information, and subdividing complex sets of distant regulatory elements into smaller intervals for detailed study. The mouse Gdf6 gene is expressed in a number of distinct embryonic locations that are involved in the patterning of skeletal and soft tissues. To identify sequences responsible for Gdf6 regulation, we first isolated a series of overlapping bacterial artificial chromosomes (BACs) that extend varying distances upstream and downstream of the gene. A LacZ reporter cassette was integrated into the Gdf6 transcription unit of each BAC using homologous recombination in bacteria. Each modified BAC was injected into fertilized mouse eggs, and founder transgenic embryos were analyzed for LacZ expression mid-gestation. The overlapping segments defined by the BAC clones revealed five separate regulatory regions that drive LacZ expression in 11 distinct anatomical locations. To further localize sequences that control expression in developing skeletal joints, we created a series of BAC constructs with precise deletions across a putative joint-control region. This approach further narrowed the critical control region to an area containing several stretches of sequence that are highly conserved between mice and humans. A distant 2.9-kilobase fragment containing the highly conserved regions is able to direct very specific expression of a minimal promoter/LacZ reporter in proximal limb joints. These results demonstrate that even distant, complex regulatory sequences can be identified using a combination of BAC scanning, BAC deletion, and comparative sequencing approaches.

    View details for DOI 10.1101/gr.1306003

    View details for Web of Science ID 000185085300010

    View details for PubMedID 12915490

  • Multiple joint and skeletal patterning defects caused by single and double mutations in the mouse Gdf6 and Gdf5 genes DEVELOPMENTAL BIOLOGY Settle, S. H., Rountree, R. B., Sinha, A., Thacker, A., Higgins, K., KINGSLEY, D. M. 2003; 254 (1): 116-130

    Abstract

    Growth/differentiation factors 5, 6, and 7 (GDF5/6/7) represent a distinct subgroup within the bone morphogenetic protein (BMP) family of secreted signaling molecules. Previous studies have shown that the Gdf5 gene is expressed in transverse stripes across developing skeletal elements and is one of the earliest known markers of joint formation during embryonic development. Although null mutations in this gene disrupt formation of some bones and joints in the skeleton, many sites are unaffected. Here, we show that the closely related family members Gdf6 and Gdf7 are expressed in different subsets of developing joints. Inactivation of the Gdf6 gene causes defects in joint, ligament, and cartilage formation at sites distinct from those seen in Gdf5 mutants, including the wrist and ankle, the middle ear, and the coronal suture between bones in the skull. Mice lacking both Gdf5 and Gdf6 show additional defects, including severe reduction or loss of some skeletal elements in the limb, additional fusions between skeletal structures, scoliosis, and altered cartilage in the intervertebral joints of the spinal column. These results show that members of the GDF5/6/7 subgroup are required for normal formation of bones and joints in the limbs, skull, and axial skeleton. The diverse effects on joint development and the different types of joints affected in the mutants suggest that members of the GDF family play a key role in establishing boundaries between many different skeletal elements during normal development. Some of the skeletal defects seen in single or double mutant mice resemble defects seen in human skeletal diseases, which suggests that these genes may be candidates that underlie some forms of carpal/tarsal coalition, conductive deafness, scoliosis, and craniosynostosis.

    View details for Web of Science ID 000180731500009

    View details for PubMedID 12606286

  • Cementum: A phosphate-sensitive tissue JOURNAL OF DENTAL RESEARCH Nociti, F. H., Berry, J. E., Foster, B. L., Gurley, K. A., KINGSLEY, D. M., Takata, T., Miyauchi, M., Somerman, M. J. 2002; 81 (12): 817-821

    Abstract

    Ectopic calcification within joints has been reported in humans and rodents exhibiting mutations in genes that regulate the level of extracellular pyrophosphate, e.g., ank and PC-1; however, periodontal effects of these mutations have not previously been examined. These initial studies using ank and PC-1 mutant mice were done to see if such mineral deposition and resulting ankylosis were occurring in the periodontium as well. Surprisingly, results indicated the absence of ankylosis; however, a marked increase in cementum formation on the root surfaces of fully developed teeth of these mutant mice was noted. Examination of ank mutant mice at earlier ages of tooth root formation indicated that this striking observation is apparent from the onset of cementogenesis. These findings suggest that cells within the periodontal region are highly responsive to changes in phosphate metabolism. This information may prove valuable in attempts to design successful therapies for regenerating periodontal tissues.

    View details for Web of Science ID 000179555900005

    View details for PubMedID 12454094

  • Mutations in ANKH cause chondrocalcinosis AMERICAN JOURNAL OF HUMAN GENETICS Pendleton, A., Johnson, M. D., Hughes, A., Gurley, K. A., Ho, A. M., Doherty, M., Dixey, J., Gillet, P., Loeuille, D., McGrath, R., REGINATO, A., Shiang, R., Wright, G., Netter, P., Williams, C., Kingsley, D. M. 2002; 71 (4): 933-940

    Abstract

    Chondrocalcinosis (CC) is a common cause of joint pain and arthritis that is caused by the deposition of calcium-containing crystals within articular cartilage. Although most cases are sporadic, rare familial forms have been linked to human chromosomes 8 (CCAL1) or 5p (CCAL2) (Baldwin et al. 1995; Hughes et al. 1995; Andrew et al. 1999). Here, we show that two previously described families with CCAL2 have mutations in the human homolog of the mouse progressive ankylosis gene (ANKH). One of the human mutations results in the substitution of a highly conserved amino acid residue within a predicted transmembrane segment. The other creates a new ATG start site that adds four additional residues to the ANKH protein. Both mutations segregate completely with disease status and are not found in control subjects. In addition, 1 of 95 U.K. patients with sporadic CC showed a deletion of a single codon in the ANKH gene. The same change was found in a sister who had bilateral knee replacement for osteoarthritis. Each of the three human mutations was reconstructed in a full-length ANK expression construct previously shown to regulate pyrophosphate levels in cultured cells in vitro. All three of the human mutations showed significantly more activity than a previously described nonsense mutation that causes severe hydroxyapatite mineral deposition and widespread joint ankylosis in mice. These results suggest that small sequence changes in ANKH are one cause of CC and joint disease in humans. Increased ANK activity may explain the different types of crystals commonly deposited in human CCAL2 families and mutant mice and may provide a useful pharmacological target for treating some forms of human CC.

    View details for Web of Science ID 000178613800019

    View details for PubMedID 12297987

  • Dysregulated expression of BMP5 in a patient with deformed helices, axial skeletal defects, and heterotopic ossification: A clue from the short-ear mouse. FELDMAN, G. J., Patel, R., Billings, P. C., KINGSLEY, D. M., Shore, E. M., Kaplan, F. S. WILEY-BLACKWELL. 2002: S499-S499
  • The genetic architecture of divergence between threespine stickleback species NATURE Peichel, C. L., Nereng, K. S., Ohgi, K. A., Cole, B. L., Colosimo, P. F., Buerkle, C. A., Schluter, D., Kingsley, D. M. 2001; 414 (6866): 901-905

    Abstract

    The genetic and molecular basis of morphological evolution is poorly understood, particularly in vertebrates. Genetic studies of the differences between naturally occurring vertebrate species have been limited by the expense and difficulty of raising large numbers of animals and the absence of molecular linkage maps for all but a handful of laboratory and domesticated animals. We have developed a genome-wide linkage map for the three-spined stickleback (Gasterosteus aculeatus), an extensively studied teleost fish that has undergone rapid divergence and speciation since the melting of glaciers 15,000 years ago. Here we use this map to analyse the genetic basis of recently evolved changes in skeletal armour and feeding morphologies seen in the benthic and limnetic stickleback species from Priest Lake, British Columbia. Substantial alterations in spine length, armour plate number, and gill raker number are controlled by genetic factors that map to independent chromosome regions. Further study of these regions will help to define the number and type of genetic changes that underlie morphological diversification during vertebrate evolution.

    View details for Web of Science ID 000172813300044

    View details for PubMedID 11780061

  • Reciprocal mouse and human limb phenotypes caused by gain- and loss-of-function mutations affecting Lmbr1 GENETICS Clark, R. M., Marker, P. C., ROESSLER, E., Dutra, A., Schimenti, J. C., Muenke, M., Kingsley, D. M. 2001; 159 (2): 715-726

    Abstract

    The major locus for dominant preaxial polydactyly in humans has been mapped to 7q36. In mice the dominant Hemimelic extra toes (Hx) and Hammertoe (Hm) mutations map to a homologous chromosomal region and cause similar limb defects. The Lmbr1 gene is entirely within the small critical intervals recently defined for both the mouse and human mutations and is misexpressed at the exact time that the mouse Hx phenotype becomes apparent during limb development. This result suggests that Lmbr1 may underlie preaxial polydactyly in both mice and humans. We have used deletion chromosomes to demonstrate that the dominant mouse and human limb defects arise from gain-of-function mutations and not from haploinsufficiency. Furthermore, we created a loss-of-function mutation in the mouse Lmbr1 gene that causes digit number reduction (oligodactyly) on its own and in trans to a deletion chromosome. The loss of digits that we observed in mice with reduced Lmbr1 activity is in contrast to the gain of digits observed in Hx mice and human polydactyly patients. Our results suggest that the Lmbr1 gene is required for limb formation and that reciprocal changes in levels of Lmbr1 activity can lead to either increases or decreases in the number of digits in the vertebrate limb.

    View details for Web of Science ID 000171744900024

    View details for PubMedID 11606546

  • The BMP family member Gdf7 is required for seminal vesicle growth, branching morphogenesis, and cytodifferentiation DEVELOPMENTAL BIOLOGY Settle, S., Marker, P., Gurley, K., Sinha, A., Thacker, A., Wang, Y. Z., Higgins, K., Cunha, G., Kingsley, D. M. 2001; 234 (1): 138-150

    Abstract

    Epithelial-mesenchymal interactions play an important role in the development of many different organs and tissues. The secretory glands of the male reproductive system, including the prostate and seminal vesicles, are derived from epithelial precursors. Signals from the underlying mesenchyme are required for normal growth, branching, and differentiation of the seminal vesicle epithelium. Here, we show that a member of the BMP family, Gdf7, is required for normal seminal vesicle development. Expression and tissue recombination experiments suggest that Gdf7 is a mesenchymal signal that acts in a paracrine fashion to control the differentiation of the seminal vesicle epithelium.

    View details for DOI 10.1006/dbio.2001.0244

    View details for Web of Science ID 000169059300011

    View details for PubMedID 11356025

  • A large-scale in situ screen provides molecular evidence for the induction of eye anterior segment structures by the developing lens DEVELOPMENTAL BIOLOGY Thut, C. J., Rountree, R. B., Hwa, M., KINGSLEY, D. M. 2001; 231 (1): 63-76

    Abstract

    The anterior segment of the vertebrate eye includes the cornea, iris, ciliary body, trabecular meshwork, and lens. Although malformations of these structures have been implicated in many human eye diseases, little is known about the molecular mechanisms that control their development. To identify genes involved in anterior segment formation, we developed a large-scale in situ hybridization screen and examined the spatial and temporal expression of over 1000 genes during eye development. This screen identified 62 genes with distinct expression patterns in specific eye structures, including several expressed in novel patterns in the anterior segment. Using these genes as developmental markers, we tested for the presence of inductive signals that control the differentiation of anterior segment tissues. Organ culture recombination experiments showed that a chick lens is capable of inducing the expression of markers of the presumptive iris and ciliary body in the developing mouse neural retina. The inducing activity from the lens acts only over short ranges and is present at multiple stages of eye development. These studies provide molecular evidence that an evolutionarily conserved signal from the lens controls tissue specification in the developing optic cup.

    View details for Web of Science ID 000167271000005

    View details for PubMedID 11180952

  • Sequence interpretation - Functional annotation of mouse genome sequences SCIENCE Nadeau, J. H., Balling, R., Barsh, G., Beier, D., Brown, S. D., Bucan, M., Camper, S., Carlson, G., Copeland, N., Eppig, J., Fletcher, C., Frankel, W. N., Ganten, D., Goldowitz, D., Goodnow, C., Guenet, J. L., Hicks, G., de Angelis, M. H., Jackson, I., Jacob, H. J., Jenkins, N., Johnson, D., Justice, M., Kay, S., Kingsley, D., Lehrach, H., Magnuson, T., Meisler, M., Poustka, A. M., Rinchik, E. M., Rossant, J., Russell, L. B., Schimenti, J., Shiroishi, T., Skarnes, W. C., Soriano, P., Stanford, W., Takahashi, J. S., Wurst, W., Zimmer, A. 2001; 291 (5507): 1251-?

    View details for Web of Science ID 000166993400028

    View details for PubMedID 11233449

  • Genetic control of bone and joint formation. Novartis Foundation symposium KINGSLEY, D. M. 2001; 232: 213-222

    Abstract

    The form and pattern of the vertebrate skeleton is thought to be strongly influenced by several fundamental morphogenetic behaviours of mesenchymal cells during embryonic development. Recent genetic and developmental studies have identified some of the genes that play an important role in controlling both the aggregation of mesenchymal cells into rough outlines of future skeletal elements (condensations), and in controlling where skeletal precursors cleave or segment to produce separate skeletal elements connected by joints. Members of the bone morphogenetic protein (BMP) family appear to play an important role in both processes. Mouse and human mutations in these genes lead to defects in formation of specific bones and joints, with striking specificity for particular anatomical locations. Results from a range of experiments suggest that these molecules may have multiple functions during normal skeletal development and patterning. A major challenge for the future is to identify genes and pathways that can maintain, repair, or stimulate the regeneration of bone and joint structures at later developmental stages.

    View details for PubMedID 11277082

  • A novel candidate gene for mouse and human preaxial polydactyly with altered expression in limbs of Hemimelic extra-toes mutant mice GENOMICS Clark, R. M., Marker, P. C., KINGSLEY, D. M. 2000; 67 (1): 19-27

    Abstract

    Polydactyly is a common malformation of vertebrate limbs. In humans a major locus for nonsyndromic pre-axial polydactyly (PPD) has been mapped previously to 7q36. The mouse Hemimelic extra-toes (Hx) mutation maps to a homologous chromosome segment and has been proposed to affect a homologous gene. To understand the molecular changes underlying PPD, we used a positional cloning approach to identify the gene or genes disrupted by the Hx mutation and a closely linked limb mutation, Hammertoe (Hm). High resolution genetic mapping identified a small candidate interval for the mouse mutations located 1.2 cM distal to the Shh locus. The nonrecombinant interval was completely cloned in bacterial artificial chromosomes and searched for genes using a combination of exon trapping, sample sequencing, and mapping of known genes. Two novel genes, Lmbr1 and Lmbr2, are entirely within the candidate interval we defined genetically. The open reading frame of both genes is intact in mutant mice, but the expression of the Lmbr1 gene is dramatically altered in developing limbs of Hx mutant mice. The correspondence between the spatial and temporal changes in Lmbr1 expression and the embryonic onset of the Hx mutant phenotype suggests that the mouse Hx mutation may be a regulatory allele of Lmbr1. The human ortholog of Lmbr1 maps within the recently described interval for human PPD, strengthening the possibility that both mouse and human limb abnormalities are due to defects in the same highly conserved gene.

    View details for Web of Science ID 000088195500003

    View details for PubMedID 10945466

  • Efficient studies of long-distance Bmp5 gene regulation using bacterial artificial chromosomes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA DiLeone, R. J., Marcus, G. A., Johnson, M. D., KINGSLEY, D. M. 2000; 97 (4): 1612-1617

    Abstract

    The regulatory regions surrounding many genes may be large and difficult to study using standard transgenic approaches. Here we describe the use of bacterial artificial chromosome clones to rapidly survey hundreds of kilobases of DNA for potential regulatory sequences surrounding the mouse bone morphogenetic protein-5 (Bmp5) gene. Simple coinjection of large insert clones with lacZ reporter constructs recapitulates all of the sites of expression observed previously with numerous small constructs covering a large, complex regulatory region. The coinjection approach has made it possible to rapidly survey other regions of the Bmp5 gene for potential control elements, to confirm the location of several elements predicted from previous expression studies using regulatory mutations at the Bmp5 locus, to test whether Bmp5 control regions act similarly on endogenous and foreign promoters, and to show that Bmp5 control elements are capable of rescuing phenotypic effects of a Bmp5 deficiency. This rapid approach has identified new Bmp5 control regions responsible for controlling the development of specific anatomical structures in the vertebrate skeleton. A similar approach may be useful for studying complex control regions surrounding many other genes important in embryonic development and human disease.

    View details for Web of Science ID 000085409600060

    View details for PubMedID 10677507

  • GDF5 coordinates bone and joint formation during digit development DEVELOPMENTAL BIOLOGY Storm, E. E., KINGSLEY, D. M. 1999; 209 (1): 11-27

    Abstract

    A functional skeletal system requires the coordinated development of many different tissue types, including cartilage, bones, joints, and tendons. Members of the Bone morphogenetic protein (BMP) family of secreted signaling molecules have been implicated as endogenous regulators of skeletal development. This is based on their expression during bone and joint formation, their ability to induce ectopic bone and cartilage, and the skeletal abnormalities present in animals with mutations in BMP family members. One member of this family, Growth/differentiation factor 5 (GDF5), is encoded by the mouse brachypodism locus. Mice with mutations in this gene show reductions in the length of bones in the limbs, altered formation of bones and joints in the sternum, and a reduction in the number of bones in the digits. The expression pattern of Gdf5 during normal development and the phenotypes seen in mice with single or double mutations in Gdf5 and Bmp5 suggested that Gdf5 has multiple functions in skeletogenesis, including roles in joint and cartilage development. To further understand the function of GDF5 in skeletal development, we assayed the response of developing chick and mouse limbs to recombinant GDF5 protein. The results from these assays, coupled with an analysis of the development of brachypodism digits, indicate that GDF5 is necessary and sufficient for both cartilage development and the restriction of joint formation to the appropriate location. Thus, GDF5 function in the digits demonstrates a link between cartilage development and joint development and is an important determinant of the pattern of bones and articulations in the digits.

    View details for Web of Science ID 000079924400002

    View details for PubMedID 10208739

  • An extensive 3 ' regulatory region controls expression of Bmp5 in specific anatomical structures of the mouse embryo GENETICS DiLeone, R. J., Russell, L. B., Kingsley, D. M. 1998; 148 (1): 401-408

    Abstract

    Bone morphogenetic proteins (BMPs) are secreted signaling molecules that control important developmental events in many different organisms. Previous studies have shown that BMPs are expressed at the earliest stages of skeletal development, and are required for formation of specific skeletal features, strongly suggesting that they are endogenous signals used to control formation of skeletal tissue. Despite the importance of BMP signaling in normal development, very little is known about the mechanisms that control the synthesis and distribution of BMP signals in vertebrates. Here, we identify a large array of cis-acting control sequences that lay out expression of the mouse Bmp5 gene in specific skeletal structures and soft tissues. Some of these elements show striking specificity for particular anatomical features within the skeleton, rather than for cartilage and bone in general. These data suggest that the vertebrate skeleton is built from the sum of many independent domains of BMP expression, each of which may be controlled by separate regulatory elements driving expression at specific anatomical locations. Surprisingly, some of the regulatory sequences in the Bmp5 gene map over 270 kb from the Bmp5 promoter, making them among the most distant elements yet identified in studies of eukaryotic gene expression.

    View details for Web of Science ID 000071494000037

    View details for PubMedID 9475750

  • Bone morphogenetic proteins in the formation and repair of cartilage, bone, and joints SKELETAL GROWTH AND DEVELOPMENT: CLINICAL ISSUES AND BASIC SCIENCE ADVANCES KINGSLEY, D. M. 1998: 87-98
  • The Bmp8 gene is expressed in developing skeletal tissue and maps near the Achondroplasia locus on mouse chromosome 4 GENOMICS DiLeone, R. J., King, J. A., Storm, E. E., Copeland, N. G., Jenkins, N. A., KINGSLEY, D. M. 1997; 40 (1): 196-198

    View details for Web of Science ID A1997WJ33600032

    View details for PubMedID 9070944

  • Spectrum of Bmp5 mutations from germline mutagenesis experiments in mice GENETICS Marker, P. C., Seung, K. J., Bland, A. E., Russell, L. B., KINGSLEY, D. M. 1997; 145 (2): 435-443

    Abstract

    Over 40 years of mutagenesis experiments using the mouse specific-locus test have produced a large number of induced germline mutations at seven loci, among them the short ear locus. We have previously shown that the short ear locus encodes bone morphogenetic protein 5 (BMP5), a member of a large family of secreted signaling molecules that play key roles in axis formation, tissue differentiation, mesenchymalepithelial interactions, and skeletal development. Here we examine 24 chemical- and radiation-induced mutations at the short ear locus. Sequence changes in the Bmp5 open reading frame confirm the importance of cysteine residues in the function of TGF beta superfamily members. The spectrum of N-ethyl-N-nitrosourea-induced mutations also provides new information about the basepair, sequence context, and strand specificity of germline mutations in mammals.

    View details for Web of Science ID A1997WM59900019

    View details for PubMedID 9071596

  • Joint patterning defects caused by single and double mutations in members of the bone morphogenetic protein (BMP) family DEVELOPMENT Storm, E. E., KINGSLEY, D. M. 1996; 122 (12): 3969-3979

    Abstract

    The mouse brachypodism locus encodes a bone morphogenetic protein (BMP)-like molecule called growth/differentiation factor 5 (GDF5). Here we show that Gdf5 transcripts are expressed in a striking pattern of transverse stripes within many skeletal precursors in the developing limb. The number, location and time of appearance of these stripes corresponds to the sites where joints will later form between skeletal elements. Null mutations in Gdf5 disrupt the formation of more than 30% of the synovial joints in the limb, leading to complete or partial fusions between particular skeletal elements, and changes in the patterns of repeating structures in the digits, wrists and ankles. Mice carrying null mutations in both Gdf5 and another BMP family member, Bmp5, show additional abnormalities not observed in either of the single mutants. These defects include disruption of the sternebrae within the sternum and abnormal formation of the fibrocartilaginous joints between the sternebrae and ribs. Previous studies have shown that members of the BMP family are required for normal development of cartilage and bone. The current studies suggest that particular BMP family members may also play an essential role in the segmentation process that cleaves skeletal precursors into separate elements. This process helps determine the number of elements in repeating series in both limbs and sternum, and is required for normal generation of the functional articulations between many adjacent structures in the vertebrate skeleton.

    View details for Web of Science ID A1996WC55400028

    View details for PubMedID 9012517

  • Mechanical and geometric changes in the growing femora of BMP-5 deficient mice BONE Mikic, B., VANDERMEULEN, M. C., KINGSLEY, D. M., Carter, D. R. 1996; 18 (6): 601-607

    Abstract

    We examined the growth-related changes in femoral geometry and torsional strength in BMP-5 deficient short-ear mice over a 22-week time interval ("long-term" changes). Four groups of female mice (n = 6 per group) were examined: short-ear animals and their heterozygous control littermates at 4 and 26 weeks of age. In agreement with findings previously observed in a mixed-gender group of adult mice (26 weeks), the femora of short-ear animals were significantly smaller in length and cross section at both ages. The magnitudes of the differences between genotypes were comparable at each age, indicating that the overall rates of appositional and endochondral growth were similar for both genotypes over the 22-week period. In the adult animals, short-ear femora were 27 +/- 7% weaker in torsional strength due to their smaller cross-sectional geometry. However, bone strength in adult short-ear mice appeared to be adequate for animal size: No significant difference was detected in maximum femoral torque when normalized by body mass. In 4-week old animals, BMP-5 deficiency was associated with a 27 +/- 6% lower body mass, but the torsional strength of the femur was not significantly different from that of controls. Cross-sectional geometry was smaller in 4-week old short-ear mice, but the apparent bone material ultimate shear stress was elevated by 33 +/- 10%, thereby resulting in a whole bone torsional strength equivalent to that of the larger control mice. While the data suggest a higher material strength in the 4-week-old short-ear animals, no significant difference in the level of bone mineralization was detectable between genotypes at either age.

    View details for Web of Science ID A1996UT99700017

    View details for PubMedID 8806002

  • The role of BMPs and GDFs in development of region-specific skeletal structures King, J. A., Storm, E. E., Marker, P. C., DiLeone, R. J., KINGSLEY, D. M. NEW YORK ACAD SCIENCES. 1996: 70-79

    View details for Web of Science ID A1996BF92H00009

    View details for PubMedID 8702185

  • THE MOUSE SNELLS WALTZER DEAFNESS GENE ENCODES AN UNCONVENTIONAL MYOSIN REQUIRED FOR STRUCTURAL INTEGRITY OF INNER-EAR HAIR-CELLS NATURE GENETICS Avraham, K. B., Hasson, T., STEEL, K. P., KINGSLEY, D. M., Russell, L. B., Mooseker, M. S., Copeland, N. G., Jenkins, N. A. 1995; 11 (4): 369-375

    Abstract

    The mouse represents an excellent model system for the study of genetic deafness in humans. Many mouse deafness mutants have been identified and the anatomy of the mouse and human ear is similar. Here we report the use of a positional cloning approach to identify the gene encoded by the mouse recessive deafness mutation, Snell's waltzer (sv). We show that sv encodes an unconventional myosin heavy chain, myosin VI, which is expressed within the sensory hair cells of the inner ear, and appears to be required for maintaining their structural integrity. The requirement for myosin VI in hearing makes this gene an excellent candidate for a human deafness disorder.

    View details for Web of Science ID A1995TH62900012

    View details for PubMedID 7493015

  • CHROMOSOMAL LOCALIZATION, EMBRYONIC EXPRESSION, AND IMPRINTING TESTS FOR BMP7 ON DISTAL MOUSE CHROMOSOME-2 GENOMICS Marker, P. C., King, J. A., Copeland, N. G., Jenkins, N. A., KINGSLEY, D. M. 1995; 28 (3): 576-580

    Abstract

    Murine Bmp7 has been assigned to distal Chromosome 2 by interspecific backcross mapping. The map location suggests close linkage to classical mouse mutations and places Bmp7 within a chromosome region thought to contain one or more unidentified imprinted genes. A direct test suggests that Bmp7 is not imprinted. An examination of embryonic RNA expression patterns shows that Bmp7 is expressed in a variety of skeletal and nonskeletal tissues. Both embryonic expression patterns and the human chromosomal sublocalization inferred from its mouse location make Bmp7 a candidate for the gene affected in some patients with Holt-Oram syndrome.

    View details for Web of Science ID A1995RQ98900030

    View details for PubMedID 7490098

  • LONG-BONE GEOMETRY AND STRENGTH IN ADULT BMP-5 DEFICIENT MICE BONE Mikic, B., VANDERMEULEN, M. C., KINGSLEY, D. M., Carter, D. R. 1995; 16 (4): 445-454

    Abstract

    Bone morphogenetic proteins (BMPs) play a critical role in early skeletal development. BMPs are also potential mediators of bone response to mechanical loading, but their role in later stages of bone growth and adaptation has yet to be studied. We characterized the postcranial skeletal defects in mature mice with BMP deficiency by measuring hind-limb muscle mass and long bone geometric, material, and torsional mechanical properties. The animals studied were 26-week-old short ear mice (n = 10) with a homozygous deletion of the BMP-5 gene and their heterozygous control litter mates (n = 15). Gender-related effects, which were found to be independent of genotype, were also examined. The femora of short ear mice were 3% shorter than in controls and had significantly lower values of many cross-sectional geometric and structural strength parameters (p < 0.05). No significant differences in ash content or material properties were detected. Lower femoral whole bone torsional strength was due to the smaller cross-sectional geometry (16% smaller section modulus) in the short ear mice. The diminished cross-sectional geometry may be commensurate with lower levels of in vivo loading, as reflected by body mass (-8%) and quadriceps mass (-11%). While no significant gender differences were found in whole bone strength or cross-sectional geometry, males had significantly greater body mass (+18%) and quadriceps mass (+15%) and lower tibio-fibular ash content (-3%). The data suggest that adult female mice have a more robust skeleton than males, relative to in vivo mechanical demands. Furthermore, although the bones of short ear mice are smaller and weaker than in control animals, they appear to be biomechanically appropriate for the in vivo mechanical loads that they experience.

    View details for Web of Science ID A1995RB63900005

    View details for PubMedID 7605705

  • BMP5 AND THE MOLECULAR, SKELETAL, AND SOFT-TISSUE ALTERATIONS IN SHORT EAR MICE DEVELOPMENTAL BIOLOGY King, J. A., Marker, P. C., Seung, K. J., KINGSLEY, D. M. 1994; 166 (1): 112-122

    Abstract

    Mutations at the mouse short ear (se) locus alter the formation and repair of skeletal structures and the development of several soft tissues. Most of the developmental effects of the gene have been studied using a spontaneous mutation reported over 70 years ago. Here we show that this mutation consists of a nonsense mutation in a secreted signaling molecule called bone morphogenetic protein 5 (BMP5). This small sequence alteration, in combination with previously reported translocation and deletion mutations, provides strong genetic evidence that BMP5 is the normal product of the se locus. Transcripts from the Bmp5 gene are expressed at the earliest stages of normal skeletal development in patterns that closely resemble the shapes of forming skeletal elements. The gene is also expressed at several sites of soft tissue abnormalities previously reported in se animals, including lungs, liver, ureter, bladder, and intestines. The combined genetic, biochemical, and expression data suggest that BMP5 is a key signal used to initiate formation of particular skeletal elements and is required for normal development of several soft tissues as well.

    View details for Web of Science ID A1994PT49200009

    View details for PubMedID 7958439

  • LIMB ALTERATIONS IN BRACHYPODISM MICE DUE TO MUTATIONS IN A NEW MEMBER OF THE TGF-BETA-SUPERFAMILY NATURE Storm, E. E., Huynh, T. V., Copeland, N. G., Jenkins, N. A., KINGSLEY, D. M., Lee, S. J. 1994; 368 (6472): 639-643

    Abstract

    The mutation brachypodism (bp) alters the length and number of bones in the limbs of mice but spares the axial skeleton. It illustrates the importance of specific genes in controlling the morphogenesis of individual skeletal elements in the tetrapod limb. We now report the isolation of three new members of the transforming growth factor-beta (TGF-beta) superfamily (growth/differentiation factors (GDF) 5,6 and 7) and show by mapping, expression patterns and sequencing that mutations in Gdf5 are responsible for skeletal alterations in bp mice. GDF5 and the closely related GDF6 and GDF7 define a new subgroup of factors related to known bone- and cartilage-inducing molecules, the bone morphogenetic proteins (BMPs). Studies of Bmp5 mutations in short ear mice have shown that at least one other BMP gene is also required for normal skeletal development. The highly specific skeletal alterations in bp and short ear mice suggest that different members of the BMP family control the formation of different morphological features in the mammalian skeleton.

    View details for Web of Science ID A1994NF39200062

    View details for PubMedID 8145850

  • THE TGF-BETA SUPERFAMILY - NEW MEMBERS, NEW RECEPTORS, AND NEW GENETIC TESTS OF FUNCTION IN DIFFERENT ORGANISMS GENES & DEVELOPMENT KINGSLEY, D. M. 1994; 8 (2): 133-146

    View details for Web of Science ID A1994MU12700001

    View details for PubMedID 8299934

  • MOUSE CHROMOSOME-9 MAMMALIAN GENOME Imai, K., KINGSLEY, D. M. 1994; 5: S139-S153

    View details for Web of Science ID A1994QD08500009

    View details for PubMedID 7719002

  • WHAT DO BMPS DO IN MAMMALS - CLUES FROM THE MOUSE SHORT-EAR MUTATION TRENDS IN GENETICS KINGSLEY, D. M. 1994; 10 (1): 16-21

    Abstract

    Bone morphogenetic proteins (BMPs) are a family of secreted signaling molecules that were originally isolated on the basis of their remarkable ability to induce the formation of ectopic bones when implanted into adult animals. The first mutations identified in a mammalian BMP gene suggest that members of this family induce the formation, patterning and repair of particular morphological features in higher animals.

    View details for Web of Science ID A1994MR68900007

    View details for PubMedID 8146910

  • Encyclopedia of the mouse genome III. October 1993. Mouse chromosome 9. Mammalian genome KINGSLEY, D. M. 1993; 4: S136-53

    View details for PubMedID 8268669

  • MOUSE CHROMOSOME-9 MAMMALIAN GENOME KINGSLEY, D. M. 1993; 4: S136-S153
  • THE MOUSE SHORT-EAR SKELETAL MORPHOGENESIS LOCUS IS ASSOCIATED WITH DEFECTS IN A BONE MORPHOGENETIC MEMBER OF THE TGF-BETA SUPERFAMILY CELL KINGSLEY, D. M., Bland, A. E., Grubber, J. M., Marker, P. C., Russell, L. B., Copeland, N. G., Jenkins, N. A. 1992; 71 (3): 399-410

    Abstract

    The mouse short ear gene is required for normal growth and patterning of skeletal structures, and for repair of bone fractures in adults. We have carried out an extensive chromosome walk in the chromosome region that surrounds this locus. Here we show that the short ear region contains the gene for a TGF beta-related protein called bone morphogenetic protein 5 (Bmp-5). This gene is deleted or rearranged in several independent mutations at the short ear locus. Mice homozygous for large deletions of the Bmp-5 coding region are viable and fertile. Mutations at the short ear locus provide an important new tool for defining the normal functions of BMPs in mammals. The specific skeletal defects seen in short-eared animals, which occur against a background of otherwise normal skeletal structures, suggest that particular aspects of skeletal morphology may be determined by individual members of a family of signaling factors that can induce the formation of cartilage and bone in vivo.

    View details for Web of Science ID A1992JW43500007

    View details for PubMedID 1339316

  • MOUSE CHROMOSOME-9 KINGSLEY, D. M. SPRINGER VERLAG. 1992: S136-S152

    View details for Web of Science ID A1992JT43900009

    View details for PubMedID 1498428

  • Mouse chromosome 9. Mammalian genome KINGSLEY, D. M. 1991; 1: S127-45

    View details for PubMedID 1799796

  • CHROMOSOMAL LOCATION OF MURINE AND HUMAN IL-1 RECEPTOR GENES GENOMICS Copeland, N. G., SILAN, C. M., KINGSLEY, D. M., Jenkins, N. A., Cannizzaro, L. A., Croce, C. M., Huebner, K., Sims, J. E. 1991; 9 (1): 44-50

    Abstract

    The gene for the type I interleukin-1 (IL-1) receptor has been mapped in both mouse and human. In the human genome, a combination of segregation analysis of rodent-human hybrid cells and chromosomal in situ hybridization has placed the gene on the long arm of chromosome 2, at band 2q12. This is near the reported map position of the loci for IL-1 alpha and IL-1 beta (2q13----2q21). The murine gene has been mapped by analysis of restriction fragment length polymorphisms in interspecific backcrosses to the centromeric end of chromosome 1, in a region that is syntenic to a portion of human chromosome 2. The murine Il-1r1 gene has thus been separated from the IL-1 genes, which lie on murine chromosome 2.

    View details for Web of Science ID A1991EP97200006

    View details for PubMedID 1672292

  • AN ANCIENT, HIGHLY CONSERVED FAMILY OF CYSTEINE-RICH PROTEIN DOMAINS REVEALED BY CLONING TYPE-I AND TYPE-II MURINE MACROPHAGE SCAVENGER RECEPTORS PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Freeman, M., Ashkenas, J., Rees, D. J., KINGSLEY, D. M., Copeland, N. G., Jenkins, N. A., Krieger, M. 1990; 87 (22): 8810-8814

    Abstract

    Scavenger receptors have been implicated in the development of atherosclerosis and other macrophage-associated functions. The bovine type I and type II scavenger receptors are multidomain transmembrane proteins that differ only by the presence in the type I receptor of an additional, extracellular cysteine-rich C-terminal domain. The isolation of type I and type II receptor cDNAs from a murine macrophage cell line, P388D1, establishes the presence of mRNAs encoding both receptor types in a single cell. Their sequences are highly similar to the bovine cDNAs. Receptor type-specific cDNA probes map to a common locus on murine chromosomes 8, suggesting that a single gene encodes both mRNAs. The type I-specific scavenger receptor cysteine-rich (SRCR) domain helps define a previously unrecognized family of remarkably well-conserved domains. Highly homologous SRCR domains (one, three, or four per polypeptide chain) are found in diverse secreted and cell-surface proteins from humans (e.g., CD5, complement factor I), mice (Ly-1), and sea urchins (speract receptor).

    View details for Web of Science ID A1990EJ60700026

    View details for PubMedID 1978939

  • CHROMOSOMAL LOCALIZATION OF 7 MEMBERS OF THE MURINE TGF-BETA SUPERFAMILY SUGGESTS CLOSE LINKAGE TO SEVERAL MORPHOGENETIC MUTANT LOCI GENOMICS Dickinson, M. E., KOBRIN, M. S., SILAN, C. M., KINGSLEY, D. M., JUSTICE, M. J., MILLER, D. A., CECI, J. D., LOCK, L. F., Lee, A., BUCHBERG, A. M., SIRACUSA, L. D., LYONS, K. M., DERYNCK, R., HOGAN, B. L., Copeland, N. G., Jenkins, N. A. 1990; 6 (3): 505-520
  • GENETIC ABLATION OF A MOUSE GENE EXPRESSED SPECIFICALLY IN BRAIN EMBO JOURNAL KINGSLEY, D. M., Rinchik, E. M., Russell, L. B., Ottiger, H. P., Sutcliffe, J. G., Copeland, N. G., Jenkins, N. A. 1990; 9 (2): 395-399

    Abstract

    The 1B1075 gene was initially identified from a cDNA clone of a rat brain messenger RNA expressed in particular subsets of CNS neurons and pituitary cells. Although the protein encoded by this gene is of unknown function, its sequence suggests that it may be related to secretogranin proteins, which are found in association with secretory granules in a variety of peptidergic endocrine and neuronal cells. Here we show that the mouse 1B1075 gene is located between the dilute (d) and short ear (se) genes on chromosome 9. Many different deletion mutations have previously been isolated in the genetic region that includes these genes. By producing mice carrying two deletions that overlap at the 1B1075 locus, the gene for this brain-specific message can be completely eliminated from otherwise viable animals. The animals missing the 1B1075 gene provide an important new tool for determining the function of this gene in the brain. In addition, these results provide a new molecular entry point for detailed characterization of other genes in the d-se region.

    View details for Web of Science ID A1990CN55700012

    View details for PubMedID 2303033

  • A MOLECULAR GENETIC-LINKAGE MAP OF MOUSE CHROMOSOME-9 WITH REGIONAL LOCALIZATIONS FOR THE GSTA, T3G, ETS-1 AND LDLR LOCI GENETICS KINGSLEY, D. M., Jenkins, N. A., Copeland, N. G. 1989; 123 (1): 165-172

    Abstract

    A 64-centiMorgan linkage map of mouse chromosome 9 was developed using cloned DNA markers and an interspecific backcross between Mus spretus and the C57BL/6J inbred strain. This map was compared to conventional genetic maps using six markers previously localized in laboratory mouse strains. These markers included thymus cell antigen-1, cytochrome P450-3, dilute, transferrin, cholecystokinin, and the G-protein alpha inhibitory subunit. No evidence was seen for segregation distortion, chromosome rearrangements, or altered genetic distances in the results from interspecific backcross mapping. Regional map locations were determined for four genes that were previously assigned to chromosome 9 using somatic cell hybrids. These genes were glutathione S-transferase Ya subunit (Gsta), the T3 gamma subunit, the low density lipoprotein receptor, and the Ets-1 oncogene. The map locations for these genes establish new regions of synteny between mouse chromosome 9 and human chromosomes 6, 11, and 19. In addition, the close linkage detected between the dilute and Gsta loci suggests that the Gsta locus may be part of the dilute/short ear complex, one of the most extensively studied genetic regions of the mouse.

    View details for Web of Science ID A1989AN07000015

    View details for PubMedID 2572508

  • A RETROVIRAL INSERTION IN THE DILUTE (D) LOCUS PROVIDES MOLECULAR ACCESS TO THIS REGION OF MOUSE CHROMOSOME-9 PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY Jenkins, N. A., Strobel, M. C., SEPERACK, P. K., KINGSLEY, D. M., Moore, K. J., Mercer, J. A., Russell, L. B., Copeland, N. G. 1989; 36: 207-220

    View details for Web of Science ID A1989AM04200016

    View details for PubMedID 2544008