Scholars@Duke
Gregory Allan Wray

Gregory Allan Wray

Professor of Biology
Biology
gwray@duke.edu
Duke Box 90325, Durham, NC 27708-0325
125 Science Drive, 4104 French Family Science Center, Durham, NC 27708

Selected Publications

Lepidopteran scale cells derive from sensory organ precursors through a canonical lineage.

Journal Article Development (Cambridge, England) · March 2025 The success of butterflies and moths is tightly linked to the origin of scales within the group. A long-standing hypothesis postulates that scales are homologous to the well-described mechanosensory bristles found in the fruit fly Drosophila melanogaster, ... Full text Cite

Single-Cell Transcriptomics Reveals Evolutionary Reconfiguration of Embryonic Cell Fate Specification in the Sea Urchin Heliocidaris erythrogramma.

Journal Article Genome biology and evolution · January 2025 Altered regulatory interactions during development likely underlie a large fraction of phenotypic diversity within and between species, yet identifying specific evolutionary changes remains challenging. Analysis of single-cell developmental transcriptomes ... Full text Open Access Cite

An RNA interference approach for functional studies in the sea urchin and its use in analysis of nodal signaling gradients.

Journal Article Developmental biology · December 2024 Dicer substrate interfering RNAs (DsiRNAs) destroy targeted transcripts using the RNA-Induced Silencing Complex (RISC) through a process called RNA interference (RNAi). This process is ubiquitous among eukaryotes. Here we report the utility of DsiRNA in em ... Full text Cite

Reprogramming of cells during embryonic transfating: overcoming a reprogramming block.

Journal Article Development (Cambridge, England) · December 2024 Regulative development, demonstrated by many animal embryos, is the ability to replace missing cells or parts. The underlying molecular mechanism(s) of that ability is not well understood. If sea urchin micromeres (skeletogenic cell progenitors) are remove ... Full text Cite

Contrasting the development of larval and adult body plans during the evolution of biphasic lifecycles in sea urchins.

Journal Article Development (Cambridge, England) · October 2024 Biphasic lifecycles are widespread among animals, but little is known about how the developmental transition between larvae and adults is regulated. Sea urchins are a unique system for studying this phenomenon because of the stark differences between their ... Full text Cite

A human-specific enhancer fine-tunes radial glia potency and corticogenesis.

Journal Article bioRxiv · April 11, 2024 Humans evolved an extraordinarily expanded and complex cerebral cortex, associated with developmental and gene regulatory modifications 1-3 . Human accelerated regions (HARs) are highly conserved genomic sequences with human-specific nucleotide substitutio ... Full text Link to item Cite

Genomic insights into Plasmodium vivax population structure and diversity in central Africa.

Journal Article Malaria journal · January 2024 BackgroundThough Plasmodium vivax is the second most common malaria species to infect humans, it has not traditionally been considered a major human health concern in central Africa given the high prevalence of the human Duffy-negative phenotype t ... Full text Cite

Hybrid Epigenomes Reveal Extensive Local Genetic Changes to Chromatin Accessibility Contribute to Divergence in Embryonic Gene Expression Between Species.

Journal Article Molecular biology and evolution · November 2023 Chromatin accessibility plays an important role in shaping gene expression, yet little is known about the genetic and molecular mechanisms that influence the evolution of chromatin configuration. Both local (cis) and distant (trans) genetic influences can ... Full text Cite

Near-Chromosomal-Level Genome Assembly of the Sea Urchin Echinometra lucunter, a Model for Speciation in the Sea.

Journal Article Genome biology and evolution · June 2023 Echinometra lucunter, the rock-boring sea urchin, is a widely distributed echinoid and a model for ecological studies of reproduction, responses to climate change, and speciation. We present a near chromosome-level genome assembly of E. lucunter, including ... Full text Open Access Cite

Feedback circuits are numerous in embryonic gene regulatory networks and offer a stabilizing influence on evolution of those networks.

Journal Article EvoDevo · June 2023 The developmental gene regulatory networks (dGRNs) of two sea urchin species, Lytechinus variegatus (Lv) and Strongylocentrotus purpuratus (Sp), have remained remarkably similar despite about 50 million years since a common ancestor. Hundreds of parallel e ... Full text Open Access Cite

CRISPR/Cas9-Mediated Disruption of Endo16 Cis-Regulatory Elements in Sea Urchin Embryos

Journal Article Fishes · February 1, 2023 Sea urchins have become significant mariculture species globally, and also serve as invertebrate model organisms in developmental biology. Cis-regulatory elements (enhancers) control development and physiology by regulating gene expression. Mutations that ... Full text Cite

Hybrid epigenomes reveal extensive local genetic changes to chromatin accessibility contribute to divergence in embryonic gene expression between species.

Journal Article bioRxiv · January 4, 2023 Chromatin accessibility plays an important role in shaping gene expression patterns across development and evolution; however, little is known about the genetic and molecular mechanisms that influence chromatin configuration itself. Because cis and trans i ... Full text Link to item Cite

Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris sea urchins.

Journal Article Nature ecology & evolution · December 2022 Changes in developmental gene regulatory networks (dGRNs) underlie much of the diversity of life, but the evolutionary mechanisms that operate on regulatory interactions remain poorly understood. Closely related species with extreme phenotypic divergence p ... Full text Cite

A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes.

Journal Article Genome biology and evolution · October 2022 Echinometra is the most widespread genus of sea urchin and has been the focus of a wide range of studies in ecology, speciation, and reproduction. However, available genetic data for this genus are generally limited to a few select loci. Here, we present a ... Full text Cite

Evolutionary Changes in the Chromatin Landscape Contribute to Reorganization of a Developmental Gene Network During Rapid Life History Evolution in Sea Urchins.

Journal Article Molecular biology and evolution · September 2022 Chromatin configuration is highly dynamic during embryonic development in animals, exerting an important point of control in transcriptional regulation. Yet there exists remarkably little information about the role of evolutionary changes in chromatin conf ... Full text Cite

Extreme phenotypic divergence and the evolution of development.

Chapter · January 2022 As analyses of developmental mechanisms extend to ever more species, it becomes important to understand not just what is conserved or altered during evolution, but why. Closely related species that exhibit extreme phenotypic divergence can be uniquely info ... Full text Cite

Transcriptomic analysis of Nodal - and BMP- associated genes during development to the juvenile seastar in Parvulastra exigua (Asterinidae).

Journal Article Marine genomics · October 2021 Featured Publication The molecular mechanisms underlying development of the pentameral body of adult echinoderms are poorly understood but are important to solve with respect to evolution of a unique body plan that contrasts with the bilateral body plan of other deuterostomes. ... Full text Cite

Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo.

Journal Article Development (Cambridge, England) · October 2021 Using scRNA-seq coupled with computational approaches, we studied transcriptional changes in cell states of sea urchin embryos during development to the larval stage. Eighteen closely spaced time points were taken during the first 24 h of development of Ly ... Full text Open Access Cite

The epidemiology of Plasmodium vivax among adults in the Democratic Republic of the Congo.

Journal Article Nature communications · July 2021 Reports of P. vivax infections among Duffy-negative hosts have accumulated throughout sub-Saharan Africa. Despite this growing body of evidence, no nationally representative epidemiological surveys of P. vivax in sub-Saharan Africa have been performed. To ... Full text Cite

Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders.

Journal Article Nat Commun · June 25, 2021 Cellular heterogeneity in the human brain obscures the identification of robust cellular regulatory networks, which is necessary to understand the function of non-coding elements and the impact of non-coding genetic variation. Here we integrate genome-wide ... Full text Link to item Cite

An early cell shape transition drives evolutionary expansion of the human forebrain.

Journal Article Cell · April 2021 Featured Publication The human brain has undergone rapid expansion since humans diverged from other great apes, but the mechanism of this human-specific enlargement is still unknown. Here, we use cerebral organoids derived from human, gorilla, and chimpanzee cells to study dev ... Full text Cite

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · April 2021 Animal gastrointestinal tracts harbor a microbiome that is integral to host function, yet species from diverse phyla have evolved a reduced digestive system or lost it completely. Whether such changes are associated with alterations in the diversity and/or ... Full text Cite

TBX5-encoded T-box transcription factor 5 variant T223M is associated with long QT syndrome and pediatric sudden cardiac death.

Journal Article Am J Med Genet A · March 2021 Featured Publication Long QT syndrome (LQTS) is a genetic disease resulting in a prolonged QT interval on a resting electrocardiogram, predisposing affected individuals to polymorphic ventricular tachycardia and sudden death. Although a number of genes have been implicated in ... Full text Open Access Link to item Cite

Methodologies for Following EMT In Vivo at Single Cell Resolution.

Journal Article Methods in molecular biology (Clifton, N.J.) · January 2021 An epithelial-mesenchymal transition (EMT) occurs in almost every metazoan embryo at the time mesoderm begins to differentiate. Several embryos have a long record as models for studying an EMT given that a known population of cells enters the EMT at a know ... Full text Cite

The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia.

Journal Article BMC biology · January 2021 Featured Publication BackgroundInhibitors of apoptosis (IAPs) are critical regulators of programmed cell death that are essential for development, oncogenesis, and immune and stress responses. However, available knowledge regarding IAP is largely biased toward humans ... Full text Cite

Ocean acidification induces distinct transcriptomic responses across life history stages of the sea urchin Heliocidaris erythrogramma.

Journal Article Molecular ecology · December 2020 Ocean acidification (OA) from seawater uptake of rising carbon dioxide emissions impairs development in marine invertebrates, particularly in calcifying species. Plasticity in gene expression is thought to mediate many of these physiological effects, but h ... Full text Cite

Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses.

Journal Article Genome biology and evolution · July 2020 Lytechinus variegatus is a camarodont sea urchin found widely throughout the western Atlantic Ocean in a variety of shallow-water marine habitats. Its distribution, abundance, and amenability to developmental perturbation make it a popular model for ecolog ... Full text Cite

Genetic basis for divergence in developmental gene expression in two closely related sea urchins.

Journal Article Nature ecology & evolution · June 2020 The genetic basis for divergence in developmental gene expression among species is poorly understood, despite growing evidence that such changes underlie many interesting traits. Here we quantify transcription in hybrids of Heliocidaris tuberculata and Hel ... Full text Cite

Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral.

Journal Article BMC genomics · May 2020 BackgroundAdaptive changes in cis-regulatory elements are an essential component of evolution by natural selection. Identifying adaptive and functional noncoding DNA elements throughout the genome is therefore crucial for understanding the relatio ... Full text Open Access Cite

Conserved and divergent expression dynamics during early patterning of the telencephalon in mouse and chick embryos.

Journal Article Progress in neurobiology · March 2020 The mammalian and the avian telencephalon are nearly indistinguishable at early embryonic vesicle stages but differ substantially in form and function at their adult stage. We sequenced and analyzed RNA populations present in mouse and chick during the ear ... Full text Cite

Transcriptomic analysis of sea star development through metamorphosis to the highly derived pentameral body plan with a focus on neural transcription factors.

Journal Article DNA research : an international journal for rapid publication of reports on genes and genomes · February 2020 The Echinodermata is characterized by a secondarily evolved pentameral body plan. While the evolutionary origin of this body plan has been the subject of debate, the molecular mechanisms underlying its development are poorly understood. We assembled a de n ... Full text Cite

Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function.

Journal Article PeerJ · January 2020 BackgroundThe emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to huma ... Full text Open Access Cite

Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function

Journal Article · 2020 Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to hum ... Full text Open Access Cite

Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach.

Journal Article Genome biology and evolution · October 2019 Changes in transcriptional regulation are thought to be a major contributor to the evolution of phenotypic traits, but the contribution of changes in chromatin accessibility to the evolution of gene expression remains almost entirely unknown. To address th ... Full text Cite

A comparative analysis of egg provisioning using mass spectrometry during rapid life history evolution in sea urchins.

Journal Article Evol Dev · July 2019 A dramatic life history switch that has evolved numerous times in marine invertebrates is the transition from planktotrophic (feeding) to lecithotrophic (nonfeeding) larval development-an evolutionary tradeoff with many important developmental and ecologic ... Full text Open Access Link to item Cite

Comparative Analyses of Chromatin Landscape in White Adipose Tissue Suggest Humans May Have Less Beigeing Potential than Other Primates.

Journal Article Genome Biol Evol · July 1, 2019 Humans carry a much larger percentage of body fat than other primates. Despite the central role of adipose tissue in metabolism, little is known about the evolution of white adipose tissue in primates. Phenotypic divergence is often caused by genetic diver ... Full text Link to item Cite

Rudolf A. Raff (1941-2019).

Journal Article Nature ecology & evolution · April 2019 Full text Cite

Identifying gene expression from single cells to single genes.

Journal Article Methods in cell biology · January 2019 Gene regulatory networks reveal how transcription factors contribute to a dynamic cascade of cellular information processing. Recent advances in technologies have enhanced the toolkit for testing GRN mechanisms and connections. Here we emphasize three appr ... Full text Cite

Embryo microinjection of the lecithotrophic sea urchin Heliocidaris erythrogramma.

Journal Article Journal of biological methods · January 2019 Microinjection is a common embryological technique used for many types of experiments, including lineage tracing, manipulating gene expression, or genome editing. Injectable reagents include mRNA overexpression, mis-expression, or dominant-negative experim ... Full text Open Access Cite

Comparative analyses of chromatin landscape in white adipose tissue suggest humans may have less beigeing potential than other primates

Journal Article · 2019 Humans carry a much larger percentage of body fat than other primates. Despite the central role of adipose tissue in metabolism, little is known about the evolution of white adipose tissue in primates. Phenotypic divergence is often caused by genetic diver ... Full text Cite

Evolution of abbreviated development inHeliocidaris erythrogrammadramatically re-wired the highly conserved sea urchin developmental gene regulatory network to decouple signaling center function from ultimate fate

Journal Article · 2019 Developmental gene regulatory networks (GRNs) describe the interactions among gene products that drive the differential transcriptional and cell regulatory states that pattern the embryo and specify distinct cell fates. GRNs are often deeply conserved, but ... Full text Cite

Integrative functional genomic analysis of human brain development and neuropsychiatric risks.

Journal Article Science · December 14, 2018 To broaden our understanding of human neurodevelopment, we profiled transcriptomic and epigenomic landscapes across brain regions and/or cell types for the entire span of prenatal and postnatal development. Integrative analysis revealed temporal, regional, ... Full text Link to item Cite

New NSF policy will stifle innovation.

Journal Article Science (New York, N.Y.) · October 2018 Full text Cite

Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia.

Journal Article Nat Commun · August 7, 2018 Schizophrenia genome-wide association studies have identified >150 regions of the genome associated with disease risk, yet there is little evidence that coding mutations contribute to this disorder. To explore the mechanism of non-coding regulatory element ... Full text Link to item Cite

Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee.

Journal Article Genome biology and evolution · March 2018 Humans experience higher rates of age-associated diseases than our closest living evolutionary relatives, chimpanzees. Environmental factors can explain many of these increases in disease risk, but species-specific genetic changes can also play a role. All ... Full text Open Access Cite

Expression of genes and proteins of the pax-six-eya-dach network in the metamorphic sea urchin: Insights into development of the enigmatic echinoderm body plan and sensory structures.

Journal Article Developmental dynamics : an official publication of the American Association of Anatomists · January 2018 BackgroundPhotoreception-associated genes of the Pax-Six-Eya-Dach network (PSEDN) are deployed for many roles in addition to photoreception development. In this first study of PSEDN genes during development of the pentameral body in sea urchins, w ... Full text Cite

Rudiment resorption as a response to starvation during larval development in the sea urchin Strongylocentrotus droebachiensis

Journal Article Canadian Journal of Zoology · January 1, 2018 Phenotypic flexibility (reversible phenotypic change) enables organisms to couple internal, ontogenetic responses with external, environmental cues. Phenotypic flexibility also provides organisms with the capacity to buffer stereotypical internal, developm ... Full text Cite

The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics.

Journal Article Molecular phylogenetics and evolution · October 2017 Multi-locus phylogenetic studies of echinoderms based on Sanger and RNA-seq technologies and the fossil record have provided evidence for the Asterozoa-Echinozoa hypothesis. This hypothesis posits a sister relationship between asterozoan classes (Asteroide ... Full text Open Access Cite

Gene expression and adaptive noncoding changes during human evolution.

Journal Article BMC genomics · June 2017 BackgroundDespite evidence for adaptive changes in both gene expression and non-protein-coding, putatively regulatory regions of the genome during human evolution, the relationship between gene expression and adaptive changes in cis-regulatory reg ... Full text Cite

Nodal and BMP expression during the transition to pentamery in the sea urchin Heliocidaris erythrogramma: insights into patterning the enigmatic echinoderm body plan.

Journal Article BMC developmental biology · February 13, 2017 BackgroundThe molecular mechanisms underlying the development of the unusual echinoderm pentameral body plan and their likeness to mechanisms underlying the development of the bilateral plans of other deuterostomes are of interest in tracing body ... Full text Cite

Genomic Characterization of the Evolutionary Potential of the Sea Urchin Strongylocentrotus droebachiensis Facing Ocean Acidification.

Journal Article Genome biology and evolution · December 2016 Ocean acidification (OA) is increasing due to anthropogenic CO2 emissions and poses a threat to marine species and communities worldwide. To better project the effects of acidification on organisms' health and persistence, an understanding is needed of the ... Full text Open Access Cite

Whole-Genome Sequences of Agricultural, Host-Associated Campylobacter coli and Campylobacter jejuni Strains.

Journal Article Genome announcements · August 2016 We report here the genome sequences of four agricultural, multidrug-resistant Campylobacter spp.: C. coli 11601 and C. jejuni 11601MD, isolated from turkey cecum and jejunum, respectively, and C. coli 6067 and C. coli 6461, isolated from turkey-house water ... Full text Cite

Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris.

Journal Article PLoS biology · March 2016 The ecologically significant shift in developmental strategy from planktotrophic (feeding) to lecithotrophic (nonfeeding) development in the sea urchin genus Heliocidaris is one of the most comprehensively studied life history transitions in any animal. Al ... Full text Cite

Never ending analysis of a century old evolutionary debate: "Unringing" the urmetazoon bell

Journal Article Frontiers in Ecology and Evolution · February 4, 2016 Our understanding of the early evolution of animals will be greatly improved if a final solution can be found to the evolutionary relationships between Porifera, Placozoa, Ctenophora, Cnidaria, and Bilateria. There have been many recent attempts to solve t ... Full text Cite

EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms.

Journal Article BMC bioinformatics · January 2016 BackgroundOne of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation transcriptome data. The current dataset is the largest assembled for echinod ... Full text Open Access Cite

Transcriptomic analysis of Nodal- and BMP-associated genes during juvenile development of the sea urchin Heliocidaris erythrogramma.

Journal Article Marine genomics · December 2015 Understanding the unusual radial body plan of echinoderms and its relationship to the bilateral plan of other deuterostomes remains a challenge. The molecular processes of embryonic and early larval development in sea urchins are well characterised, but th ... Full text Cite

Molecular clocks and the early evolution of metazoan nervous systems.

Journal Article Philosophical transactions of the Royal Society of London. Series B, Biological sciences · December 2015 The timing of early animal evolution remains poorly resolved, yet remains critical for understanding nervous system evolution. Methods for estimating divergence times from sequence data have improved considerably, providing a more refined understanding of ... Full text Cite

The PsychENCODE project.

Journal Article Nat Neurosci · December 2015 Recent research on disparate psychiatric disorders has implicated rare variants in genes involved in global gene regulation and chromatin modification, as well as many common variants located primarily in regulatory regions of the genome. Understanding pre ... Full text Open Access Link to item Cite

High spatial resolution proteomic comparison of the brain in humans and chimpanzees.

Journal Article The Journal of comparative neurology · October 2015 We performed high-throughput mass spectrometry at high spatial resolution from individual regions (anterior cingulate and primary motor, somatosensory, and visual cortices) and layers of the neocortex (layers III, IV, and V) and cerebellum (granule cell la ... Full text Cite

Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees.

Journal Article Genome Biol Evol · July 10, 2015 Although transcriptomic profiling has become the standard approach for exploring molecular differences in the primate brain, very little is known about how the expression levels of gene transcripts relate to downstream protein abundance. Moreover, it is un ... Full text Open Access Link to item Cite

Analysis of synaptic gene expression in the neocortex of primates reveals evolutionary changes in glutamatergic neurotransmission.

Journal Article Cerebral cortex (New York, N.Y. : 1991) · June 2015 Increased relative brain size characterizes the evolution of primates, suggesting that enhanced cognition plays an important part in the behavioral adaptations of this mammalian order. In addition to changes in brain anatomy, cognition can also be regulate ... Full text Cite

Evolution of gene expression network underlying a disease state

Conference INTEGRATIVE AND COMPARATIVE BIOLOGY · April 1, 2015 Link to item Cite

Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex.

Journal Article Curr Biol · March 16, 2015 The human neocortex differs from that of other great apes in several notable regards, including altered cell cycle, prolonged corticogenesis, and increased size [1-5]. Although these evolutionary changes most likely contributed to the origin of distinctive ... Full text Open Access Link to item Cite

Does evolutionary theory need a rethink?

Journal Article Nature · October 2014 Full text Cite

Genetic comparisons yield insight into the evolution of enamel thickness during human evolution.

Journal Article Journal of human evolution · August 2014 Enamel thickness varies substantially among extant hominoids and is a key trait with significance for interpreting dietary adaptation, life history trajectory, and phylogenetic relationships. There is a strong link in humans between enamel formation and mu ... Full text Cite

Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears.

Journal Article Cell · May 2014 Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyper-lipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear ... Full text Cite

Transcriptomic analysis of the highly derived radial body plan of a sea urchin.

Journal Article Genome biology and evolution · April 2014 With their complex life cycle and highly derived body plan, echinoderms are unique among bilaterians. Although early development has been intensively studied, the molecular mechanisms underlying development of the adult echinoderm and its unusual radial bo ... Full text Cite

High-coverage sequencing and annotated assemblies of the budgerigar genome.

Journal Article Gigascience · 2014 BACKGROUND: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and unders ... Full text Open Access Link to item Cite

The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network.

Journal Article PLoS biology · October 2013 Regulatory interactions buffer development against genetic and environmental perturbations, but adaptation requires phenotypes to change. We investigated the relationship between robustness and evolvability within the gene regulatory network underlying dev ... Full text Cite

Social environment influences the relationship between genotype and gene expression in wild baboons.

Journal Article Philosophical transactions of the Royal Society of London. Series B, Biological sciences · May 2013 Variation in the social environment can have profound effects on survival and reproduction in wild social mammals. However, we know little about the degree to which these effects are influenced by genetic differences among individuals, and conversely, the ... Full text Cite

Genomics and the evolution of phenotypic traits

Journal Article Annual Review of Ecology, Evolution, and Systematics · January 1, 2013 Evolutionary genetics has entered an unprecedented era of discovery, catalyzed in large part by the development of technologies that provide information about genome sequence and function. An important benefit is the ability to move beyond a handful of mod ... Full text Cite

Insights from a chimpanzee adipose stromal cell population: opportunities for adult stem cells to expand primate functional genomics.

Journal Article Genome biology and evolution · January 2013 Comparisons between humans and chimpanzees are essential for understanding traits unique to each species. However, linking important phenotypic differences to underlying molecular changes is often challenging. The ability to generate, differentiate, and pr ... Full text Cite

Genetics of gene expression responses to temperature stress in a sea urchin gene network.

Journal Article Molecular ecology · September 2012 Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter the contribution of additive genetic variation to gene expression during development of the purple sea urc ... Full text Cite

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.

Journal Article PLoS Genet · June 2012 Understanding the molecular basis for phenotypic differences between humans and other primates remains an outstanding challenge. Mutations in non-coding regulatory DNA that alter gene expression have been hypothesized as a key driver of these phenotypic di ... Full text Link to item Cite

Conservation and function of noncoding RNAs in primate evolution

Conference INTEGRATIVE AND COMPARATIVE BIOLOGY · April 1, 2012 Link to item Cite

Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus.

Journal Article Evolution & development · March 2012 Despite the fact that noncoding sequences comprise a substantial fraction of functional sites within all genomes, the evolutionary mechanisms that operate on genetic variation within regulatory elements remain poorly understood. In this study, we examine t ... Full text Cite

Changes in gene expression associated with reproductive maturation in wild female baboons.

Journal Article Genome biology and evolution · January 2012 Changes in gene expression during development play an important role in shaping morphological and behavioral differences, including between humans and nonhuman primates. Although many of the most striking developmental changes occur during early developmen ... Full text Cite

Reconstitution of the human biome as the most reasonable solution for epidemics of allergic and autoimmune diseases.

Journal Article Med Hypotheses · October 2011 A wide range of hyperimmune-associated diseases plague post-industrial society, with a prevalence and impact that is staggering. Strong evidence points towards a loss of helminths from the ecosystem of the human body (the human biome) as the most important ... Full text Link to item Cite

Evolution. CNCing is believing.

Journal Article Science (New York, N.Y.) · August 2011 Full text Cite

Genomic signatures of diet-related shifts during human origins.

Journal Article Proceedings. Biological sciences · April 2011 There are numerous anthropological analyses concerning the importance of diet during human evolution. Diet is thought to have had a profound influence on the human phenotype, and dietary differences have been hypothesized to contribute to the dramatic morp ... Full text Cite

Allele-specific gene expression in a wild nonhuman primate population.

Journal Article Molecular ecology · February 2011 Natural populations hold enormous potential for evolutionary genetic studies, especially when phenotypic, genetic and environmental data are all available on the same individuals. However, untangling the genotype-phenotype relationship in natural populatio ... Full text Cite

Comparative expression analysis of the phosphocreatine circuit in extant primates: Implications for human brain evolution.

Journal Article Journal of human evolution · February 2011 While the hominid fossil record clearly shows that brain size has rapidly expanded over the last ~2.5 M.yr. the forces driving this change remain unclear. One popular hypothesis proposes that metabolic adaptations in response to dietary shifts supported gr ... Full text Cite

Genomic signatures of diet-related shifts in primate evolution

Journal Article Proceedings of the Royal Society of London B · 2011 Cite

Generation-biased gene expression in a bryophyte model system.

Journal Article Molecular biology and evolution · January 2011 The evolution of land plants is tightly linked to the evolution of the alternation of generations. Because alternating ploidal generations share their genomes, investigating generation-biased gene expression can give insight into the evolution of life cycl ... Full text Cite

A potential role for glucose transporters in the evolution of human brain size.

Journal Article Brain, behavior and evolution · January 2011 Differences in cognitive abilities and the relatively large brain are among the most striking differences between humans and their closest primate relatives. The energy trade-off hypothesis predicts that a major shift in energy allocation among tissues occ ... Full text Cite

Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populations.

Journal Article Trends in genetics : TIG · August 2010 Ecological and evolutionary studies of wild primates hold important keys to understanding both the shared characteristics of primate biology and the genetic and phenotypic differences that make specific lineages, including our own, unique. Although complem ... Full text Cite

Contrasts between adaptive coding and noncoding changes during human evolution.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · April 2010 Changes in non-protein-coding regulatory DNA sequences have been proposed to play distinctive roles in adaptive evolution. We analyzed correlations between gene functions and evidence for positive selection in a common statistical framework across several ... Full text Cite

Multiple Functional Variants in cis Modulate PDYN Expression.

Journal Article Molecular biology and evolution · February 2010 Understanding genetic variation and its functional consequences within cis-regulatory regions remains an important challenge in human genetics and evolution. Here, we present a fine-scale functional analysis of segregating variation within the cis-regulato ... Full text Cite

Developmental evolution: how beetles evolved their shields.

Journal Article Current biology : CB · January 2010 Beetle forewings are modified into hardened structures called elytra. A recent study indicates that the evolution of elytra involved co-opting genes for exoskeleton formation into the wing development gene network of beetles on at least three separate occa ... Full text Cite

The evolution of gene regulatory interactions

Journal Article BioScience · January 1, 2010 Changes in the timing and level at which genes are expressed are known to play an important role in evolution, but the mechanisms underlying changes in gene expression remain relatively obscure. Until quite recently, evolutionary biologists, like most biol ... Full text Cite

Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain.

Journal Article Genome biology and evolution · January 2010 Despite striking differences in cognition and behavior between humans and our closest primate relatives, several studies have found little evidence for adaptive change in protein-coding regions of genes expressed primarily in the brain. Instead, changes in ... Full text Cite

Extensive changes in the expression of the opioid genes between humans and chimpanzees.

Journal Article Brain, behavior and evolution · January 2010 The various means by which the body perceives, transmits, and resolves the experiences of pain and nociception are mediated by a host of molecules, including neuropeptides within the opioid gene signaling pathway. The peptide ligands and receptors encoded ... Full text Cite

Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin.

Journal Article Genome biology and evolution · January 2010 Comparisons of genomic sequence between divergent species can provide insight into the action of natural selection across many distinct classes of proteins. Here, we examine the extent of positive selection as a function of tissue-specific and stage-specif ... Full text Cite

A pipeline to determine RT-QPCR control genes for evolutionary studies: Application to primate gene expression across multiple tissues

Journal Article PLoS ONE · 2010 Because many species-specific phenotypic differences are assumed to be caused by differential regulation of gene expression, many recent investigations have focused on measuring transcript abundance. Despite the availability of high throughput platforms, q ... Full text Cite

Evolution of functional genetic variation at immune loci in wild baboons.

Conference AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY · January 1, 2010 Link to item Cite

Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation.

Journal Article Molecular biology and evolution · September 2009 Variation in gene expression is an important contributor to phenotypic diversity within and between species. Although this variation often has a genetic component, identification of the genetic variants driving this relationship remains challenging. In par ... Full text Cite

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships.

Journal Article Nucleic acids research · July 2009 Transcriptional regulation is mediated by the collective binding of proteins called transcription factors to cis-regulatory elements. A handful of factors are known to function at particular distances from the transcription start site, although the extent ... Cite

Evolution of a malaria resistance gene in wild primates.

Journal Article Nature · July 2009 The ecology, behaviour and genetics of our closest living relatives, the nonhuman primates, should help us to understand the evolution of our own lineage. Although a large amount of data has been amassed on primate ecology and behaviour, much less is known ... Full text Cite

Comparative embryology without a microscope: using genomic approaches to understand the evolution of development.

Journal Article Journal of biology · January 2009 Until recently, understanding developmental conservation and change has relied on embryological comparisons and analyses of single genes. Several studies, including one recently published in BMC Biology, have now taken a genomic approach to this classical ... Full text Cite

Reply to "Rapidly evolving human promoter regions"

Journal Article Nature Genetics · November 1, 2008 Full text Cite

Genetics. Enhancing gene regulation.

Journal Article Science (New York, N.Y.) · September 2008 Full text Cite

Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs.

Journal Article Genome research · March 2008 Lemurs and the other strepsirrhine primates are of great interest to the primate genomics community due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitoc ... Full text Cite

Evolutionary and ecological functional genomics.

Journal Article Heredity · February 2008 Full text Cite

Enhancing gene regulation

Journal Article Science · 2008 Cite

Growth and patterning are evolutionarily dissociated in the vestigial wing discs of workers of the red imported fire ant, Solenopsis invicta.

Journal Article Journal of experimental zoology. Part B, Molecular and developmental evolution · December 2007 Over the last decade, it has become clear that organismal form is largely determined by developmental and evolutionary changes in the growth and pattern formation of tissues. Yet, there is little known about how these two integrated processes respond to en ... Full text Cite

Ontogeny in the fossil record: Diversification of body plans and the evolution of "aberrant" symmetry in Paleozoic echinoderms

Journal Article Paleobiology · December 1, 2007 Echinoderms have long been characterized by the presence of ambulacra that exhibit pentaradiate symmetry and define five primary body axes. In reality, truly pentaradial ambulacral symmetry is a condition derived only once in the evolutionary history of ec ... Full text Cite

When two is better than one.

Journal Article Cell · October 2007 Gene duplication and divergence has long been considered an important route to adaptation and phenotypic evolution. Reporting in Nature, Hittinger and Carroll (2007) provide the first clear example of adaptations in both regulatory regions and protein-codi ... Full text Cite

The evolutionary significance of cis-regulatory mutations.

Journal Article Nature reviews. Genetics · March 2007 For decades, evolutionary biologists have argued that changes in cis-regulatory sequences constitute an important part of the genetic basis for adaptation. Although originally based on first principles, this claim is now empirically well supported: numerou ... Full text Cite

When two is better than one

Journal Article Cell · 2007 Cite

Convergent adaptation of human lactase persistence in Africa and Europe.

Journal Article Nature genetics · January 2007 A SNP in the gene encoding lactase (LCT) (C/T-13910) is associated with the ability to digest milk as adults (lactase persistence) in Europeans, but the genetic basis of lactase persistence in Africans was previously unknown. We conducted a genotype-phenot ... Full text Cite

Tracing the ancestry of the great white shark, Carcharodon carcharias, using morphometric analyses of fossil teeth

Journal Article Journal of Vertebrate Paleontology · December 11, 2006 The evolutionary origin of the great white shark (Carcharodon carcharias) is unclear, with debate centering around two principal hypotheses. The first, based on similarity in tooth shape, claims that C. carcharias originated from a group of extinct mako sh ... Full text Cite

Functional analysis of cis-regulatory evolution in humans and other primates

Journal Article INTEGRATIVE AND COMPARATIVE BIOLOGY · December 1, 2006 Link to item Cite

Endo16 is required for gastrulation in the sea urchin Lytechinus variegatus.

Journal Article Development, growth & differentiation · October 2006 The Endo16 gene encodes a large extracellular protein with several functional domains that provide some insight into the role of this protein during embryonic development. We isolated the full-length cDNA sequence from Lytechinus variegatus and utilized mo ... Full text Cite

Ancient polymorphism and functional variation in the primate MHC-DQA1 5' cis-regulatory region.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · October 2006 Precise regulation of MHC gene expression is critical to vertebrate immune surveillance and response. Polymorphisms in the 5' proximal promoter region of the human class II gene HLA-DQA1 have been shown to influence its transcriptional regulation and may c ... Full text Cite

The evolution of embryonic gene expression in sea urchins.

Journal Article Integrative and comparative biology · June 2006 Many evolutionary modifications in development and life history derive from changes in embryonic gene expression. However, the genetic variation affecting gene expression in natural populations is not well understood, nor are the evolutionary mechanisms th ... Full text Cite

Evolution: spot on (and off).

Journal Article Nature · April 2006 Full text Cite

Spot on (and off)

Journal Article Nature · 2006 Cite

The evolutionary dynamics of alpha-satellite.

Journal Article Genome research · January 2006 Alpha-satellite is a family of tandemly repeated sequences found at all normal human centromeres. In addition to its significance for understanding centromere function, alpha-satellite is also a model for concerted evolution, as alpha-satellite repeats are ... Full text Cite

Ancient and recent positive selection transformed opioid cis-regulation in humans.

Journal Article PLoS biology · December 2005 Changes in the cis-regulation of neural genes likely contributed to the evolution of our species' unique attributes, but evidence of a role for natural selection has been lacking. We found that positive natural selection altered the cis-regulation of human ... Full text Cite

Ancient and recent positive selection transformed opioid cis-regulation in humans.

Journal Article PLoS biology · December 1, 2005 Changes in the cis-regulation of neural genes likely contributed to the evolution of our species' unique attributes, but evidence of a role for natural selection has been lacking. We found that positive natural selection altered the cis-regulation of human ... Cite

Arrays in rays: terminal addition in echinoderms and its correlation with gene expression.

Journal Article Evolution & development · November 2005 The echinoderms are deuterostomes that superimpose radial symmetry upon bilateral larval morphology. Consequently, they are not the first animals that come to mind when the concepts of segmentation and terminal addition are being discussed. However, it has ... Full text Cite

Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · June 2005 The evolutionary mechanisms that operate on genetic variation within transcriptional regulatory sequences are not well understood. We present here an evolutionary analysis of an exceptionally well characterized cis-regulatory region, the endo16 promoter of ... Full text Cite

Positive selection on MMP3 regulation has shaped heart disease risk.

Journal Article Current biology : CB · September 2004 BackgroundThe evolutionary forces of mutation, natural selection, and genetic drift shape the pattern of phenotypic variation in nature, but the roles of these forces in defining the distributions of particular traits have been hard to disentangle ... Full text Cite

Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the factor VII locus in humans.

Journal Article Genetics · June 2004 The abundance of cis-regulatory polymorphisms in humans suggests that many may have been important in human evolution, but evidence for their role is relatively rare. Four common polymorphisms in the 5' promoter region of factor VII (F7), a coagulation fac ... Full text Cite

Molecular phylogeny of naidid worms (Annelida: Clitellata)

Journal Article Molecular Phylogeny and Evolution · 2004 Cite

Culture of echinoderm larvae through metamorphosis.

Journal Article Methods in cell biology · January 2004 Full text Cite

Molecular phylogeny of naidid worms (Annelida: Clitellata) based on cytochrome oxidase I.

Journal Article Molecular phylogenetics and evolution · January 2004 Naidids are tiny, primarily freshwater oligochaete annelids which reproduce asexually by fission. We investigated the phylogenetic relationships within this group by sequencing 1224 bp of the mitochondrial gene cytochrome oxidase I (COI) from 26 species of ... Full text Cite

Simulations of evolutionary radiations and their application to understanding the probability of a Cambrian explosion

Journal Article Journal of Paleontology · January 1, 2004 A molecular survey of animal phylogeny (Wray et al., 1996) recovered the presumed correct temporal order of the phylogenetic splits Protostomata- Deuterostomata, Echinodermata-Chordata, and Agnatha-Gnathostomata in studies of six of seven gene sequences. T ... Full text Cite

Positive selection on a human-specific transcription factor binding site regulating IL4 expression.

Journal Article Current biology : CB · December 2003 A single nucleotide polymorphism in the promoter of the multifunctional cytokine Interleukin 4 (IL4) affects the binding of NFAT, a key transcriptional activator of IL4 in T cells. This regulatory polymorphism influences the balance of cytokine signaling i ... Full text Cite

The evolution of transcriptional regulation in eukaryotes.

Journal Article Molecular biology and evolution · September 2003 Gene expression is central to the genotype-phenotype relationship in all organisms, and it is an important component of the genetic basis for evolutionary change in diverse aspects of phenotype. However, the evolution of transcriptional regulation remains ... Full text Cite

Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation.

Journal Article Development (Cambridge, England) · September 2003 Evolutionary changes in transcriptional regulation undoubtedly play an important role in creating morphological diversity. However, there is little information about the evolutionary dynamics of cis-regulatory sequences. This study examines the functional ... Full text Cite

The effects of selection against spurious transcription factor binding sites.

Journal Article Molecular biology and evolution · June 2003 Most genomes contain nucleotide sequences with no known function; such sequences are assumed to be free of constraints, evolving only according to the vagaries of mutation. Here we show that selection acts to remove spurious transcription factor binding si ... Full text Cite

Identification of asteroid genera with species capable of larval cloning.

Journal Article The Biological bulletin · June 2003 Asexual reproduction in larvae, larval cloning, is a recently recognized component of the complex life histories of asteroids. We compare DNA sequences of mitochondrial tRNA genes (Ala, Leu, Asn, Pro, and Gln) from larvae in the process of cloning collecte ... Full text Cite

Transcriptional regulation and the evolution of development.

Journal Article The International journal of developmental biology · January 2003 A growing body of evidence suggests that changes in transcriptional regulation form an important part of the genetic basis for the evolution of development. At a microevolutionary level, all the necessary conditions are present: populations harbor abundant ... Cite

Stasis, change, and functional constraint in the evolution of animal body plans, whatever they may be

Journal Article Vie et Milieu · December 1, 2002 The phrase "body plan" or "bauplan" has been used to mean (1) the characteristic features of a phylum or other taxon of high rank, (2) architectural features of animals (such as symmetry; modular units; types of body walls, body cavities, body openings, an ... Cite

Abundant raw material for cis-regulatory evolution in humans.

Journal Article Molecular biology and evolution · November 2002 Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in ... Full text Cite

Getting a head in the world

Journal Article Natural History · October 2002 Cite

Evolution of the gene network underlying wing polyphenism in ants.

Journal Article Science (New York, N.Y.) · July 2002 Wing polyphenism in ants evolved once, 125 million years ago, and has been a key to their amazing evolutionary success. We characterized the expression of several genes within the network underlying the wing primordia of reproductive (winged) and sterile ( ... Full text Cite

The g-value paradox.

Journal Article Evolution & development · March 2002 Full text Cite

Gene expression and larval evolution: changing roles of distal-less and orthodenticle in echinoderm larvae.

Journal Article Evolution & development · March 2002 We describe the expression of the homeobox genes orthodenticle (Otx) and distal-less (Dlx) during the larval development of seven species representing three classes of echinoderms: Holothuroidea, Asteroidea, and Echinoidea. Several expression domains are c ... Full text Cite

Do convergent developmental mechanisms underlie convergent phenotypes?

Journal Article Brain, behavior and evolution · January 2002 Convergence is a pervasive evolutionary process, affecting many aspects of phenotype and even genotype. Relatively little is known about convergence in developmental processes, however, nor about the degree to which convergence in development underlies con ... Full text Cite

Dating branches on the tree of life using DNA.

Journal Article Genome biology · January 2002 The use of DNA sequences to estimate the timing of evolutionary events is increasingly popular, although it is fraught with practical difficulties. But the exponential growth of relevant information and improved methods of analysis are providing increasing ... Full text Cite

Rapid evolution of cis-regulatory sequences via local point mutations.

Journal Article Molecular biology and evolution · September 2001 Although the evolution of protein-coding sequences within genomes is well understood, the same cannot be said of the cis-regulatory regions that control transcription. Yet, changes in gene expression are likely to constitute an important component of pheno ... Full text Cite

Evolution of regeneration and fission in annelids: insights from engrailed- and orthodenticle-class gene expression.

Journal Article Development (Cambridge, England) · July 2001 The recent explosion of information on the role of regulatory genes in embryogenesis provides an excellent opportunity to study how these genes participate in post-embryonic developmental processes. We present a detailed comparison of regulatory gene expre ... Full text Cite

Resolving the Hox Paradox

Journal Article Science · June 22, 2001 From DNA to Diversity Molecular Genetics and the Evolution of Animal Design. Sean B. Carroll, Jennifer K. Grenier, and Scott D. Weatherbee. Blackwell Science, Malden, MA, 2001. 230 pp. Paper, $44.95, ... Full text Cite

Rapid appearance of new transcription factor binding sites by local point mutation

Journal Article Molecular Biology and Evolution · 2001 Cite

The evolution of embryonic patterning mechanisms in animals.

Journal Article Seminars in cell & developmental biology · December 2000 Animals exhibit an enormous diversity of life cycles and larval morphologies. The developmental basis for this diversity is not well understood. It is clear, however, that mechanisms of pattern formation in early embryos differ significantly among and with ... Full text Cite

The evolution and development of left-right asymmetry in echinoderms.

Journal Article AMERICAN ZOOLOGIST · December 1, 2000 Link to item Cite

A sea urchin genome project: sequence scan, virtual map, and additional resources.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · August 2000 Results of a first-stage Sea Urchin Genome Project are summarized here. The species chosen was Strongylocentrotus purpuratus, a research model of major importance in developmental and molecular biology. A virtual map of the genome was constructed by sequen ... Full text Cite

Peering ahead (cautiously).

Journal Article Evolution & development · May 2000 Full text Cite

Developmental regulatory genes and echinoderm evolution.

Journal Article Systematic biology · March 2000 Modified interactions among developmental regulatory genes and changes in their expression domains are likely to be an important part of the developmental basis for evolutionary changes in morphology. Although developmental regulatory genes are now being s ... Full text Cite

The evolution of embryonic patterning mechanisms in animals

Journal Article Seminars in Cell and Developmental Biology · 2000 Cite

Controversy and consensus in asteroid systernatics: New insights to ordinal and familial relationships

Journal Article American Zoologist · January 1, 2000 SYNOPSIS. Phylogenetic approaches have sparked controversy in asteroid systematics since 1987. Despite recent attempts at resolving these differences and evidence of some consensus, our understanding of relationships among asteroid taxa remains unsatisfact ... Full text Cite

Developmental regulatory genes and echinoderm evolution

Journal Article Systematic Biology · 2000 Cite

Peering ahead (cautiously)

Journal Article Evolution and Development · 2000 Cite

Rearing larvae of sea urchins and sea stars for developmental studies.

Journal Article Methods in molecular biology (Clifton, N.J.) · January 2000 Full text Cite

Gene expression during echinoderm metamorphosis.

Journal Article Zygote (Cambridge, England) · January 2000 Cite

The evolution of sea urchin development

Conference REGULATORY PROCESSES IN DEVELOPMENT · January 1, 2000 Link to item Cite

Chronicling the birth of a discipline.

Journal Article Evolution & development · July 1999 Full text Cite

Evolutionary dissociations between homologous genes and homologous structures.

Journal Article Novartis Foundation symposium · January 1999 Phenotype is encoded in the genome in an indirect manner: each morphological structure is the product of many interacting genes, and most regulatory genes have several distinct developmental roles and phenotypic consequences. The lack of a simple and consi ... Full text Cite

When is homology not homology?

Journal Article Current opinion in genetics & development · December 1998 Although genes have specific phenotypic consequences in a given species, this functional relationship can clearly change during the course of evolution. Many cases of evolutionary dissociations between homologous genes and homologous morphological features ... Full text Cite

Promoter logic.

Journal Article Science (New York, N.Y.) · March 1998 Full text Cite

Cloning of zebrafish vsx1: expression of a paired-like homeobox gene during CNS development.

Journal Article Developmental genetics · January 1998 vsx1 is a homeobox gene encoding a paired-type homeodomain and a CVC domain that was originally cloned from an adult goldfish retinal library. We previously reported the spatiotemporal expression pattern of vsx1 in the adult and developing retina of zebraf ... Full text Cite

Homology and developmental genes.

Journal Article Trends in genetics : TIG · November 1997 Full text Cite

Radical alterations in the roles of homeobox genes during echinoderm evolution.

Journal Article Nature · October 1997 Echinoderms possess one of the most highly derived body architectures of all metazoan phyla, with radial symmetry, a calcitic endoskeleton, and a water vascular system. How these dramatic morphological changes evolved has been the subject of extensive spec ... Full text Cite

Archenteron precursor cells can organize secondary axial structures in the sea urchin embryo.

Journal Article Development (Cambridge, England) · September 1997 Local cell-cell signals play a crucial role in establishing major tissue territories in early embryos. The sea urchin embryo is a useful model system for studying these interactions in deuterostomes. Previous studies showed that ectopically implanted micro ... Full text Cite

The origin and evolution of animal appendages.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · May 1997 Animals have evolved diverse appendages adapted for locomotion, feeding and other functions. The genetics underlying appendage formation are best understood in insects and vertebrates. The expression of the Distal-less (Dll) homeoprotein during arthropod l ... Full text Cite

The 'paradox' of polyembryony: A review of the cases and a hypothesis for its evolution

Journal Article Evolutionary Ecology · January 1, 1997 Animal polyembryony appears to be paradoxical because it clones an unproven genotype at the expense of genetic diversity in a clutch. However, it is employed by at least 18 taxa in six phyla (excluding instances of occasional twinning). Most polyembryony o ... Full text Cite

Parallel evolution of nonfeeding larvae in echinoids

Journal Article Systematic Biology · January 1, 1996 The switch from feeding to nonfeeding larvae is an ecologically important transformation that has evolved on several separate occasions within the echinoids. In each case, this life history transformation has been accompanied by extensive changes in larval ... Full text Cite

Molecular evidence for deep Precambrian divergences among metazoan phyla

Journal Article Science · January 1, 1996 A literal reading of the fossil record suggests that the animal phyla diverged in an 'explosion' near the beginning of the Cambrian period. Calibrated rates of molecular sequence divergence were used to test this hypothesis. Seven independent data sets sug ... Full text Cite

Punctuated evolution of embryos

Journal Article Science · February 24, 1995 Cite

The 'paradox' of polyembryony

Journal Article Trends in Ecology & Evolution · January 1, 1995 Full text Cite

Comparing patterns of evolution: larval and adult life history stages and ribosomal RNA of post-Palaeozoic echinoids

Journal Article Philosophical Transactions - Royal Society of London, B · January 1, 1995 A total-evidence approach to the phylogeny of 29 extant echinoids has been taken, combined data from larval morphology, adult morphology, small subunit rRNA complete gene sequence and large subunit rRNA partial gene sequence: a total of 176 morphological a ... Full text Cite

The evolution of cell lineage in echinoderms

Journal Article Integrative and Comparative Biology · December 1, 1994 SYNOPSIS. Metazoan embryos in various phyla and classes often utilize quite different processes to specify cell fates during embryogenesis. These differences have been interpreted either as constraints, necessary for fabricating distinct adult body plans, ... Full text Cite

The evolution of echinoderm development is driven by several distinct factors

Journal Article Development · January 1, 1994 We analyzed a comparative data base of gene expression, cell fate specification, and morphogenetic movements from several echinoderms to determine why developmental processes do and do not evolve. Mapping this comparative data onto explicit phylogenetic fr ... Cite

The evolution of echinoderm development is driven by several distinct factors.

Journal Article Development (Cambridge, England). Supplement · January 1994 We analyzed a comparative data base of gene expression, cell fate specification, and morphogenetic movements from several echinoderms to determine why developmental processes do and do not evolve. Mapping this comparative data onto explicit phylogenetic fr ... Cite

Developmental evolution: new paradigms and paradoxes.

Journal Article Developmental genetics · January 1994 Full text Cite

Rates of evolution in developmental processes

Journal Article Integrative and Comparative Biology · December 1, 1992 The tempo and mode of morphological evolution are influenced by several factors, among which evolutionary transformations in developmental processes are likely to be important. Comparing the embryos of extant species in an explicit phylogenetic fram work a ... Full text Cite

Rates of evolution in developmental processes

Journal Article American Zoologist · 1992 The tempo and mode of morphological evolution are influenced by several factors, among which evolutionary transformations in developmental processes are likely to be important. Comparing the embryos of extant species in an explicit phylogenetic framework a ... Cite

The evolution of larval morphology during the post-Paleozoic radiation of echinoids

Journal Article Paleobiology · January 1, 1992 .—The post-Paleozoic radiation of echinoids entailed a rapid diversification not only of adult morphology, but also of larval morphology. The timing, order, and phylogenetic distribution of evolutionary transformations in echinopluteus larvae are reconstru ... Full text Cite

Mechanism of an Alternate Type of Echinoderm Blastula Formation: The Wrinkled Blastula of the Sea Urchin Heliocidaris erythrogramma direct development/echinoderm development/morphogenesis/sea urchin embryos/wrinkled blastula

Journal Article Development, Growth & Differentiation · January 1, 1991 While most indirect‐developing echinoderms (possessing a feeding larval stage) form a hollow, smooth‐walled blastula, most direct‐developing species form a wrinkled blastula. The process of wrinkled blastula formation was examined in the direct‐developing ... Full text Cite

The evolution of developmental strategy in marine invertebrates

Journal Article Trends in Ecology and Evolution · January 1, 1991 Developmental mode varies widely in most animal phyla. These differences in developmental strategy exert a profound influence on the ecology and evolution of closely related species. The mechanistic alterations in ontogeny that lead to switches in developm ... Full text Cite

The dorsoventral axis is specified prior to first cleavage in the direct developing sea urchin Heliocidaris erythrogramma.

Journal Article Development (Cambridge, England) · November 1990 Previous fate mapping studies as well as the culture of isolated blastomeres have revealed that the dorsoventral axis is specified as early as the 2-cell stage in the embryos of the direct developing echinoid, Heliocidaris erythrogramma. Normally, the firs ... Full text Cite

Novel origins of lineage founder cells in the direct-developing sea urchin Heliocidaris erythrogramma.

Journal Article Developmental biology · September 1990 The lineage and fate of each blastomere in the 32-cell embryo of the direct-developing sea urchin Heliocidaris erythrogramma have been traced by microinjection of tetramethylrhodamine-dextran. The results reveal substantive evolutionary modifications of th ... Full text Cite

The "lecithotrophic" sea urchin Heliocidaris erythrogramma lacks typical yolk platelets and yolk glycoproteins.

Journal Article Developmental biology · March 1990 The sea urchin Heliocidaris tuberculata undergoes typical development, forming an echinoid pluteus larva, whereas H. erythrogramma undergoes direct development via a highly modified, nonfeeding larva. Using a polyclonal antibody prepared against yolk glyco ... Full text Cite

Heterochrony and other mechanisms of radical evolutionary change in early development

Journal Article Evolutionary innovations · January 1, 1990 Examines the view that developmental processes which happen together or sequentially in time are not necessarily tightly coupled mechanistically and may be shifted relative to each other in evolution without disrupting development. Heterochrony is the most ... Cite

An analysis of the phenotypic effects of certain colour pattern genes in Heliconius (Lepidoptera: Nymphalidae)

Journal Article Biological Journal of the Linnean Society · January 1, 1990 The colour patterns of Heliconius butterflies are built up from an array of serially homologous pattern elements known as the nymphalid groundplan. An analysis of the phenotypic effects of ten genetic loci from H. melpomene and H. cydno reveals that each a ... Full text Cite

Early inductive interactions are involved in restricting cell fates of mesomeres in sea urchin embryos.

Journal Article Developmental biology · November 1989 Isolated intact caps of animal blastomeres, obtained from either 8- or 16-cell embryos, differentiate as swollen ectodermal vesicles. These findings agree with earlier studies demonstrating that mesomeres contribute only to larval ectoderm during normal de ... Full text Cite

Evolutionary modification of cell lineage in the direct-developing sea urchin Heliocidaris erythrogramma.

Journal Article Developmental biology · April 1989 The sea urchin Heliocidaris erythrogramma undergoes direct development, bypassing the usual echinoid pluteus larva. We present an analysis of cell lineage in H. erythrogramma as part of a definition of the mechanistic basis for this evolutionary change in ... Full text Cite

Heterochrony: Developmental mechanisms and evolutionary results

Journal Article Journal of Evolutionary Biology · January 1, 1989 The concept of heterochrony, that the relative timing of ontogenetic events can shift during evolution, has been a major paradigm for understanding the role of developmental processes in evolution. In this paper we consider heterochrony from the perspectiv ... Full text Cite

The origin of spicule-forming cells in a 'primitive' sea urchin (Eucidaris tribuloides) which appears to lack primary mesenchyme cells.

Journal Article Development (Cambridge, England) · June 1988 The calcareous larval skeleton of euechinoid sea urchins is synthesized by primary mesenchyme cells which ingress prior to gastrulation. In embryos of the cidaroid sea urchin Eucidaris tribuloides, no mesenchyme cells ingress before gastrulation, yet larva ... Full text Cite

Homologies in the colour patterns of the genus Heliconius (Lepidoptera: Nymphalidae)

Journal Article Biological Journal of the Linnean Society · January 1, 1988 The colour patterns of Heliconius butterflies are composed from a relatively simple set of pattern elements whose homologues are recognizable throughout the genus. Although Heliconius colour patterns look quite different from those of most nymphalids, thes ... Full text Cite

THE EMBRYONIC MESENCHYME IN A PRIMITIVE SEA-URCHIN, EUCIDARIS-TRIBULOIDES

Journal Article JOURNAL OF CELL BIOLOGY · November 1, 1986 Link to item Cite

Homologies in the colour patterns of the genus Charaxes (Lepidoptera: Nymphalidae)

Journal Article Biological Journal of the Linnean Society · January 1, 1986 The phylogenetically and morphologically diverse patterns of Charaxes can be reduced to a simple set of pattern elements which can be homologized throughout the genus. At least five types of correspondence (homologies) exist among pattern elements: those b ... Full text Cite

Ontogeny, phylogeny and evolution of form: An algorithmic approach

Journal Article Systematic Zoology · January 1, 1986 A computer model that simulates general aspects of ontogeny is presented as a heuristic device for studying the relationship between ontogenetic changes and the evolution of morphologies. The model consists of a set of developmental rules limited to known ... Full text Cite