Scholars@Duke
Anne Daphne Yoder

Anne Daphne Yoder

Braxton Craven Distinguished Professor of Evolutionary Biology
Biology
anne.yoder@duke.edu
Box 90338, Durham, NC 27708-0338
128 Biol Sciences Bldg, Durham, NC 27708
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Selected Publications

Telomere dynamics during hibernation in a tropical primate.

Journal Article Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology · April 2024 Hibernation is a widespread metabolic strategy among mammals for surviving periods of food scarcity. During hibernation, animals naturally alternate between metabolically depressed torpor bouts and energetically expensive arousals without ill effects. As a ... Full text Cite

Genetic variation in Loudetia simplex supports the presence of ancient grasslands in Madagascar

Journal Article Plants People Planet · March 1, 2024 Societal Impact Statement: Recognizing Loudetia-dominated grasslands were widespread prior to human colonization highlights that open ecosystems were and continue to be an important component of Madagascar's biodiversity. A better understanding of the plan ... Full text Cite

Interspecies Papillomavirus Type Infection and a Novel Papillomavirus Type in Red Ruffed Lemurs (Varecia rubra).

Journal Article Viruses · December 2023 The Papillomaviridae are a family of vertebrate-infecting viruses of oncogenic potential generally thought to be host species- and tissue-specific. Despite their phylogenetic relatedness to humans, there is a scarcity of data on papillomaviruses (PV ... Full text Open Access Cite

Estimation of species divergence times in presence of cross-species gene flow.

Journal Article Systematic biology · August 2023 Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene fl ... Full text Cite

Characterization of Diverse Anelloviruses, Cressdnaviruses, and Bacteriophages in the Human Oral DNA Virome from North Carolina (USA).

Journal Article Viruses · August 2023 The diversity of viruses identified from the various niches of the human oral cavity-from saliva to dental plaques to the surface of the tongue-has accelerated in the age of metagenomics. This rapid expansion demonstrates that our understanding of oral vir ... Full text Cite

Diversification processes in Gerp's mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar's humid rainforests.

Journal Article Ecology and evolution · July 2023 Madagascar exhibits exceptionally high levels of biodiversity and endemism. Models to explain the diversification and distribution of species in Madagascar stress the importance of historical variability in climate conditions which may have led to the form ... Full text Cite

Phylogenomic analyses provide insights into primate evolution.

Journal Article Science (New York, N.Y.) · June 2023 Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, includ ... Full text Cite

Identification of diverse papillomaviruses in captive black-and-white ruffed lemurs (Varecia variegata).

Journal Article Archives of virology · December 2022 Papillomaviruses (PVs) are host-species-specific and tissue-specific viruses that infect a diverse array of vertebrate hosts, including humans and non-human primates, with varying pathogenic outcomes. Although primate PVs have been studied extensively, no ... Full text Cite

Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests.

Journal Article Molecular ecology · October 2022 Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The historical perspective was that Madagascar's grasslands had anthropogenic origins, but emerging evidence suggests that grasslands were a component o ... Full text Cite

RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results.

Journal Article Proceedings. Biological sciences · August 2022 Microsatellites have been a workhorse of evolutionary genetic studies for decades and are still commonly in use for estimating signatures of genetic diversity at the population and species level across a multitude of taxa. Yet, the very high mutation rate ... Full text Cite

Variation in gut microbiome structure across the annual hibernation cycle in a wild primate.

Journal Article FEMS microbiology ecology · July 2022 The gut microbiome can mediate host metabolism, including facilitating energy-saving strategies like hibernation. The dwarf lemurs of Madagascar (Cheirogaleus spp.) are the only obligate hibernators among primates. They also hibernate in the subtropics, an ... Full text Open Access Cite

RADseq Data Suggest Occasional Hybridization between Microcebus murinus and M. ravelobensis in Northwestern Madagascar.

Journal Article Genes · May 2022 The occurrence of natural hybridization has been reported in a wide range of organisms, including primates. The present study focuses on the endemic lemurs of Madagascar, primates for which only a few species occur in sympatry or parapatry with congeners, ... Full text Cite

Initiation of the Primate Genome Project.

Journal Article Zoological research · March 2022 Full text Cite

Body Mass and Tail Girth Predict Hibernation Expression in Captive Dwarf Lemurs.

Journal Article Physiological and biochemical zoology : PBZ · March 2022 AbstractHibernation, a metabolic strategy, allows individuals to reduce energetic demands in times of energetic deficits. Hibernation is pervasive in nature, occurring in all major mammalian lineages and geographical regions; however, its expression is var ... Full text Open Access Cite

The Earth BioGenome Project 2020: Starting the clock.

Journal Article Proc Natl Acad Sci U S A · January 25, 2022 Full text Link to item Cite

The Mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates.

Journal Article eLife · January 2022 In the past decade, several studies have estimated the human per-generation germline mutation rate using large pedigrees. More recently, estimates for various nonhuman species have been published. However, methodological differences among studies in detect ... Full text Cite

The challenge and promise of estimating the de novo mutation rate from whole-genome comparisons among closely related individuals.

Journal Article Molecular ecology · December 2021 Germline mutations are the raw material for natural selection, driving species evolution and the generation of earth's biodiversity. Without this driver of genetic diversity, life on earth would stagnate. Yet, it is a double-edged sword. An excess of mutat ... Full text Cite

Gut Microbial Diversity and Ecological Specialization in Four Sympatric Lemur Species Under Lean Conditions

Journal Article International Journal of Primatology · December 1, 2021 The gut microbiome is gaining recognition for its role in primate nutrition, but we stand to benefit from microbiome comparisons across diverse hosts and environmental conditions. We compared gut microbiome structure in four lemur species from four phyloge ... Full text Open Access Cite

Living in tiny fragments: a glimpse at the ecology of Goodman's mouse lemurs (Microcebus lehilahytsara) in the relic forest of Ankafobe, Central Highlands, Madagascar.

Journal Article Primates; journal of primatology · November 2021 Habitat fragmentation is one of the major types of anthropogenic change, though fragmented landscapes predate human intervention. At present, the Central Highlands of Madagascar are covered by extensive grasslands interspersed with small discrete forest pa ... Full text Cite

Telomere dynamics during hibernation in a tropical primate.

Journal Article Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology · April 2024 Hibernation is a widespread metabolic strategy among mammals for surviving periods of food scarcity. During hibernation, animals naturally alternate between metabolically depressed torpor bouts and energetically expensive arousals without ill effects. As a ... Full text Cite

Genetic variation in Loudetia simplex supports the presence of ancient grasslands in Madagascar

Journal Article Plants People Planet · March 1, 2024 Societal Impact Statement: Recognizing Loudetia-dominated grasslands were widespread prior to human colonization highlights that open ecosystems were and continue to be an important component of Madagascar's biodiversity. A better understanding of the plan ... Full text Cite

Interspecies Papillomavirus Type Infection and a Novel Papillomavirus Type in Red Ruffed Lemurs (Varecia rubra).

Journal Article Viruses · December 2023 The Papillomaviridae are a family of vertebrate-infecting viruses of oncogenic potential generally thought to be host species- and tissue-specific. Despite their phylogenetic relatedness to humans, there is a scarcity of data on papillomaviruses (PV ... Full text Open Access Cite

Estimation of species divergence times in presence of cross-species gene flow.

Journal Article Systematic biology · August 2023 Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene fl ... Full text Cite

Characterization of Diverse Anelloviruses, Cressdnaviruses, and Bacteriophages in the Human Oral DNA Virome from North Carolina (USA).

Journal Article Viruses · August 2023 The diversity of viruses identified from the various niches of the human oral cavity-from saliva to dental plaques to the surface of the tongue-has accelerated in the age of metagenomics. This rapid expansion demonstrates that our understanding of oral vir ... Full text Cite

Diversification processes in Gerp's mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar's humid rainforests.

Journal Article Ecology and evolution · July 2023 Madagascar exhibits exceptionally high levels of biodiversity and endemism. Models to explain the diversification and distribution of species in Madagascar stress the importance of historical variability in climate conditions which may have led to the form ... Full text Cite

Phylogenomic analyses provide insights into primate evolution.

Journal Article Science (New York, N.Y.) · June 2023 Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, includ ... Full text Cite

Identification of diverse papillomaviruses in captive black-and-white ruffed lemurs (Varecia variegata).

Journal Article Archives of virology · December 2022 Papillomaviruses (PVs) are host-species-specific and tissue-specific viruses that infect a diverse array of vertebrate hosts, including humans and non-human primates, with varying pathogenic outcomes. Although primate PVs have been studied extensively, no ... Full text Cite

Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests.

Journal Article Molecular ecology · October 2022 Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The historical perspective was that Madagascar's grasslands had anthropogenic origins, but emerging evidence suggests that grasslands were a component o ... Full text Cite

RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results.

Journal Article Proceedings. Biological sciences · August 2022 Microsatellites have been a workhorse of evolutionary genetic studies for decades and are still commonly in use for estimating signatures of genetic diversity at the population and species level across a multitude of taxa. Yet, the very high mutation rate ... Full text Cite

Variation in gut microbiome structure across the annual hibernation cycle in a wild primate.

Journal Article FEMS microbiology ecology · July 2022 The gut microbiome can mediate host metabolism, including facilitating energy-saving strategies like hibernation. The dwarf lemurs of Madagascar (Cheirogaleus spp.) are the only obligate hibernators among primates. They also hibernate in the subtropics, an ... Full text Open Access Cite

RADseq Data Suggest Occasional Hybridization between Microcebus murinus and M. ravelobensis in Northwestern Madagascar.

Journal Article Genes · May 2022 The occurrence of natural hybridization has been reported in a wide range of organisms, including primates. The present study focuses on the endemic lemurs of Madagascar, primates for which only a few species occur in sympatry or parapatry with congeners, ... Full text Cite

Initiation of the Primate Genome Project.

Journal Article Zoological research · March 2022 Full text Cite

Body Mass and Tail Girth Predict Hibernation Expression in Captive Dwarf Lemurs.

Journal Article Physiological and biochemical zoology : PBZ · March 2022 AbstractHibernation, a metabolic strategy, allows individuals to reduce energetic demands in times of energetic deficits. Hibernation is pervasive in nature, occurring in all major mammalian lineages and geographical regions; however, its expression is var ... Full text Open Access Cite

The Earth BioGenome Project 2020: Starting the clock.

Journal Article Proc Natl Acad Sci U S A · January 25, 2022 Full text Link to item Cite

The Mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates.

Journal Article eLife · January 2022 In the past decade, several studies have estimated the human per-generation germline mutation rate using large pedigrees. More recently, estimates for various nonhuman species have been published. However, methodological differences among studies in detect ... Full text Cite

The challenge and promise of estimating the de novo mutation rate from whole-genome comparisons among closely related individuals.

Journal Article Molecular ecology · December 2021 Germline mutations are the raw material for natural selection, driving species evolution and the generation of earth's biodiversity. Without this driver of genetic diversity, life on earth would stagnate. Yet, it is a double-edged sword. An excess of mutat ... Full text Cite

Gut Microbial Diversity and Ecological Specialization in Four Sympatric Lemur Species Under Lean Conditions

Journal Article International Journal of Primatology · December 1, 2021 The gut microbiome is gaining recognition for its role in primate nutrition, but we stand to benefit from microbiome comparisons across diverse hosts and environmental conditions. We compared gut microbiome structure in four lemur species from four phyloge ... Full text Open Access Cite

Living in tiny fragments: a glimpse at the ecology of Goodman's mouse lemurs (Microcebus lehilahytsara) in the relic forest of Ankafobe, Central Highlands, Madagascar.

Journal Article Primates; journal of primatology · November 2021 Habitat fragmentation is one of the major types of anthropogenic change, though fragmented landscapes predate human intervention. At present, the Central Highlands of Madagascar are covered by extensive grasslands interspersed with small discrete forest pa ... Full text Cite

Molecular Adaptation to Folivory and the Conservation Implications for Madagascar’s Lemurs

Journal Article Frontiers in Ecology and Evolution · October 6, 2021 The lemurs of Madagascar include numerous species characterized by folivory across several families. Many extant lemuriform folivores exist in sympatry in Madagascar’s remaining forests. These species avoid feeding competition by adopting different dietary ... Full text Open Access Cite

Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur.

Journal Article Heredity · August 2021 Mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of de novo mutations ... Full text Cite

Comparative analyses of two primate species diverged by more than 60 million years show different rates but similar distribution of genome-wide UV repair events.

Journal Article BMC genomics · August 2021 BackgroundNucleotide excision repair is the primary DNA repair mechanism that removes bulky DNA adducts such as UV-induced pyrimidine dimers. Correspondingly, genome-wide mapping of nucleotide excision repair with eXcision Repair sequencing (XR-se ... Full text Cite

Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, "subfossil" koala lemur Megaladapis edwardsi.

Conference Proceedings of the National Academy of Sciences of the United States of America · June 2021 No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal "subfossil" remains we can reconstruct some of the biology and behavioral ecology of gian ... Full text Cite

Comparative genomic analysis of sifakas (Propithecus) reveals selection for folivory and high heterozygosity despite endangered status.

Journal Article Science advances · April 2021 Sifakas (genus Propithecus) are critically endangered, large-bodied diurnal lemurs that eat leaf-based diets and show corresponding anatomical and microbial adaptations to folivory. We report on the genome assembly of Coquerel's sifaka (P. coquer ... Full text Cite

Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent.

Journal Article Systematic biology · February 2021 Featured Publication Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic revision has prompted understandable concern tha ... Full text Cite

Molecular Clocks without Rocks: New Solutions for Old Problems.

Journal Article Trends in genetics : TIG · November 2020 Molecular data have been used to date species divergences ever since they were described as documents of evolutionary history in the 1960s. Yet, an inadequate fossil record and discordance between gene trees and species trees are persistently problematic. ... Full text Cite

Next-generation technologies applied to age-old challenges in Madagascar

Journal Article Conservation Genetics · October 1, 2020 Madagascar is a biodiversity hotspot that is facing rapid rates of deforestation, habitat destruction, and poverty. Urgent action is required to document the status of biodiversity to facilitate efficacious conservation plans. With the recent advent of por ... Full text Cite

Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species.

Journal Article American journal of primatology · September 2020 Delimitation of cryptic species is increasingly based on genetic analyses but the integration of distributional, morphological, behavioral, and ecological data offers unique complementary insights into species diversification. We surveyed communities of no ... Full text Cite

Probabilities of Unranked and Ranked Anomaly Zones under Birth-Death Models.

Journal Article Molecular biology and evolution · May 2020 A labeled gene tree topology that is more probable than the labeled gene tree topology matching a species tree is called "anomalous." Species trees that can generate such anomalous gene trees are said to be in the "anomaly zone." Here, probabilities of "un ... Full text Cite

Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar's hibernating dwarf lemurs.

Journal Article Heredity · January 2020 Madagascar's biodiversity is notoriously threatened by deforestation and climate change. Many of these organisms are rare, cryptic, and severely threatened, making population-level sampling unrealistic. Such is the case with Madagascar's dwarf lemurs (genu ... Full text Cite

Comparative Genomic Analysis of the Pheromone Receptor Class 1 Family (V1R) Reveals Extreme Complexity in Mouse Lemurs (Genus, Microcebus) and a Chromosomal Hotspot across Mammals.

Journal Article Genome Biol Evol · January 1, 2020 Sensory gene families are of special interest for both what they can tell us about molecular evolution and what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental r ... Full text Link to item Cite

The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs.

Journal Article American journal of primatology · October 2019 Research on animal microbiomes is increasingly aimed at determining the evolutionary and ecological factors that govern host-microbiome dynamics, which are invariably intertwined and potentially synergistic. We present three empirical studies related to th ... Full text Cite

Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species.

Journal Article Molecular biology and evolution · October 2019 Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of postspeciation gene flow that can produce a mosaic ... Full text Cite

Applications of 3D printing in small animal magnetic resonance imaging.

Journal Article J Med Imaging (Bellingham) · April 2019 Three-dimensional (3D) printing has significantly impacted the quality, efficiency, and reproducibility of preclinical magnetic resonance imaging. It has vastly expanded the ability to produce MR-compatible parts that readily permit customization of animal ... Full text Link to item Cite

What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species

Journal Article Biological Journal of the Linnean Society · August 1, 2018 As is true of virtually every realm of the biological sciences, our understanding of speciation is increasingly informed by the genomic revolution of the past decade. Investigators can ask detailed questions relating to both the extrinsic (e.g. inter- and ... Full text Cite

Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes.

Journal Article Microbial ecology · July 2018 Bamboo specialization is one of the most extreme examples of convergent herbivory, yet it is unclear how this specific high-fiber diet might selectively shape the composition of the gut microbiome compared to host phylogeny. To address these questions, we ... Full text Cite

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case.

Journal Article Systematic biology · July 2018 Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the Cretaceous-Paleogene (K-Pg) boundary and ... Full text Cite

Tropical heterothermy is "cool": The expression of daily torpor and hibernation in primates.

Journal Article Evolutionary anthropology · July 2018 Living nonhuman primates generally inhabit tropical forests, and torpor is regarded as a strategy employed by cold-adapted organisms. Yet, some primates employ daily torpor or hibernation (heterothermy) under obligatory, temporary, or emergency circumstanc ... Full text Cite

Neutral Theory Is the Foundation of Conservation Genetics.

Journal Article Molecular biology and evolution · June 2018 Kimura's neutral theory of molecular evolution has been essential to virtually every advance in evolutionary genetics, and by extension, is foundational to the field of conservation genetics. Conservation genetics utilizes the key concepts of neutral theor ... Full text Cite

The ecosystem services of animal microbiomes.

Journal Article Molecular ecology · April 2018 Microbiologists often evaluate microbial community dynamics by formulating functional hypotheses based on ecological processes. Indeed, many of the methods and terms currently used to describe animal microbiomes derive from ecology and evolutionary biology ... Full text Cite

Evolutionary genomics of Verreaux's sifaka (Propithecus verreauxi)

Conference AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY · April 1, 2018 Link to item Cite

Warning SINEs: Alu elements, evolution of the human brain, and the spectrum of neurological disease.

Journal Article Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · March 2018 Alu elements are a highly successful family of primate-specific retrotransposons that have fundamentally shaped primate evolution, including the evolution of our own species. Alus play critical roles in the formation of neurological networks and the epigen ... Full text Cite

Transcriptomics in the wild: Hibernation physiology in free-ranging dwarf lemurs.

Journal Article Molecular ecology · February 2018 Hibernation is an adaptive strategy some mammals use to survive highly seasonal or unpredictable environments. We present the first investigation on the transcriptomics of hibernation in a natural population of primate hibernators: Crossley's dwarf lemurs ... Full text Cite

Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs.

Journal Article Gut microbes · January 2018 Many studies have demonstrated the effects of host diet on gut microbial membership, metagenomics, and fermentation individually; but few have attempted to interpret the relationship among these biological phenomena with respect to host features (e.g. gut ... Full text Cite

Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus).

Journal Article BMC Biol · November 16, 2017 BACKGROUND: The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications. Here, we present an iterative approach to h ... Full text Open Access Link to item Cite

The Alu neurodegeneration hypothesis: A primate-specific mechanism for neuronal transcription noise, mitochondrial dysfunction, and manifestation of neurodegenerative disease.

Journal Article Alzheimers Dement · July 2017 It is hypothesized that retrotransposons have played a fundamental role in primate evolution and that enhanced neurologic retrotransposon activity in humans may underlie the origin of higher cognitive function. As a potential consequence of this enhanced a ... Full text Open Access Link to item Cite

The effect of body mass and diet composition on torpor patterns in a Malagasy primate (Microcebus murinus).

Journal Article Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology · May 2017 One of the most obvious physiological changes accompanying seasonal heterothermy in mammals is a fattening stage preceding periods of resource scarcity. This phenomenon reflects the interplay of both diet and physiology. Though the accrual of fat stores is ... Full text Cite

The challenges faced by living stock collections in the USA.

Journal Article eLife · March 2017 Many discoveries in the life sciences have been made using material from living stock collections. These collections provide a uniform and stable supply of living organisms and related materials that enhance the reproducibility of research and minimize the ... Full text Cite

Down for the count: Cryptosporidium infection depletes the gut microbiome in Coquerel's sifakas.

Journal Article Microbial ecology in health and disease · January 2017 Background: The gut microbiome (GMB) is the first line of defense against enteric pathogens, which are a leading cause of disease and mortality worldwide. One such pathogen, the protozoan Cryptosporidium, causes a variety of digestive disorde ... Full text Cite

Population and Conservation Genetics in an Endangered Lemur, Indri indri, Across Three Forest Reserves in Madagascar

Journal Article International Journal of Primatology · December 1, 2016 Population decline and fragmentation often lead to reduced genetic diversity and population differentiation. Habitat destruction throughout Madagascar has caused population decline and extinction of many endemic species. Lemur populations, including those ... Full text Cite

Gene Expression Profiling in the Hibernating Primate, Cheirogaleus Medius.

Journal Article Genome biology and evolution · August 2016 Hibernation is a complex physiological response that some mammalian species employ to evade energetic demands. Previous work in mammalian hibernators suggests that hibernation is activated not by a set of genes unique to hibernators, but by differential ex ... Full text Cite

Hibernation in a primate: does sleep occur?

Journal Article R Soc Open Sci · August 2016 During hibernation, critical physiological processes are downregulated and thermogenically induced arousals are presumably needed periodically to fulfil those physiological demands. Among the processes incompatible with a hypome tabolic state is sleep. How ... Full text Link to item Cite

Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar's forests past.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · July 2016 Phylogeographic analysis can be described as the study of the geological and climatological processes that have produced contemporary geographic distributions of populations and species. Here, we attempt to understand how the dynamic process of landscape c ... Full text Cite

Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs.

Journal Article Molecular ecology · May 2016 Implementation of the coalescent model in a Bayesian framework is an emerging strength in genetically based species delimitation studies. By providing an objective measure of species diagnosis, these methods represent a quantitative enhancement to the anal ... Full text Cite

Implications of lemuriform extinctions for the Malagasy flora.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · May 2016 Madagascar's lemurs display a diverse array of feeding strategies with complex relationships to seed dispersal mechanisms in Malagasy plants. Although these relationships have been explored previously on a case-by-case basis, we present here the first comp ... Full text Cite

Blood transcriptomes reveal novel parasitic zoonoses circulating in Madagascar's lemurs.

Journal Article Biology letters · January 2016 Zoonotic diseases are a looming threat to global populations, and nearly 75% of emerging infectious diseases can spread among wildlife, domestic animals and humans. A 'One World, One Health' perspective offers us an ideal framework for understanding and po ... Full text Cite

Phylogeography of the arid-adapted Malagasy bullfrog, Laliostoma labrosum, influenced by past connectivity and habitat stability.

Journal Article Molecular phylogenetics and evolution · November 2015 The rainforest biome of eastern Madagascar is renowned for its extraordinary biodiversity and restricted distribution ranges of many species, whereas the arid western region of the island is relatively species poor. We provide insight into the biogeography ... Full text Cite

Assessing the utility of whole genome amplified DNA for next-generation molecular ecology.

Journal Article Molecular ecology resources · September 2015 DNA quantity can be a hindrance in ecological and evolutionary research programmes due to a range of factors including endangered status of target organisms, available tissue type, and the impact of field conditions on preservation methods. A potential sol ... Full text Cite

Shifting ranges and conservation challenges for lemurs in the face of climate change

Journal Article Ecology and Evolution · March 1, 2015 Geospatial modeling is one of the most powerful tools available to conservation biologists for estimating current species ranges of Earth's biodiversity. Now, with the advantage of predictive climate models, these methods can be deployed for understanding ... Full text Cite

Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs.

Journal Article Journal of human evolution · February 2015 Humans first arrived on Madagascar only a few thousand years ago. Subsequent habitat destruction and hunting activities have had significant impacts on the island's biodiversity, including the extinction of megafauna. For example, we know of 17 recently ex ... Full text Cite

Multilocus phylogenetic and geospatial analyses illuminate diversification patterns and the biogeographic history of Malagasy endemic plated lizards (Gerrhosauridae: Zonosaurinae).

Journal Article Journal of evolutionary biology · February 2015 Although numerous studies have attempted to find single unifying mechanisms for generating Madagascar's unique flora and fauna, little consensus has been reached regarding the relative importance of climatic, geologic and ecological processes as catalysts ... Full text Cite

Shifting ranges and conservation challenges for lemurs in the face of climate change

Journal Article Ecology and Evolution · 2015 Geospatial modeling is one of the most powerful tools available to conservation biologists for estimating current species ranges of Earth’s biodiversity. Now, with the advantage of predictive climate models, these methods can be deployed for understanding ... Full text Open Access Cite

Alteration of the rat cecal microbiome during colonization with the helminth Hymenolepis diminuta.

Journal Article Gut Microbes · 2015 The microbiome is now widely recognized as being important in health and disease, and makes up a substantial subset of the biome within the ecosystem of the vertebrate body. At the same time, multicellular, eukaryotic organisms such as helminths are being ... Full text Link to item Cite

Patterns of gut bacterial colonization in three primate species.

Journal Article PloS one · January 2015 Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the ... Full text Cite

Population genetics of the Mauritian flying fox, Pteropus Niger

Journal Article Acta Chiropterologica · December 1, 2014 The Mauritius flying fox Pteropus niger is distributed on the islands of Mauritius and La Réunion in the western Indian Ocean. Although recent studies have examined the phylogenetics and systematics of this genus, relatively few have assessed the populatio ... Full text Cite

A deep divergence time between sister species of eidolon (Pteropodidae) with evidence for widespread Panmixia

Journal Article Acta Chiropterologica · December 1, 2014 The pteropodid fruit bat genus Eidolon is comprised of two extant species: E. dupreanum on Madagascar and E. helvum on the African mainland and offshore islands. Recent population genetic studies of E. helvum indicate widespread panmixia across the contine ... Full text Cite

Next-generation approaches to advancing eco-immunogenomic research in critically endangered primates.

Journal Article Molecular ecology resources · November 2014 High-throughput sequencing platforms are generating massive amounts of genomic data from nonmodel species, and these data sets are valuable resources that can be mined to advance a number of research areas. An example is the growing amount of transcriptome ... Full text Cite

A necessarily complex model to explain the biogeography of the amphibians and reptiles of Madagascar.

Journal Article Nature communications · October 2014 Pattern and process are inextricably linked in biogeographic analyses, though we can observe pattern, we must infer process. Inferences of process are often based on ad hoc comparisons using a single spatial predictor. Here, we present an alternative appro ... Full text Cite

Comparative genomics of mammalian hibernators using gene networks.

Journal Article Integrative and comparative biology · September 2014 In recent years, the study of the molecular processes involved in mammalian hibernation has shifted from investigating a few carefully selected candidate genes to large-scale analysis of differential gene expression. The availability of high-throughput dat ... Full text Cite

Theme and variations: heterothermy in mammals.

Journal Article Integrative and comparative biology · September 2014 This collection of articles is focused on the evolutionary dynamics of heterothermy in mammals, specifically torpor and hibernation. Topics cover a wide range from evolutionary genetics, physiology, ecology, and applications to human health. ... Full text Cite

The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms.

Journal Article BMC genomics · August 2014 BackgroundMolecular characterization of highly diverse gene families can be time consuming, expensive, and difficult, especially when considering the potential for relatively large numbers of paralogs and/or pseudogenes. Here we investigate the ut ... Full text Cite

Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution.

Journal Article Retrovirology · August 2014 BackgroundFoamy viruses (FVs) are a unique subfamily of retroviruses that are widely distributed in mammals. Owing to the availability of sequences from diverse mammals coupled with their pattern of codivergence with their hosts, FVs have one of t ... Full text Cite

The founding of Mauritian endemic coffee trees by a synchronous long-distance dispersal event.

Journal Article Journal of evolutionary biology · June 2014 The stochastic process of long-distance dispersal is the exclusive means by which plants colonize oceanic islands. Baker's rule posits that self-incompatible plant lineages are unlikely to successfully colonize oceanic islands because they must achieve a c ... Full text Cite

Multilocus coalescent analyses reveal the demographic history and speciation patterns of mouse lemur sister species.

Journal Article BMC evolutionary biology · March 2014 BackgroundDebate continues as to whether allopatric speciation or peripatric speciation through a founder effect is the predominant force driving evolution in vertebrates. The mouse lemurs of Madagascar are a system in which evolution has generate ... Full text Cite

Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates.

Journal Article Genome biology and evolution · January 2014 Vomeronasal receptor genes have frequently been invoked as integral to the establishment and maintenance of species boundaries among mammals due to the elaborate one-to-one correspondence between semiochemical signals and neuronal sensory inputs. Here, we ... Full text Cite

Gene flow happens.

Journal Article Evolutionary anthropology · January 2014 Debate over what is a species was already considered old hat when Darwin wrote his seminal abstract (as he called it) more than 150 years ago.(1) Endless papers, workshops, and symposia have been presented in an effort to "solve" the species problem. Yet, ... Full text Cite

Species-specific assembly of the gut microbiota in lemurs

Conference INTEGRATIVE AND COMPARATIVE BIOLOGY · January 1, 2014 Link to item Cite

Extinction risks and the conservation of Madagascar's reptiles.

Journal Article PloS one · January 2014 BackgroundAn understanding of the conservation status of Madagascar's endemic reptile species is needed to underpin conservation planning and priority setting in this global biodiversity hotspot, and to complement existing information on the islan ... Full text Cite

The molecular evolutionary dynamics of the vomeronasal receptor (class 1) genes in primates: a gene family on the verge of a functional breakdown.

Journal Article Frontiers in neuroanatomy · January 2014 Olfaction plays a critical role in both survival of the individual and in the propagation of species. Studies from across the mammalian clade have found a remarkable correlation between organismal lifestyle and molecular evolutionary properties of receptor ... Full text Cite

Life history profiles for 27 strepsirrhine primate taxa generated using captive data from the Duke Lemur Center.

Journal Article Scientific data · January 2014 Since its establishment in 1966, the Duke Lemur Center (DLC) has accumulated detailed records for nearly 4,200 individuals from over 40 strepsirrhine primate taxa-the lemurs, lorises, and galagos. Here we present verified data for 3,627 individuals of 27 t ... Full text Cite

Latitude drives diversification in Madagascar's endemic dry forest rodent eliurus myoxinus (subfamily Nesomyinae)

Journal Article Biological Journal of the Linnean Society · November 1, 2013 Numerous hypotheses have been proposed for the historical processes governing the rich endemism of Madagascar's biodiversity. The 'watershed model' suggests that drier climates in the recent geological past have resulted in the contraction of forests aroun ... Full text Cite

Two New Species of Mouse Lemurs (Cheirogaleidae: Microcebus) from Eastern Madagascar

Journal Article International Journal of Primatology · June 1, 2013 The number of newly discovered Malagasy vertebrate taxa has multiplied in recent years, emphasizing the importance of complete taxon sampling for phylogenetics, biogeography, functional ecology, and conservation biology, especially in such a biodiversity h ... Full text Cite

The lemur revolution starts now: the genomic coming of age for a non-model organism.

Journal Article Molecular phylogenetics and evolution · February 2013 Morris Goodman was a revolutionary. Together with a mere handful of like-minded scientists, Morris established himself as a leader in the molecular phylogenetic revolution of the 1960s. The effects of this revolution are most evident in this journal, which ... Full text Cite

Evolution. Fossils versus clocks.

Journal Article Science (New York, N.Y.) · February 2013 Full text Cite

Neuroethology: Do hibernating primates sleep?

Journal Article Nova Acta Leopoldina · 2013 Cite

Underground hibernation in a primate.

Journal Article Scientific reports · January 2013 Hibernation in mammals is a remarkable state of heterothermy wherein metabolic rates are reduced, core body temperatures reach ambient levels, and key physiological functions are suspended. Typically, hibernation is observed in cold-adapted mammals, though ... Full text Cite

Review of the systematic status of Sceloporus arenicolus Degenhardt and Jones, 1972 with an estimate of divergence time.

Journal Article Zootaxa · January 2013 The sagebrush lizards (Sceloporus graciosus group) consist of four taxa (S. graciosus graciosus, S. graciosus gracilis, S. graciosus vandenburgianus, and S. arenicolus) distributed in western North America. Of these, S. arenicolus is morphologically, behav ... Full text Cite

The relationship of sleep with temperature and metabolic rate in a hibernating primate.

Journal Article PLoS One · 2013 STUDY OBJECTIVES: It has long been suspected that sleep is important for regulating body temperature and metabolic-rate. Hibernation, a state of acute hypothermia and reduced metabolic-rate, offers a promising system for investigating those relationships. ... Full text Open Access Link to item Cite

Sequence data from new plastid and nuclear cosii regions resolves early diverging lineages in coffea (Rubiaceae)

Journal Article Systematic Botany · October 1, 2012 Resolving phylogenetic relationships within the economically important genus Coffea (Rubiaceae) has proven to be difficult due to low levels of plastid and nuclear ITS sequence divergence. The recent identification of a large number of conserved, single-co ... Full text Cite

Defining spatial and temporal patterns of phylogeographic structure in Madagascar's iguanid lizards (genus Oplurus).

Journal Article Molecular ecology · August 2012 Understanding the remarkably high species diversity and levels of endemism found among Madagascar's flora and fauna has been the focus of many studies. One hypothesis that has received much attention proposes that Quaternary climate fluctuations spurred di ... Full text Cite

Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics.

Journal Article Molecular biology and evolution · June 2012 The systematics and speciation literature is rich with discussion relating to the potential for gene tree/species tree discordance. Numerous mechanisms have been proposed to generate discordance, including differential selection, long-branch attraction, ge ... Full text Cite

Comparative RNA sequencing reveals substantial genetic variation in endangered primates.

Journal Article Genome research · April 2012 Comparative genomic studies in primates have yielded important insights into the evolutionary forces that shape genetic diversity and revealed the likely genetic basis for certain species-specific adaptations. To date, however, these studies have focused o ... Full text Cite

Effects of anthropogenic disturbance on indri (Indri indri) health in Madagascar.

Journal Article American journal of primatology · July 2011 Anthropogenic habitat disturbance impairs ecosystem health by fragmenting forested areas, introducing environmental contamination, and reducing the quality of habitat resources. The effect of this disturbance on wildlife health is of particular concern in ... Full text Cite

Integrating statistical genetic and geospatial methods brings new power to phylogeography.

Journal Article Molecular phylogenetics and evolution · May 2011 The field of phylogeography continues to grow in terms of power and accessibility. Initially uniting population genetics and phylogenetics, it now spans disciplines as diverse as geology, statistics, climatology, ecology, physiology, and bioinformatics to ... Full text Cite

Increased population sampling confirms low genetic divergence among Pteropus (Chiroptera: Pteropodidae) fruit bats of Madagascar and other western Indian Ocean islands.

Journal Article PLoS currents · March 2011 Fruit bats of the genus Pteropus occur throughout the Austral-Asian region west to islands off the eastern coast of Africa. Recent phylogenetic analyses of Pteropus from the western Indian Ocean found low sequence divergence and poor phylogenetic resolutio ... Full text Cite

Expression and trans-specific polymorphism of self-incompatibility RNases in coffea (Rubiaceae).

Journal Article PloS one · January 2011 Self-incompatibility (SI) is widespread in the angiosperms, but identifying the biochemical components of SI mechanisms has proven to be difficult in most lineages. Coffea (coffee; Rubiaceae) is a genus of old-world tropical understory trees in which the v ... Full text Cite

Phylogeny and biogeography of western Indian Ocean Rousettus (Chiroptera: Pteropodidae).

Journal Article Journal of mammalogy · June 2010 We examined patterns of genetic variation in Rousettus madagascariensis from Madagascar and R. obliviosus from the Comoros (Grande Comore, Anjouan, and Mohéli). Genetic distances among individuals on the basis of 1,130 base pairs of the mitoc ... Full text Cite

Conservation. CITES designation for endangered rosewood in Madagascar.

Journal Article Science (New York, N.Y.) · May 2010 Full text Cite

Delimiting species without nuclear monophyly in Madagascar's mouse lemurs.

Journal Article PloS one · March 2010 BackgroundSpeciation begins when populations become genetically separated through a substantial reduction in gene flow, and it is at this point that a genetically cohesive set of populations attain the sole property of species: the independent evo ... Full text Open Access Cite

Phylogeography's past, present, and future: 10 years after Avise, 2000.

Journal Article Molecular phylogenetics and evolution · January 2010 Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and population genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of ... Full text Cite

Multiple colonisations of the western Indian Ocean by Pteropus fruit bats (Megachiroptera: Pteropodidae): the furthest islands were colonised first.

Journal Article Molecular phylogenetics and evolution · May 2009 We investigate the genetic relationships between purported island species of Pteropus fruit bat (Megachiroptera) from the western Indian Ocean islands using mitochondrial DNA sequencing in order to infer the pattern of colonisation of this biogeographic re ... Full text Cite

Species delimitation in lemurs: multiple genetic loci reveal low levels of species diversity in the genus Cheirogaleus.

Journal Article BMC evolutionary biology · February 2009 BackgroundSpecies are viewed as the fundamental unit in most subdisciplines of biology. To conservationists this unit represents the currency for global biodiversity assessments. Even though Madagascar belongs to one of the top eight biodiversity ... Full text Cite

Phylogeny and evolution of Malagasy plated lizards.

Journal Article Molecular phylogenetics and evolution · February 2009 The endemic plated lizards (Gerrhosauridae) of Madagascar are one of the most diverse groups of lizards on the island (19 species) and are found in all ecoregions. On an island that presents so many interesting biological questions, plated lizards are an i ... Full text Cite

Anonymous nuclear markers for Malagasy plated lizards (Zonosaurus).

Journal Article Molecular ecology resources · January 2009 We report the development of 18, single-copy, anonymous nuclear loci from the Malagasy plated lizard Zonosaurus madagascariensis. More than 140 clones from a genomic library were examined and 38 potential loci tested across both closely and distantly relat ... 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

Population genetic analysis of Myzopoda (Chiroptera: Myzopodidae) in Madagascar

Journal Article Journal of Mammalogy · February 1, 2008 The chiropteran family Myzopodidae is endemic to Madagascar and is characterized by several unique morphologies, such as sessile adhesive discs on the thumb and sole. A new species, Myzopoda schliemanni, was recently described from western Madagascar that ... Full text Cite

The role of molecular genetics in sculpting the future of integrative biogeography

Journal Article Progress in Physical Geography · January 1, 2008 We review the expanding role of molecular genetics in the emergence of a vibrant and vital integrative biogeography. The enormous growth over the past several decades in the number and variety of molecular-based phylogenetic and population genetics studies ... Full text Cite

Lemurs.

Journal Article Current biology : CB · October 2007 Full text Cite

Multiple nuclear loci reveal patterns of incomplete lineage sorting and complex species history within western mouse lemurs (Microcebus).

Journal Article Molecular phylogenetics and evolution · May 2007 Mouse lemurs (genus Microcebus) are nocturnal primates endemic to the island of Madagascar. Until recently, they were classified as two species, one from eastern and one from western Madagascar. Previously published analyses of morphometric and mitochondri ... Full text Cite

Evolution of a tumorigenic property conferred by glycophosphatidyl-inositol membrane anchors of carcinoembryonic antigen gene family members during the primate radiation.

Journal Article Molecular biology of the cell · April 2007 GPI membrane anchors of cell surface glycoproteins have been shown to confer functional properties that are different from their transmembrane (TM)-anchored counterparts. For the human carcinoembryonic antigen (CEA) family, a subfamily of the immunoglobuli ... Full text Cite

Working at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae).

Journal Article Molecular ecology · February 2007 New applications of genetic data to questions of historical biogeography have revolutionized our understanding of how organisms have come to occupy their present distributions. Phylogenetic methods in combination with divergence time estimation can reveal ... Full text Open Access Cite

Evolutionary origins of malagasy primates.

Journal Article AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY · January 1, 2007 Link to item Cite

Has vicariance or dispersal been the predominant biogeographic force in Madagascar? Only time will tell

Journal Article Annual Review of Ecology, Evolution, and Systematics · December 18, 2006 Madagascar is one of the world's hottest biodiversity hot spots due to its diverse, endemic, and highly threatened biota. This biota shows a distinct signature of evolution in isolation, both in the high levels of diversity within lineages and in the imbal ... Full text Cite

Incongruence between genetic and morphological diversity in Microcebus griseorufus of Beza Mahafaly.

Journal Article BMC evolutionary biology · November 2006 BackgroundThe past decade has seen a remarkable increase in the number of recognized mouse lemur species (genus Microcebus). As recently as 1994, only two species of mouse lemur were recognized according to the rules of zoological nomenclature. Th ... Full text Cite

A new species of Emballonura (Chiroptera: Emballonuridae) from the dry regions of madagascar

Journal Article American Museum Novitates · January 1, 2006 We describe a new species of bat in the genus Emballonura (Chiroptera: Emballonuridae), E. tiavato, from the dry forest regions of Madagascar. This species is distinguished from the only other member of this genus found on the island, E. atrata, and extral ... Full text Cite

A multidimensional approach for detecting species patterns in malagasy vertebrates

Chapter · October 28, 2005 The biodiversity of Madagascar is extraordinarily distinctive, diverse, and endangered. It is therefore urgent that steps be taken to document, describe, interpret, and protect this exceptional biota. As a collaborative group of field and laboratory biolog ... Full text Cite

Evidence from opsin genes rejects nocturnality in ancestral primates.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · October 2005 It is firmly believed that ancestral primates were nocturnal, with nocturnality having been maintained in most prosimian lineages. Under this traditional view, the opsin genes in all nocturnal prosimians should have undergone similar degrees of functional ... Full text Cite

A multidimensional approach for detecting species patterns in Malagasy vertebrates.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · May 2005 The biodiversity of Madagascar is extraordinarily distinctive, diverse, and endangered. It is therefore urgent that steps be taken to document, describe, interpret, and protect this exceptional biota. As a collaborative group of field and laboratory biolog ... Full text Cite

Ancient DNA from giant extinct lemurs confirms single origin of Malagasy primates.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · April 2005 The living Malagasy lemurs constitute a spectacular radiation of >50 species that are believed to have evolved from a common ancestor that colonized Madagascar in the early Tertiary period. Yet, at least 15 additional Malagasy primate species, some of whic ... Full text Cite

The biogeography of Madagascar: where to turn when the fossils aren’t there.

Journal Article Paleontological Society Papers · 2005 Cite

Illumination of cryptic species boundaries in long-tailed shrew tenrecs (Mammalia: Tenrecidae; Microgale), with new insights into geographic variation and distributional constraints

Journal Article Biological Journal of the Linnean Society · September 1, 2004 The increasing use of mitochondrial DNA (mtDNA) to explore and test species limits among morphologically similar species is potentially compromised by phenomena poorly reflective of organismal history and speciation, including (but not limited to) stochast ... Full text Cite

Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context.

Journal Article Molecular ecology · April 2004 The lemurs of Madagascar are a unique radiation of primates that show an extraordinary diversity of lifestyles, morphologies and behaviours. However, very little is known about the relative antiquity of lemuriform clades due to the lack of terrestrial foss ... Full text Cite

Structure and function of CC-chemokine receptor 5 homologues derived from representative primate species and subspecies of the taxonomic suborders Prosimii and Anthropoidea.

Journal Article Journal of virology · November 2003 A chemokine receptor from the seven-transmembrane-domain G-protein-coupled receptor superfamily is an essential coreceptor for the cellular entry of human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) strains. To investigate ... Full text Cite

Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene Loci and calibration points, with application to a radiation of cute-looking mouse lemur species.

Journal Article Systematic biology · October 2003 Divergence time and substitution rate are seriously confounded in phylogenetic analysis, making it difficult to estimate divergence times when the molecular clock (rate constancy among lineages) is violated. This problem can be alleviated to some extent by ... Full text Cite

Single origin of Malagasy Carnivora from an African ancestor.

Journal Article Nature · February 2003 The Carnivora are one of only four orders of terrestrial mammals living in Madagascar today. All four (carnivorans, primates, rodents and lipotyphlan insectivores) are placental mammals with limited means for dispersal, yet they occur on a large island tha ... Full text Cite

The phylogeny of Rosoideae (Rosaceae) based on sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA and the trnL/F region of chloroplast DNA

Journal Article International Journal of Plant Sciences · January 1, 2003 The phylogeny of Rosoideae was investigated using 44 species. Here we report new sequence data from the chloroplast trnL/F region as well as an increased sample of species. The analysis of these new data, along with previously used data from the nuclear ri ... Full text Cite

Molecular evidence of reproductive isolation in sympatric sibling species of mouse lemurs

Journal Article International Journal of Primatology · December 1, 2002 Recent morphological and molecular phylogenetic studies of mouse lemurs (Microcebus) living in the western and southern regions of Madagascar have shown that specific diversity had been considerably underestimated. In large part, this underestimate was due ... Full text Cite

Ancient DNA

Chapter · 2002 Cite

Using secondary structure to identify ribosomal numts: cautionary examples from the human genome.

Journal Article Molecular biology and evolution · January 2002 The identification of inadvertently sequenced mitochondrial pseudogenes (numts) is critical to any study employing mitochondrial DNA sequence data. Failure to discriminate numts correctly can confound phylogenetic reconstruction and studies of molecular ev ... Full text Cite

Ancient DNA from Megaladapis edwardsi.

Journal Article Folia primatologica; international journal of primatology · November 2001 Full text Cite

Failure of the ILD to determine data combinability for slow loris phylogeny.

Journal Article Systematic biology · June 2001 Tests for incongruence as an indicator of among-data partition conflict have played an important role in conditional data combination. When such tests reveal significant incongruence, this has been interpreted as a rationale for not combining data into a s ... Full text Cite

Remarkable species diversity in Malagasy mouse lemurs (primates, Microcebus).

Journal Article Proceedings of the National Academy of Sciences of the United States of America · October 2000 Phylogenetic analysis of mtDNA sequence data confirms the observation that species diversity in the world's smallest living primate (genus Microcebus) has been greatly underestimated. The description of three species new to science, and the resurrection of ... Full text Cite

Genetic tests of the taxonomic status of the ring-tailed lemur (Lemur catta) from the high mountain zone of the Andringitra Massif, Madagascar

Journal Article Journal of Zoology · September 25, 2000 A recent survey of the high-mountain zone of the Madagascar Parc National (PN) d'Andringitra revealed the presence of an apparently isolated troop of the ring-tailed lemur Lemur catta. These animals display phenotypic and ecological characteristics that ar ... Full text Cite

Estimation of primate speciation dates using local molecular clocks.

Journal Article Molecular biology and evolution · July 2000 Protein-coding genes of the mitochondrial genomes from 31 mammalian species were analyzed to estimate the speciation dates within primates and also between rats and mice. Three calibration points were used based on paleontological data: one at 20-25 MYA fo ... Full text Cite

Estimation of the transition/transversion rate bias and species sampling.

Journal Article Journal of molecular evolution · March 1999 The transition/transversion (ti/tv) rate ratios are estimated by pairwise sequence comparison and joint likelihood analysis using mitochondrial cytochrome b genes of 28 primate species, representing both the Strepsirrhini (lemurs and lories) and the Anthro ... Full text Cite

Phylogeny of the Lemuridae: Effects of character and taxon sampling on resolution of species relationships within Eulemur

Journal Article Cladistics · January 1, 1999 DNA sequences from three mitochondrial genes and one nuclear gene were analyzed to determine the phylogeny of the Malagasy primate family Lemuridae. Whether analyzed separately or in combination, the data consistently indicate that Eulemur species comprise ... Full text Cite

An infinitude of connecting links

Journal Article Trends in Ecology & Evolution · March 1997 Full text Cite

Back to the future: A synthesis of strepsirrhine systematics

Journal Article Evolutionary Anthropology · January 1, 1997 The strepsirrhine primates, defined here as living tooth-combed primates, their immediate ancestor, and all of its descendants, are a diverse assemblage of mammals, viewed by some as exemplars of the richness of evolutionary innovation and by others as uni ... Full text Cite

Molecular evolutionary dynamics of cytochrome b in strepsirrhine primates: the phylogenetic significance of third-position transversions.

Journal Article Molecular biology and evolution · December 1996 DNA sequences of the complete cytochrome b gene are shown to contain robust phylogenetic signal for the strepsirrhine primates (i.e., lemurs and lorises). The phylogeny derived from these data conforms to other molecular studies of strepsirrhine relationsh ... Full text Cite

Ancient single origin for Malagasy primates.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · May 1996 We report new evidence that bears decisively on a long-standing controversy in primate systematics. DNA sequence data for the complete cytochrome b gene, combined with an expanded morphological data set, confirm the results of a previous study and again in ... Full text Cite

Relative position of the Cheirogaleidae in strepsirhine phylogeny: a comparison of morphological and molecular methods and results.

Journal Article American journal of physical anthropology · May 1994 An examination of previous morphological and molecular studies of strepsirhine systematics suggests a conflict between the two types of data. Cladistic analyses of morphological data have indicated that the Malagasy primate family Cheirogaleidae is the sis ... Full text Cite

Molecules and morphology in Primate Systematics: An introduction

Journal Article American Journal of Physical Anthropology · January 1, 1994 Full text Cite

Cranial anatomy of Ignacius graybullianus and the affinities of the Plesiadapiformes

Journal Article American Journal of Physical Anthropology · January 1, 1992 A nearly complete cranium of Ignacius graybullianus provides increased understanding of the cranial anatomy of Plesiadapiformes. In nearly all details of cranial anatomy, Ignacius differs markedly from primates. USNM 421608 exhibits a long tapering snout, ... Full text Cite

The applications and limitations of ontogenetic comparisons for phylogeny reconstruction: the case of the strepsirhine internal carotid artery

Journal Article Journal of Human Evolution · January 1, 1992 Ontogeny and phylogeny together determine organismal form and consequently, the two should be reciprocally illuminating. Ontogeny contributes valuable information for phylogenetic studies, not because it is a window into phylogeny, but because ontogenetic ... Full text Cite

A PHYLOGENETIC SYSTEMATIC STUDY OF THE TRUE LORISES

Journal Article AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY · February 1, 1989 Link to item Cite