Robert W Murphy

Robert W Murphy
University of Toronto | U of T · Department of Ecology and Evolutionary Biology

Ph.D.

About

699
Publications
175,810
Reads
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12,837
Citations
Citations since 2017
230 Research Items
6821 Citations
201720182019202020212022202302004006008001,0001,2001,400
201720182019202020212022202302004006008001,0001,2001,400
201720182019202020212022202302004006008001,0001,2001,400
201720182019202020212022202302004006008001,0001,2001,400
Introduction
My research tests hypotheses in evolutionary genomics, phylogenetics, biogeography, and conservation. Some studies venture into methods, de novo software and alpha taxonomy. The research is internationally collaborative and involves researchers from China, Russia, Germany, Mexico, Brazil, Vietnam, Australia, USA and elsewhere. My curiosity is not bounded by species, but rather involves all forms of life, although it tends to concentrate on amphibians and reptiles.
Additional affiliations
August 2007 - March 2020
Kunming Institute of Zoology CAS
Position
  • Senior Researcher
June 1985 - March 2020
University of Toronto
Position
  • Professor
September 1984 - February 2020
Royal Ontario Museum
Position
  • Sr. Curator
Education
September 1976 - March 1982
September 1973 - June 1976
San Francisco State University
Field of study
  • Herpetology

Publications

Publications (699)
Article
Full-text available
Determining the functional consequences of karyotypic changes is invariably challenging because evolution has a tendency to obscure many of its own footprints, such as accumulated mutations, recombination events and demographic perturbations. Here we describe the assembly of a chromosome-level reference genome of the gayal (Bos frontalis) thereby r...
Article
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The systematics of the Cricetid genus Neodon have long been fraught with uncertainty due to sampling issues and a lack of comprehensive datasets. To gain better insights into the phylogeny and evolution of Neodon , we systematically sampled Neodon across the Hengduan and Himalayan Mountains, which cover most of its range in China. Analyses of skull...
Article
Defense against ultraviolet (UV) radiation exposure is essential for survival, especially in high-elevation species. Although some specific genes involved in UV response have been reported, the full view of UV defense mechanisms remains largely unexplored. Herein, we used integrated approaches to analyze UV responses in the highest-elevation frog,...
Article
We describe a new species of kukri snake from Da Lat City and its vicinity in Lam Dong Province, southern Vietnam on the basis of morphological characters of four specimens, including two males and two females. Oligodon tuani sp. nov. differs from other congeners by a combination of the following characters: large size in adults (TL ≤ 888 mm); 19 d...
Article
The biodiversity within tropical dry forests (TDFs) is astounding and yet poorly catalogued due to inadequate sampling and the presence of cryptic species. In the Mexican TDF, endemic species are common, and the landscape has been continually altered by geological and anthropogenic changes. To understand how landscape and environmental variables ha...
Preprint
Full-text available
Abstract. Inferring phylogenies among intraspecific individuals often yields unresolved relationships (i.e., polytomies). Consequently, methods that compute distance-based abstract networks, like Median-Joining Networks (MJNs), are thought to be more appropriate tools for reconstructing such relationships than traditional trees. MJNs visualize all...
Article
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The Hong Kong Whipping Frog (Polypedates megacephalus) is widespread on Hainan Island and yet nothing is known about its history. To investigate this, we use sequences of a partial fragment of mitochondrial ND1 and its flanking region from 248 individuals taken from 30 localities. Analyses reveal low genetic diversity and commonly shared haplotypes...
Article
Full-text available
Background Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra...
Article
Full-text available
Evolutionary biologists are always interested in deciphering the geographic context of diversification, therefore they introduced the concept of comparative phylogeography, which helps to identify common mechanisms that contribute to shared genetic structures among organisms from the same region. Here, we used multi-locus genetic data along with en...
Article
Maintenance of genetic diversity at adaptive loci may facilitate invasions by non-native species by allowing populations to adapt to novel environments, despite the loss of diversity at neutral loci that typically occurs during founder events. To evaluate this prediction, we compared genetic diversity at MHC and cytochrome b (cytb) loci from 20 pop...
Article
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Effective conservation of threatened biota relies on accurate assessments and scientific guidance. As an unfortunate example, Chinese giant salamanders (Andrias, CGS) remain critically endangered in nature. Misguided conservation efforts, e.g., commercial propagation and releasing of millions of likely non-indigenous or interspecific hybrids, have...
Article
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Speciation plays a central role in evolutionary studies, and particularly how reproductive isolation evolves. The origins and persistence of reproductive isolation are distinct processes that require separate evaluations. Treating them separately clarifies the drivers of speciation and then it is possible to link the processes to understand large-s...
Article
During a small mammal survey in Wanglang National Natural Reserve, Sichuan, China in August–October 2018, we collected four specimens of an Asiatic striped squirrel (genus Tamiops) that could not be assigned morphologically to any described species. Phylogenetic analyses of CYTB and nuDNA sequences strongly supported them in the genus Tamiops. The...
Preprint
Full-text available
Defense against increasing ultraviolet radiation (UV) exposure is essential for survival, especially in high-elevation species. Although some specific genes involved in UV response have been reported, the full view of UV-defense mechanisms remains largely unexplored. Herein, we analyzed UV responses in the highest-elevation frog, Nanorana parkeri ,...
Preprint
Full-text available
Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 MYA, yet the genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remain largely unknown. Additionally, many populations have declined drastically due to anthropogenic...
Article
Full-text available
en While species boundaries between conspicuously divergent populations of the medically important snake genus Sinomicrurus are well established, instances of erratic chromatic and meristic variation continue to confound taxonomists, since the mid-1800s. This predicament can be attributed to an inadequate molecular phylogenetic framework and the la...
Article
Full-text available
The evolutionary outcomes of high‐elevation adaptation have been extensively described. However, whether widely distributed high‐elevation endemic animals adopt uniform mechanisms during adaptation to different elevational environments remains unknown, especially with respect to extreme high elevation environments. To explore this, we analyze pheno...
Preprint
Full-text available
Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molec...
Article
Full-text available
Deharveng's blind lizard, Dibamus deharvengi Ineich, 1999, was described more than 20 years ago based on a single male specimen (MNHN 1997.6515) collected in 1995 from Binh Chau, Xuyen Moc district, Ba Ria-Vung Tau province, Vietnam. The unique specimen was broken into two parts: the first section includes head and neck and the other consists of bo...
Article
Montane frogs of the genus Quasipaa Dubois, 1992 occur from southern China to Southeast Asia (Frost 2021). Analyses of mtDNA (Cytb) and nuDNA data (Rag1, Rag2, Rhod, Tyr) for samples from 93 localities throughout its distribution yield a phylogeny. Clades A and B occur in Southeast Asia, clade C in northern Yangtze River, China, clade D in southwes...
Article
A new vine snake, genus Ahaetulla, from Soc Trang Province, southern Vietnam is described based on morphological data and nucleotide sequences from COI and Cytb. Ahaetulla rufusoculara sp. nov. is diagnosed by the following morphological characters: bright red eyes; snout without dermal appendage; internasal separated from supralabial by loreal; bo...
Article
A new species of the genus Gekko Laurenti, 1768 is described from Phu Yen Province, southern Vietnam based on morphological and molecular evidence. Gekko phuyenensis sp. nov. differs from other congeners by its moderate size, with a snout-vent length of 90.2-92.8 mm; nares in contact with rostral; internasal 1; interorbitals 35 or 36; ventrals 30-3...
Article
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Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for n...
Article
Full-text available
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1–4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evalu...
Article
Leaf-toed geckos (Phyllodactylus) exhibit much cryptic diversity, at least in North America. However, the origins of Central American taxa and their relationships with North American congeners remain unknown. The P. tuberculosus species complex is ideal for evolutionary and biogeographic studies because its geographic distribution extends from nort...
Article
We describe a new species of the genus Subdoluseps Freitas, Datta-Roy, Karanth, Grismer & Siler from a coastal area in southern Vietnam. Subdoluseps vietnamensis sp. nov. is characterized by the following morphological characters: medium size in adults (snout-vent length up to 48.7 mm); tail length/snout-vent length ratio 1.04; toes not reaching fi...
Article
Emerging infectious diseases are on the rise in many different taxa, including, among others, the amphibian batrachochytrids, the snake fungal disease and the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) virus, responsible for Coronavirus disease 2019 (COVID-19) in mammals. Following the onset of the pandemic linked to COVID-19, eas...
Preprint
Full-text available
Background The reconstruction of phylogenetic relationships for allopolyploids using genomic data is challenging because hybridization and polyploidy can blur history. In cyprinids, one allopolyploidization event involves goldfish and common carp, yet little is known about the origins of other cyprinid polyploid lineages, including their maternal a...
Article
A new skink of the genus Scincella Mittleman, 1950, from Binh Phuoc Province, southern Vietnam is described based on morphological data, including hemipenial characters, and nucleotide sequences from COI. The following morphological characters diagnose Scincella baraensis sp. nov.: relatively small size in adults (snout-vent length up to 49.2 mm);...
Article
Herein, we describe a new agamid species of the genus Acanthosaura from Central Highlands of Vietnam: Gia Lai Province, Kon Chu Rang NR, and Kon Tum Province: Kon Plông and Ngoc Linh Mountain based on morphological and molecular data. Acanthosaura prasina sp. nov. is distinguished from all congeners by a combination of the following morphological c...
Article
Full-text available
Understanding the influence of geographic features on the evolutionary history and population structure of a species can assist wildlife managers in delimiting genetic units (GUs) for conservation and management. Landscape features including mountains, low elevation depressions, and even roads can influence connectivity and gene flow among Agassiz’...
Article
We utilize the efficient GBS technique to obtain thousands of nuclear loci and SNPs to reconstruct the evolutionary history of Mexican leaf-toed geckos (Phyllodactylus). Through the incorporation of unprecedented sampling for this group of geckos, in combination with genomic data analysis, we generate mostly consistent phylogenetic hypotheses using...
Article
Full-text available
A persistent enigma is the rarity of polyploidy in animals, compared to its prevalence in plants. Although animal polyploids are thought to experience deleterious genomic chaos during initial polyploidization and subsequent rediploidization processes, this hypothesis has not been tested. We provide an improved reference-quality de novo genome for a...
Preprint
Full-text available
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species. To address this issue, the international Genome 10K (G10K) consortium has worked over a five-year period to evaluate an...
Article
Full-text available
Background: The hybridization of female D. raddei and male D. valentini gave rise to the parthenogenetic Caucasian rock lizard Darevskia unisexualis. A previously identified genetic polymorphism in the species consisted of one common and two allozyme clones. Analysis of microsatellites and single nucleotide polymorphisms (SNPs) from the three spec...
Article
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Among 14 species of forest skinks (genus Sphenomorphus) in Vietnam, seven were recorded from southern part of the country. Shea's forest skink, S. sheai, was described from Kon Tum Plateau based on a single female. Similarly, the tridigital forest skink, S. tridigitus, was also described based on a single putrid and desiccated specimen found dead o...
Article
The genus Amolops (“torrent frogs”) is one of the most species-rich genera in Ranidae, with 59 recognized species. This genus currently includes six species groups diagnosed mainly by morphology. Several recent molecular studies indicated that the classification of species groups within Amolops remains controversial, and key nodes in the phylogeny...
Article
Full-text available
A new species of Sinomicrurus Slowinski, Boundy, and Lawson, 2001 is described herein based on a series of specimens. The new species, Sinomicrurus peinani sp. nov., occurs in southern China and northern Vietnam. Sinomicrurus peinani sp. nov. is distinguished from its congeners by the following combination of characters: (1) 30–35 black crossbands...
Article
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Myanmar, a biodiversity hotspot, harbors a striking diversity and endemism of species. Despite this, its herpetofauna remains one of the least explored in continental Asia due to restrictions of crossing political boundaries and infrastructure in remote regions. Many species in adjacent China and India are hypothesized to occur in Myanmar but recor...
Article
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The transition of terrestrial snakes to marine life approximately 10 million years ago (Ma) is ideal for exploring adaptive evolution. Sea snakes possess phenotype specializations including laterally compressed bodies, paddle-shaped tails, valvular nostrils, cutaneous respiration, elongated lungs and salt glands yet knowledge on the genetic underpi...
Article
Full-text available
Background: Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated...
Preprint
Background: Crocidura , the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated...
Preprint
Full-text available
Neodon , genus of a short time evolutionary history, was reported to be diverged from its relatives in early stage of Pleistocene. Only 4 species were well documented in Neodon for a long period of time until last years when a systematic work described and added three new species, adjusted three species used to belong to Lasiopodomys, Phaiomys, Mic...
Article
Historically Panaspis wahlbergi (Smith, 1849) has been the only assignable species present in Kenya. Recent studies have shown that it comprises multiple cryptic species and the nominal species is now restricted to southern Africa. Newly collected mitochondrial data (16S rRNA) helped to resolve the status of the Kenyan populations, which revealed t...
Article
Full-text available
Species of Xenophrys are conserved morphologically and live primarily in forests. In Thailand, the genus harbors many cryptic species. Herein we report the collection of specimens from Doi Inthanon, Chiang Mai Province, northern Thailand, which were identified previously as X. minor. Molecular and morphological analyses find that these specimens di...
Article
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Deep seas have extremely harsh conditions including high hydrostatic pressure, total darkness, cold, and little food and oxygen. The adaptations of fishes to deep-sea environment apparently have occurred independently many times. The genetic basis of adaptation for obtaining their energy remains unknown. Mitochondria play a central role in aerobic...
Article
Full-text available
Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards and snakes, amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a con...
Article
Full-text available
Abstract Inaccurate taxonomic assessment of threatened populations can hinder conservation prioritization and management, with human‐mediated population movements obscuring biogeographic patterns and confounding reconstructions of evolutionary history. Giant salamanders were formerly distributed widely across China, and are interpreted as a single...
Article
Full-text available
The Mojave Desert Tortoise, Gopherus agassizii (Family Testudinidae), is a large terrestrial species that can reach >370 mm in straight midline carapace length (CL) but most individuals are smaller. Both sexes reach adulthood at 12 to 21 years and ca. 180 mm CL. The species is sexually dimorphic, with males typically larger than females; sexual cha...
Preprint
Background: Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. In China, the taxonomy has been primarily based on cursory morphological comparisons and molecular phylogenetic relationships of the genus remain unexplored. In order to understand the phylogeny of this group in China, we estimated the first mul...
Preprint
Full-text available
Background: Crocidura , the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated...
Article
Full-text available
Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused base...
Article
Ba Den is an isolated mountain in southern Vietnam and home to two endemic species of lizards. Herein, we describe another endemic species, a new skink of the genus Scincella Mittleman, 1950, from the area based on morphological data, including hemipenial characters and nucleotide sequences of COI. The following morphological characters diagnose Sc...
Article
Full-text available
Adaptations to extreme environmental conditions are intriguing. Animal skin, which directly interacts with external environment, plays diverse and important roles in adaptive evolution. The thin and bare skin of amphibians is sensitive to external environmental conditions and, thus, it facilitates investigations into adaptations for living in extre...
Data
Breeding males of this species have keratinized spines on their upper jaws, which are used as weapons in the fight. Each male usually lowers its head and struggles to put it under the body of the opponent, extends the forelimbs forward and slightly upward to try to grasp the opponent and steady it on the spines, and pushes forward with the hindlimb...