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Papers by Robert Murphy

Research paper thumbnail of List of Snakes of Tam-Dao Mountain Ridge (Tonkin, Vietnam)

Russian Journal of Herpetology, 2011

The full list of species of snakes inhabiting Tam-Dao mountain ridge is presented.

Research paper thumbnail of A Redescription of Vibrissaphora ailaonica with a New Record in Vietnam

Russian Journal of Herpetology, 2011

Specimens of Vibrissaphora ailaonica were collected on Mt. Fan Si Pan, Lao Cai Province, Vietnam.... more Specimens of Vibrissaphora ailaonica were collected on Mt. Fan Si Pan, Lao Cai Province, Vietnam. Prior to this, the species was known only from two localities in southern Yunnan, China. This collection represents not only the southern-most distribution for the genus, but also a new species record for Vietnam. We provide a redescription of V. ailaonica , and comments on its ecology and reproductive biology.

Research paper thumbnail of Phylogeny of genus Scutiger (Amphibia: Megophryidae): a re-evaluation

Asiatic herpetological research., 1997

A re-analysis of a published data set from Ye et al. (1992) indicates that their phylogeny for th... more A re-analysis of a published data set from Ye et al. (1992) indicates that their phylogeny for the genus Sc~rtiger does not reflect the most parsimonious explanation of the data. The consensus of the resulting trees from the original data set is a "bush" with only three resolved nodes. A re-evaluation of the character states, and their respective polarizations, resulted in alternative phylogenetic hypotheses. However, measures of homoplasy and data consistency for the re-evaluated topologies were relatively low, suggesting that little confidence could be obtained in these relationships. More data are needed to generate a defensible hypothesis of the relationships within the genus Scutiger.

Research paper thumbnail of The taxonomic status of the rosy boa Lichanura roseofusca (Serpentes: Boidae)

The Great Basin naturalist., 1980

Evidence is presented indicating that lAchanura roseofusca and Lkhanum triiirgata are conspecific... more Evidence is presented indicating that lAchanura roseofusca and Lkhanum triiirgata are conspecific. Data include the report of an intermediate specimen from El Arco, Baja California Norte, a site midway between the previously known peninsular ranges of the two species; captive hybridization provides additional support for the conclusion.

Research paper thumbnail of The speciation continuum: ecological and chromosomal divergence in the Simulium arcticum complex (Diptera: Simuliidae)

Biological Journal of the Linnean Society, 2015

Chromosome inversions may be involved in adaptation and speciation. We investigate ecological div... more Chromosome inversions may be involved in adaptation and speciation. We investigate ecological diversification among members of the Simulium arcticum species complex at different stages of chromosome divergence. Our analyses focus on two geographical scales. First, we assess ecological divergence of sibling species throughout North America using niche modelling methods. Then, using canonical correspondence analysis, we investigate habitat associations of sibling species and cytotypes in the northern Rocky Mountains ecoregion, where cytotypes tend to occur. Despite significant overlap in predicted distributions, all sibling species are ecologically unique. On the other hand, we discover various degrees of ecological divergence for cytotypes. Some cytotypes are ecologically distinct and perhaps are in their initial stages of incipient speciation. Other cytotypes are ecologically associated with one another or with particular sibling species. Thus, for members of the S. arcticum complex, ecological and chromosomal differences tend to develop early in lineage formation. Ecological distinctiveness of sibling species and cytotypes suggests that local adaptation may be involved in diversification of these chromosomal forms.

Research paper thumbnail of Comparison of base composition and codon usage in insect mitochondrial genomes

Genes & Genomics, 2009

Insects, the most biodiverse taxonomic group, have high AT content in their mitochondrial genomes... more Insects, the most biodiverse taxonomic group, have high AT content in their mitochondrial genomes. Although codon usage te nds to be AT-rich, base composition and codon usage of mitochondrial genomes may vary among taxa. Thus, we compare base composition and codon usage patterns of 49 insect mitochondri al genomes. For protein coding genes , AT content is as high as SOOIo in the Hymenoptera and Lepidoptera and as low as 72% in the Orthopotera. The AT content is high at positions 1 and 3, but A content is low at position 2. A close correlation occurs between codon usa ge and tRNA abundance in nuclear genomes. Optimal codons can pair well with the anticodons of the most abun dant tRNAs. One tRNA gene translates a synonymous codon family in vertebrate mitochondrial genomes and. these tRNA ann codons can pair with optimal codons. However, opti mal codons cannot pair with anticodons in mtDNA of Cochliomyia hominivorax (Diptera: Calliphoridae). Ten opti mal codons cannot pair with tRNA anticodons in all 49 insect mi• tochondrial genomes : non-optimal codon-anticodon usage is conunon and codon usage is not influenced by tRNA abundance. Key words: insect mitochondrial gen ome, codon usa ge, tRNA anticodon, non-optimal codon-anticodon usage. INTRODUCTIO N Ins ect mitochondrial genomes (mtDNA) exist as closed circular st rands with 13 protein-coding genes, *To whom correspondence shoul d be addressed.

Research paper thumbnail of Genetic Assessments and Parentage Analysis of Captive Bolson Tortoises (Gopherus flavomarginatus) Inform Their “Rewilding” in New Mexico

PLoS ONE, 2014

The Bolson tortoise (Gopherus flavomarginatus) is the first species of extirpated megafauna to be... more The Bolson tortoise (Gopherus flavomarginatus) is the first species of extirpated megafauna to be repatriated into the United States. In September 2006, 30 individuals were translocated from Arizona to New Mexico with the long-term objective of restoring wild populations via captive propagation. We evaluated mtDNA sequences and allelic diversity among 11 microsatellite loci from the captive population and archived samples collected from wild individuals in Durango, Mexico (n = 28). Both populations exhibited very low genetic diversity and the captive population captured roughly 97.5% of the total wild diversity, making it a promising founder population. Genetic screening of other captive animals (n = 26) potentially suitable for reintroduction uncovered multiple hybrid G. flavomarginatus6G. polyphemus, which were ineligible for repatriation; only three of these individuals were verified as purebred G. flavomarginatus. We used these genetic data to inform mate pairing, reduce the potential for inbreeding and to monitor the maintenance of genetic diversity in the captive population. After six years of successful propagation, we analyzed the parentage of 241 hatchlings to assess the maintenance of genetic diversity. Not all adults contributed equally to successive generations. Most yearly cohorts of hatchlings failed to capture the diversity of the parental population. However, overlapping generations of tortoises helped to alleviate genetic loss because the entire six-year cohort of hatchlings contained the allelic diversity of the parental population. Polyandry and sperm storage occurred in the captives and future management strategies must consider such events.

Research paper thumbnail of Low metabolic rate in a nocturnal desert lizard, an arbylus switaki murphy (Sauria: Gekkonidae)

Comparative Biochemistry and Physiology Part A: Physiology, 1982

Metabolic rates were measured in two xeric-adapted gekkonid lizards, Ai~arby1u.s switaki and Cole... more Metabolic rates were measured in two xeric-adapted gekkonid lizards, Ai~arby1u.s switaki and Coleonyx uariegatus. 2. Standard metabolic rates (SMR) were 0.074ml 0,Ighr in A. switaki and were 70% of the value predicted on the basis of mass from regression equations. The SMR of 0.146 ml 0 2 / g hr in C. uariegattis is similar to the predicted value for a lizard of this mass. 3. During intense act~vity, metabolic rates of 0.378 and 0.804 ml 0 2 / g hr were measured in A. switakl and C. variegatus, respectively. 4. Various theories to explain reduced SMR in lizards are discussed, and it is concluded that none is entirely satisfactory, and caution should be exercised in interpreting the adaptive significance of reduced SMR.

Research paper thumbnail of Allozyme variation patterns and multiple hybridization origins: Clonal variation among four sibling parthenogenetic Caucasian rock lizards

Genetica, 2000

Allozyme electrophoresis of four sibling parthenogenetic Caucasian rock lizards Darevskia unisexu... more Allozyme electrophoresis of four sibling parthenogenetic Caucasian rock lizards Darevskia unisexualis, D. uzzelli, D. sapphirina, and D. bendimahiensis found seven clones and five variable loci. The data supported the hypothesis that D. raddei and D. valentini are the parental species of all four parthenogens. Variation patterns in Darevskia were summarized. Species that originated from a single F 1 typically consisted of one widespread clone with a few rare clones. Species with multiple origins displayed variation only slightly higher than species with a single origin. This is contrary to other genera of parthenogenetic lizards, in which cases massive clonal variations were observed.

Research paper thumbnail of Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amphibia)

Zoologica Scripta, 2012

Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amph... more Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amphibia).-Zoologica Scripta, 00, 000-000. The treefrog genus Rhacophorus, a large genus with 80 species, has a wide range, occurring eastward from India to China, Japan, Southeast Asia, the Greater Sunda Islands and the Philippines. The phylogenetic relationships and taxonomic recognition of many species are very controversial. To stabilize the taxonomy, the phylogenetic relationships among about 52 species are investigated from 96 samples using mtDNA sequence data. Matrilineal relationships based on maximum likelihood and Bayesian inference methods resolve three well-supported lineages (A, B and C), although the phylogenetic relationships among three lineages remain ambiguous. Analyses support recognition of two previously assigned subgenera, Leptomantis and Rhacophorus, and these correspond to lineages A and B, respectively. Given that we have three strongly supported lineages, that these lineages are morphologically distinct, and the constrained geographic distributions of these groups, we recognize each lineage as a taxon. Subgenus Leptomantis includes species mainly from Malaysia, Indonesia and the Philippines. Subgenus Rhacophorus contains a mix of species occurring in India, Indochina and southern China. Lineage C accommodates species distributed mostly in East Asia, including Japan and China. Based on genetic and morphological data from type localities, the taxonomic recognition of some species needs to be reconsidered. Rhacophorus pingbianensis and Polypedates spinus are considered as junior synonyms of Rhacophorus duboisi. Specimens of Rhacophorus rhodopus from Vietnam and Hainan, China likely represent an undescribed, cryptic species.

Research paper thumbnail of Phylogeny and biogeography of water skinks of the genus Tropidophorus (Reptilia: Scincidae): a molecular approach

Zoologica Scripta, 2006

Phylogenetic relationships of the Oriental semiaquatic lygosomine skinks of the genus Tropidophor... more Phylogenetic relationships of the Oriental semiaquatic lygosomine skinks of the genus Tropidophorus were inferred from 1219 base positions of mitochondrial 12S and 16S rRNA genes. Results of the phylogenetic analyses incorporating data for representatives of other lygosomine genera indicated that the basal phylogenetic split within Tropidophorus separated a clade of continental Indochinese species exclusive of T. cocincinensis and T. microlepis from one comprising T. cocincinensis, T. microlepis and species from Borneo, Sulawesi and the Philippines. Of the latter group, the two continental species form the sister taxon to a clade comprising the island species. Diversification among species in Indochina and among Borneo, the Philippines and Sulawesi was likely concentrated in the Miocene, with no apparent dispersal among these regions during the Pleistocene. The body depression recognized in several Indochinese species is likely to have occurred twice in parallel as an adaptation to ...

Research paper thumbnail of Phylogenetic relationships of megophryid frogs of the genus Leptobrachium (Amphibia, Anura) as revealed by mtDNA gene sequences

Molecular Phylogenetics and Evolution, 2010

By investigating genealogical relationships, we estimated the phylogenetic history and biogeograp... more By investigating genealogical relationships, we estimated the phylogenetic history and biogeography in the megophryid genus Leptobrachium (sensu lato, including Vibrissaphora) from southern China, Indochina, Thailand and the Sundaland. The genealogical relationships among the 30 named and unnamed taxa were estimated using 2009 bp of sequences from the mitochondrial DNA genes 12S rRNA, tRNA val , and 16S rRNA using maximum parsimony, maximum likelihood, and Bayesian inference methods. The genus Leptobrachium was a well-supported monophyletic group that contained two major clades. One clade had three subclades primarily from disjunct regions including Borneo, Peninsular Malaysia and Java, and Thailand. The Bornean subclade included one species each from the Philippines and Sumatra. The other major clade consisted of two subclades, one from Indochina and the other from southern China (Vibrissaphora). Divergence times estimated an old evolutionary history of each subclade, one that could not be explained by the geohistory of Southeast Asian major landmasses.

Research paper thumbnail of COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae)

Molecular Ecology Resources, 2011

The 5&amp... more The 5' region of the mitochondrial DNA (mtDNA) gene cytochrome c oxidase I (COI) is the standard marker for DNA barcoding. However, because COI tends to be highly variable in amphibians, sequencing is often challenging. Consequently, another mtDNA gene, 16S rRNA gene, is often advocated for amphibian barcoding. Herein, we directly compare the usefulness of COI and 16S in discriminating species of hynobiid salamanders using 130 individuals. Species identification and classification of these animals, which are endemic to Asia, are often based on morphology only. Analysis of Kimura 2-parameter genetic distances (K2P) documents the mean intraspecific variation for COI and 16S rRNA genes to be 1.4% and 0.3%, respectively. Whereas COI can always identify species, sometimes 16S cannot. Intra- and interspecific genetic divergences occasionally overlap in both markers, thus reducing the value of a barcoding gap to identify genera. Regardless, COI is the better DNA barcoding marker for hynobiids. In addition to the comparison of two potential markers, high levels of intraspecific divergence in COI (>5%) suggest that both Onychodactylus fischeri and Salamandrella keyserlingii might be composites of cryptic species.

Research paper thumbnail of Molecular approaches identify known species, reveal cryptic species and verify host specificity of Chinese Philotrypesis (Hymenoptera: Pteromalidae)

Molecular Ecology Resources, 2013

Philotrypesis, a major component of the fig wasp community (Hymenoptera: Pteromalidae), is a mode... more Philotrypesis, a major component of the fig wasp community (Hymenoptera: Pteromalidae), is a model taxon for studying male fighting and mating behaviour. Its extreme sexual dimorphism and male polymorphism render species identification uncertain and in‐depth research on its ecology, behaviour and other evolutionary topics challenging. The fig wasps’ enclosed habitat within the syconia makes their mating behaviour inaccessible, to the extent of matching conspecific females and males. In this study, we combine morphological and molecular analyses to identify species of Philotrypesis sampled from south China and to associate their extraordinarily dimorphic genders and labile male morphologies. Morphological evaluations of females identify 22 species and 28 male morphs. The mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 2 data detect 21 species using females, and 15 species among the males. Most of the males match the species as delimited by females. Both markers reveal cryptic species in P. quadrisetosa on Ficus vasculosa. Most species of wasps live on one species of fig but three species co‐occur in two hosts (F. microcarpa and F. benjamina), which indicates host switching.

Research paper thumbnail of Biogeographical patterns of Chinese spiders (Arachnida: Araneae) based on a parsimony analysis of endemicity

Journal of Biogeography, 2008

Aim The distributions of Chinese spiders are used to form biotic regions and to infer biogeograp... more Aim The distributions of Chinese spiders are used to form biotic regions and to infer biogeographical patterns.Location China.Methods China was initially divided into 294 quadrats of 2° latitude by 2° longitude. The distributions of 958 species of spiders were summarized for each quadrat. Subsequently, these quadrats were pooled into 28 areas based on topographical characteristics and to a lesser extent on the distributions of spiders. Parsimony analysis of endemicity (PAE) was used to classify the 28 areas based on the shared distributional patterns of spiders.Results China was found to have seven major biogeographical regions based on the distributional patterns of spiders: Western Northern region (clade B2: Tibetan Plateau and Inner Mongolia‐Xinjiang subregions), Central Northern region (clade B3), Eastern Northern region (clade B4), Central region (clade C2), Eastern Southern region (clade C3), Western Southern region (clade C4), and Central Southern region (clade C5).Main c...

Research paper thumbnail of Polyandry and multiple paternities in the threatened Agassiz’s desert tortoise, Gopherus agassizii

Conservation Genetics, 2011

We used data from 17 to 20 microsatellite markers to investigate the incidence of multiple patern... more We used data from 17 to 20 microsatellite markers to investigate the incidence of multiple paternities in wild Agassiz's desert tortoises, Gopherus agassizii. Neonates were sampled from clutches of eggs laid by wild mothers in nesting enclosures at Edwards Air Force Base and at the Marine Corps Air Ground Combat Center, California. We genotyped 28 clutches from 26 females sampling an average of six neonates per clutch. The number of paternal alleles was used to determine the minimum number of sires for each clutch. Based on conservative criteria requiring evidence from at least two loci to determine multiple paternity, a minimum of 64% of females were polyandrous, while a minimum of 57% of clutches were sired by multiple males. This formed one of the highest incidences of multiple paternities recorded to date in any species of tortoise. The high number of microsatellite loci involved in the analyses allowed detection of multiple paternities in clutches where this may have been missed if fewer loci were used. Our results highlighted the potential pitfalls of quantitatively comparing paternity studies based on differing sampling strategies. Finally, we summarized the conservation implications of the high rate of multiple paternities in this threatened species.

Research paper thumbnail of Trends in nuclear DNA content among amphibians and reptiles

Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 1996

Research paper thumbnail of Identification of two metallothionein genes and their roles in stress responses of Musca domestica toward hyperthermy and cadmium tolerance

Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 2011

Stress proteins such as metallothioneins (MTs) play a key role in cellular protection against env... more Stress proteins such as metallothioneins (MTs) play a key role in cellular protection against environmental stressors. In nature, insects such as houseflies (Musca domestica) are commonly exposed to multiple stressors including heavy metals (e.g. Cadmium, Cd) and high temperatures. In this paper, we identify two novel MT genes from the cDNAs of M. domestica, MdMT1 and MdMT2, which putatively encode 40 and 42 amino acid residues respectively. Expression of the two MTs' mRNAs, which are examined in the fat body, gut, hemocyte, and the epidermis. From our study, we saw that the expression of MdMT1 and MdMT2 are enhanced by Cd and thermal stress. Levels of expression are highest at 10 mM Cd 2+ within a 24-h period, and expressions increase significantly with exposure to 10 mM Cd for 12 h. Levels of the mRNAs are up-regulated after heat shock and that of MdMT2 reaches its maximum peak faster than MdMT1. Both of the MT genes might be involved in a transient systemic tolerance response to stressors and they may play important roles in heavy metal and high temperature tolerance in the housefly. To detect whether or not the MTs bind heavy metals, the target genes are cloned into the prokaryotic expression vector pET-DsbA to obtain fusion protein expressed in Escherichia coli BL21 (DE3). Recombinant DsbA-MdMT1 significantly increases tolerance of the host bacteria to Cd 2+ , but DsbA-MdMT2 is absent. These differential characteristics will facilitate future investigations into the physiological functions of MTs.

Research paper thumbnail of Isozyme evidence for independently derived, duplicate G3PDH loci among squamate reptiles

Canadian Journal of Zoology, 1991

We report evidence for several independent gene duplications for the locus encoding the enzyme gl... more We report evidence for several independent gene duplications for the locus encoding the enzyme glycerol-3-phosphate dehydrogenase (G3PDH) in squamate reptiles. Evidence for the duplication comes from population genetic studies demonstrating "fixed" heterozygosity in all members of some lizard species, the documentation of independent allelic heterozygosity at each of the two G3PDH loci in these same species, and tissue-specific gene expression surveys in a taxonomically diverse array of groups. The duplicated condition is present at both low and high taxonomic levels (selected populations of the phrynosomatid lizard Sceloporus grammicus, and almost all snakes, respectively), and appears to represent the derived condition in most of these groups. One notable exception is the colubrid snake genus Masticophis, which appears to be characterized by an apomorphic secondary silencing event. Evolutionary implications of the duplication and silencing events within squamates are dis...

Research paper thumbnail of The problematic phylogenetic analysis of interlocus heteropolymer isozyme characters: a case study from sea snakes and cobras

Canadian Journal of Zoology, 1988

Multiple cases of parallel advancement (isozyme silencing) of L-lactate dehydrogenase heterotetra... more Multiple cases of parallel advancement (isozyme silencing) of L-lactate dehydrogenase heterotetramer isozymes are encountered when the observed isozyme patterns are superimposed on a well-corroborated cladogram depicting the phylogenetic relationships of some sea snakes, cobras, and coral snakes. This finding may be common among similar data sets because of parallel evolution and the inability to discern transformation sequences. Thus, the utility of this isozyme character in phylogenetic investigations may be severely limited, depending on the taxonomic group or level of universality being investigated.

Research paper thumbnail of List of Snakes of Tam-Dao Mountain Ridge (Tonkin, Vietnam)

Russian Journal of Herpetology, 2011

The full list of species of snakes inhabiting Tam-Dao mountain ridge is presented.

Research paper thumbnail of A Redescription of Vibrissaphora ailaonica with a New Record in Vietnam

Russian Journal of Herpetology, 2011

Specimens of Vibrissaphora ailaonica were collected on Mt. Fan Si Pan, Lao Cai Province, Vietnam.... more Specimens of Vibrissaphora ailaonica were collected on Mt. Fan Si Pan, Lao Cai Province, Vietnam. Prior to this, the species was known only from two localities in southern Yunnan, China. This collection represents not only the southern-most distribution for the genus, but also a new species record for Vietnam. We provide a redescription of V. ailaonica , and comments on its ecology and reproductive biology.

Research paper thumbnail of Phylogeny of genus Scutiger (Amphibia: Megophryidae): a re-evaluation

Asiatic herpetological research., 1997

A re-analysis of a published data set from Ye et al. (1992) indicates that their phylogeny for th... more A re-analysis of a published data set from Ye et al. (1992) indicates that their phylogeny for the genus Sc~rtiger does not reflect the most parsimonious explanation of the data. The consensus of the resulting trees from the original data set is a "bush" with only three resolved nodes. A re-evaluation of the character states, and their respective polarizations, resulted in alternative phylogenetic hypotheses. However, measures of homoplasy and data consistency for the re-evaluated topologies were relatively low, suggesting that little confidence could be obtained in these relationships. More data are needed to generate a defensible hypothesis of the relationships within the genus Scutiger.

Research paper thumbnail of The taxonomic status of the rosy boa Lichanura roseofusca (Serpentes: Boidae)

The Great Basin naturalist., 1980

Evidence is presented indicating that lAchanura roseofusca and Lkhanum triiirgata are conspecific... more Evidence is presented indicating that lAchanura roseofusca and Lkhanum triiirgata are conspecific. Data include the report of an intermediate specimen from El Arco, Baja California Norte, a site midway between the previously known peninsular ranges of the two species; captive hybridization provides additional support for the conclusion.

Research paper thumbnail of The speciation continuum: ecological and chromosomal divergence in the Simulium arcticum complex (Diptera: Simuliidae)

Biological Journal of the Linnean Society, 2015

Chromosome inversions may be involved in adaptation and speciation. We investigate ecological div... more Chromosome inversions may be involved in adaptation and speciation. We investigate ecological diversification among members of the Simulium arcticum species complex at different stages of chromosome divergence. Our analyses focus on two geographical scales. First, we assess ecological divergence of sibling species throughout North America using niche modelling methods. Then, using canonical correspondence analysis, we investigate habitat associations of sibling species and cytotypes in the northern Rocky Mountains ecoregion, where cytotypes tend to occur. Despite significant overlap in predicted distributions, all sibling species are ecologically unique. On the other hand, we discover various degrees of ecological divergence for cytotypes. Some cytotypes are ecologically distinct and perhaps are in their initial stages of incipient speciation. Other cytotypes are ecologically associated with one another or with particular sibling species. Thus, for members of the S. arcticum complex, ecological and chromosomal differences tend to develop early in lineage formation. Ecological distinctiveness of sibling species and cytotypes suggests that local adaptation may be involved in diversification of these chromosomal forms.

Research paper thumbnail of Comparison of base composition and codon usage in insect mitochondrial genomes

Genes & Genomics, 2009

Insects, the most biodiverse taxonomic group, have high AT content in their mitochondrial genomes... more Insects, the most biodiverse taxonomic group, have high AT content in their mitochondrial genomes. Although codon usage te nds to be AT-rich, base composition and codon usage of mitochondrial genomes may vary among taxa. Thus, we compare base composition and codon usage patterns of 49 insect mitochondri al genomes. For protein coding genes , AT content is as high as SOOIo in the Hymenoptera and Lepidoptera and as low as 72% in the Orthopotera. The AT content is high at positions 1 and 3, but A content is low at position 2. A close correlation occurs between codon usa ge and tRNA abundance in nuclear genomes. Optimal codons can pair well with the anticodons of the most abun dant tRNAs. One tRNA gene translates a synonymous codon family in vertebrate mitochondrial genomes and. these tRNA ann codons can pair with optimal codons. However, opti mal codons cannot pair with anticodons in mtDNA of Cochliomyia hominivorax (Diptera: Calliphoridae). Ten opti mal codons cannot pair with tRNA anticodons in all 49 insect mi• tochondrial genomes : non-optimal codon-anticodon usage is conunon and codon usage is not influenced by tRNA abundance. Key words: insect mitochondrial gen ome, codon usa ge, tRNA anticodon, non-optimal codon-anticodon usage. INTRODUCTIO N Ins ect mitochondrial genomes (mtDNA) exist as closed circular st rands with 13 protein-coding genes, *To whom correspondence shoul d be addressed.

Research paper thumbnail of Genetic Assessments and Parentage Analysis of Captive Bolson Tortoises (Gopherus flavomarginatus) Inform Their “Rewilding” in New Mexico

PLoS ONE, 2014

The Bolson tortoise (Gopherus flavomarginatus) is the first species of extirpated megafauna to be... more The Bolson tortoise (Gopherus flavomarginatus) is the first species of extirpated megafauna to be repatriated into the United States. In September 2006, 30 individuals were translocated from Arizona to New Mexico with the long-term objective of restoring wild populations via captive propagation. We evaluated mtDNA sequences and allelic diversity among 11 microsatellite loci from the captive population and archived samples collected from wild individuals in Durango, Mexico (n = 28). Both populations exhibited very low genetic diversity and the captive population captured roughly 97.5% of the total wild diversity, making it a promising founder population. Genetic screening of other captive animals (n = 26) potentially suitable for reintroduction uncovered multiple hybrid G. flavomarginatus6G. polyphemus, which were ineligible for repatriation; only three of these individuals were verified as purebred G. flavomarginatus. We used these genetic data to inform mate pairing, reduce the potential for inbreeding and to monitor the maintenance of genetic diversity in the captive population. After six years of successful propagation, we analyzed the parentage of 241 hatchlings to assess the maintenance of genetic diversity. Not all adults contributed equally to successive generations. Most yearly cohorts of hatchlings failed to capture the diversity of the parental population. However, overlapping generations of tortoises helped to alleviate genetic loss because the entire six-year cohort of hatchlings contained the allelic diversity of the parental population. Polyandry and sperm storage occurred in the captives and future management strategies must consider such events.

Research paper thumbnail of Low metabolic rate in a nocturnal desert lizard, an arbylus switaki murphy (Sauria: Gekkonidae)

Comparative Biochemistry and Physiology Part A: Physiology, 1982

Metabolic rates were measured in two xeric-adapted gekkonid lizards, Ai~arby1u.s switaki and Cole... more Metabolic rates were measured in two xeric-adapted gekkonid lizards, Ai~arby1u.s switaki and Coleonyx uariegatus. 2. Standard metabolic rates (SMR) were 0.074ml 0,Ighr in A. switaki and were 70% of the value predicted on the basis of mass from regression equations. The SMR of 0.146 ml 0 2 / g hr in C. uariegattis is similar to the predicted value for a lizard of this mass. 3. During intense act~vity, metabolic rates of 0.378 and 0.804 ml 0 2 / g hr were measured in A. switakl and C. variegatus, respectively. 4. Various theories to explain reduced SMR in lizards are discussed, and it is concluded that none is entirely satisfactory, and caution should be exercised in interpreting the adaptive significance of reduced SMR.

Research paper thumbnail of Allozyme variation patterns and multiple hybridization origins: Clonal variation among four sibling parthenogenetic Caucasian rock lizards

Genetica, 2000

Allozyme electrophoresis of four sibling parthenogenetic Caucasian rock lizards Darevskia unisexu... more Allozyme electrophoresis of four sibling parthenogenetic Caucasian rock lizards Darevskia unisexualis, D. uzzelli, D. sapphirina, and D. bendimahiensis found seven clones and five variable loci. The data supported the hypothesis that D. raddei and D. valentini are the parental species of all four parthenogens. Variation patterns in Darevskia were summarized. Species that originated from a single F 1 typically consisted of one widespread clone with a few rare clones. Species with multiple origins displayed variation only slightly higher than species with a single origin. This is contrary to other genera of parthenogenetic lizards, in which cases massive clonal variations were observed.

Research paper thumbnail of Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amphibia)

Zoologica Scripta, 2012

Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amph... more Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amphibia).-Zoologica Scripta, 00, 000-000. The treefrog genus Rhacophorus, a large genus with 80 species, has a wide range, occurring eastward from India to China, Japan, Southeast Asia, the Greater Sunda Islands and the Philippines. The phylogenetic relationships and taxonomic recognition of many species are very controversial. To stabilize the taxonomy, the phylogenetic relationships among about 52 species are investigated from 96 samples using mtDNA sequence data. Matrilineal relationships based on maximum likelihood and Bayesian inference methods resolve three well-supported lineages (A, B and C), although the phylogenetic relationships among three lineages remain ambiguous. Analyses support recognition of two previously assigned subgenera, Leptomantis and Rhacophorus, and these correspond to lineages A and B, respectively. Given that we have three strongly supported lineages, that these lineages are morphologically distinct, and the constrained geographic distributions of these groups, we recognize each lineage as a taxon. Subgenus Leptomantis includes species mainly from Malaysia, Indonesia and the Philippines. Subgenus Rhacophorus contains a mix of species occurring in India, Indochina and southern China. Lineage C accommodates species distributed mostly in East Asia, including Japan and China. Based on genetic and morphological data from type localities, the taxonomic recognition of some species needs to be reconsidered. Rhacophorus pingbianensis and Polypedates spinus are considered as junior synonyms of Rhacophorus duboisi. Specimens of Rhacophorus rhodopus from Vietnam and Hainan, China likely represent an undescribed, cryptic species.

Research paper thumbnail of Phylogeny and biogeography of water skinks of the genus Tropidophorus (Reptilia: Scincidae): a molecular approach

Zoologica Scripta, 2006

Phylogenetic relationships of the Oriental semiaquatic lygosomine skinks of the genus Tropidophor... more Phylogenetic relationships of the Oriental semiaquatic lygosomine skinks of the genus Tropidophorus were inferred from 1219 base positions of mitochondrial 12S and 16S rRNA genes. Results of the phylogenetic analyses incorporating data for representatives of other lygosomine genera indicated that the basal phylogenetic split within Tropidophorus separated a clade of continental Indochinese species exclusive of T. cocincinensis and T. microlepis from one comprising T. cocincinensis, T. microlepis and species from Borneo, Sulawesi and the Philippines. Of the latter group, the two continental species form the sister taxon to a clade comprising the island species. Diversification among species in Indochina and among Borneo, the Philippines and Sulawesi was likely concentrated in the Miocene, with no apparent dispersal among these regions during the Pleistocene. The body depression recognized in several Indochinese species is likely to have occurred twice in parallel as an adaptation to ...

Research paper thumbnail of Phylogenetic relationships of megophryid frogs of the genus Leptobrachium (Amphibia, Anura) as revealed by mtDNA gene sequences

Molecular Phylogenetics and Evolution, 2010

By investigating genealogical relationships, we estimated the phylogenetic history and biogeograp... more By investigating genealogical relationships, we estimated the phylogenetic history and biogeography in the megophryid genus Leptobrachium (sensu lato, including Vibrissaphora) from southern China, Indochina, Thailand and the Sundaland. The genealogical relationships among the 30 named and unnamed taxa were estimated using 2009 bp of sequences from the mitochondrial DNA genes 12S rRNA, tRNA val , and 16S rRNA using maximum parsimony, maximum likelihood, and Bayesian inference methods. The genus Leptobrachium was a well-supported monophyletic group that contained two major clades. One clade had three subclades primarily from disjunct regions including Borneo, Peninsular Malaysia and Java, and Thailand. The Bornean subclade included one species each from the Philippines and Sumatra. The other major clade consisted of two subclades, one from Indochina and the other from southern China (Vibrissaphora). Divergence times estimated an old evolutionary history of each subclade, one that could not be explained by the geohistory of Southeast Asian major landmasses.

Research paper thumbnail of COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae)

Molecular Ecology Resources, 2011

The 5&amp... more The 5' region of the mitochondrial DNA (mtDNA) gene cytochrome c oxidase I (COI) is the standard marker for DNA barcoding. However, because COI tends to be highly variable in amphibians, sequencing is often challenging. Consequently, another mtDNA gene, 16S rRNA gene, is often advocated for amphibian barcoding. Herein, we directly compare the usefulness of COI and 16S in discriminating species of hynobiid salamanders using 130 individuals. Species identification and classification of these animals, which are endemic to Asia, are often based on morphology only. Analysis of Kimura 2-parameter genetic distances (K2P) documents the mean intraspecific variation for COI and 16S rRNA genes to be 1.4% and 0.3%, respectively. Whereas COI can always identify species, sometimes 16S cannot. Intra- and interspecific genetic divergences occasionally overlap in both markers, thus reducing the value of a barcoding gap to identify genera. Regardless, COI is the better DNA barcoding marker for hynobiids. In addition to the comparison of two potential markers, high levels of intraspecific divergence in COI (>5%) suggest that both Onychodactylus fischeri and Salamandrella keyserlingii might be composites of cryptic species.

Research paper thumbnail of Molecular approaches identify known species, reveal cryptic species and verify host specificity of Chinese Philotrypesis (Hymenoptera: Pteromalidae)

Molecular Ecology Resources, 2013

Philotrypesis, a major component of the fig wasp community (Hymenoptera: Pteromalidae), is a mode... more Philotrypesis, a major component of the fig wasp community (Hymenoptera: Pteromalidae), is a model taxon for studying male fighting and mating behaviour. Its extreme sexual dimorphism and male polymorphism render species identification uncertain and in‐depth research on its ecology, behaviour and other evolutionary topics challenging. The fig wasps’ enclosed habitat within the syconia makes their mating behaviour inaccessible, to the extent of matching conspecific females and males. In this study, we combine morphological and molecular analyses to identify species of Philotrypesis sampled from south China and to associate their extraordinarily dimorphic genders and labile male morphologies. Morphological evaluations of females identify 22 species and 28 male morphs. The mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 2 data detect 21 species using females, and 15 species among the males. Most of the males match the species as delimited by females. Both markers reveal cryptic species in P. quadrisetosa on Ficus vasculosa. Most species of wasps live on one species of fig but three species co‐occur in two hosts (F. microcarpa and F. benjamina), which indicates host switching.

Research paper thumbnail of Biogeographical patterns of Chinese spiders (Arachnida: Araneae) based on a parsimony analysis of endemicity

Journal of Biogeography, 2008

Aim The distributions of Chinese spiders are used to form biotic regions and to infer biogeograp... more Aim The distributions of Chinese spiders are used to form biotic regions and to infer biogeographical patterns.Location China.Methods China was initially divided into 294 quadrats of 2° latitude by 2° longitude. The distributions of 958 species of spiders were summarized for each quadrat. Subsequently, these quadrats were pooled into 28 areas based on topographical characteristics and to a lesser extent on the distributions of spiders. Parsimony analysis of endemicity (PAE) was used to classify the 28 areas based on the shared distributional patterns of spiders.Results China was found to have seven major biogeographical regions based on the distributional patterns of spiders: Western Northern region (clade B2: Tibetan Plateau and Inner Mongolia‐Xinjiang subregions), Central Northern region (clade B3), Eastern Northern region (clade B4), Central region (clade C2), Eastern Southern region (clade C3), Western Southern region (clade C4), and Central Southern region (clade C5).Main c...

Research paper thumbnail of Polyandry and multiple paternities in the threatened Agassiz’s desert tortoise, Gopherus agassizii

Conservation Genetics, 2011

We used data from 17 to 20 microsatellite markers to investigate the incidence of multiple patern... more We used data from 17 to 20 microsatellite markers to investigate the incidence of multiple paternities in wild Agassiz's desert tortoises, Gopherus agassizii. Neonates were sampled from clutches of eggs laid by wild mothers in nesting enclosures at Edwards Air Force Base and at the Marine Corps Air Ground Combat Center, California. We genotyped 28 clutches from 26 females sampling an average of six neonates per clutch. The number of paternal alleles was used to determine the minimum number of sires for each clutch. Based on conservative criteria requiring evidence from at least two loci to determine multiple paternity, a minimum of 64% of females were polyandrous, while a minimum of 57% of clutches were sired by multiple males. This formed one of the highest incidences of multiple paternities recorded to date in any species of tortoise. The high number of microsatellite loci involved in the analyses allowed detection of multiple paternities in clutches where this may have been missed if fewer loci were used. Our results highlighted the potential pitfalls of quantitatively comparing paternity studies based on differing sampling strategies. Finally, we summarized the conservation implications of the high rate of multiple paternities in this threatened species.

Research paper thumbnail of Trends in nuclear DNA content among amphibians and reptiles

Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 1996

Research paper thumbnail of Identification of two metallothionein genes and their roles in stress responses of Musca domestica toward hyperthermy and cadmium tolerance

Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 2011

Stress proteins such as metallothioneins (MTs) play a key role in cellular protection against env... more Stress proteins such as metallothioneins (MTs) play a key role in cellular protection against environmental stressors. In nature, insects such as houseflies (Musca domestica) are commonly exposed to multiple stressors including heavy metals (e.g. Cadmium, Cd) and high temperatures. In this paper, we identify two novel MT genes from the cDNAs of M. domestica, MdMT1 and MdMT2, which putatively encode 40 and 42 amino acid residues respectively. Expression of the two MTs' mRNAs, which are examined in the fat body, gut, hemocyte, and the epidermis. From our study, we saw that the expression of MdMT1 and MdMT2 are enhanced by Cd and thermal stress. Levels of expression are highest at 10 mM Cd 2+ within a 24-h period, and expressions increase significantly with exposure to 10 mM Cd for 12 h. Levels of the mRNAs are up-regulated after heat shock and that of MdMT2 reaches its maximum peak faster than MdMT1. Both of the MT genes might be involved in a transient systemic tolerance response to stressors and they may play important roles in heavy metal and high temperature tolerance in the housefly. To detect whether or not the MTs bind heavy metals, the target genes are cloned into the prokaryotic expression vector pET-DsbA to obtain fusion protein expressed in Escherichia coli BL21 (DE3). Recombinant DsbA-MdMT1 significantly increases tolerance of the host bacteria to Cd 2+ , but DsbA-MdMT2 is absent. These differential characteristics will facilitate future investigations into the physiological functions of MTs.

Research paper thumbnail of Isozyme evidence for independently derived, duplicate G3PDH loci among squamate reptiles

Canadian Journal of Zoology, 1991

We report evidence for several independent gene duplications for the locus encoding the enzyme gl... more We report evidence for several independent gene duplications for the locus encoding the enzyme glycerol-3-phosphate dehydrogenase (G3PDH) in squamate reptiles. Evidence for the duplication comes from population genetic studies demonstrating "fixed" heterozygosity in all members of some lizard species, the documentation of independent allelic heterozygosity at each of the two G3PDH loci in these same species, and tissue-specific gene expression surveys in a taxonomically diverse array of groups. The duplicated condition is present at both low and high taxonomic levels (selected populations of the phrynosomatid lizard Sceloporus grammicus, and almost all snakes, respectively), and appears to represent the derived condition in most of these groups. One notable exception is the colubrid snake genus Masticophis, which appears to be characterized by an apomorphic secondary silencing event. Evolutionary implications of the duplication and silencing events within squamates are dis...

Research paper thumbnail of The problematic phylogenetic analysis of interlocus heteropolymer isozyme characters: a case study from sea snakes and cobras

Canadian Journal of Zoology, 1988

Multiple cases of parallel advancement (isozyme silencing) of L-lactate dehydrogenase heterotetra... more Multiple cases of parallel advancement (isozyme silencing) of L-lactate dehydrogenase heterotetramer isozymes are encountered when the observed isozyme patterns are superimposed on a well-corroborated cladogram depicting the phylogenetic relationships of some sea snakes, cobras, and coral snakes. This finding may be common among similar data sets because of parallel evolution and the inability to discern transformation sequences. Thus, the utility of this isozyme character in phylogenetic investigations may be severely limited, depending on the taxonomic group or level of universality being investigated.