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Article ; Online: Punctuated Equilibrium or Gradualism in the Lizard Genus Sceloporus? Lost in Plesiograms and a Forest of Trees.

Murphy, Robert W / Lovejoy, Nathan R

Cladistics : the international journal of the Willi Hennig Society

2021 Volume 14, Issue 1, Page(s) 95–103

Abstract: Conclusions about the rates of evolution among a group of organisms are only are only as sound as the phylogeny upon which the conclusions are based. We re-evaluated the rates of allozyme evolution amoung lizards of the speciose genus Sceloporus. The ... ...

Abstract	- Conclusions about the rates of evolution among a group of organisms are only are only as sound as the phylogeny upon which the conclusions are based. We re-evaluated the rates of allozyme evolution amoung lizards of the speciose genus Sceloporus. The initial evaluation was suspect because a modification of the invalid, presence or absence method of data coding was employed in genealogical estimation. We recoded the allozyme data using the locus as the character and observed that the previous best explanation of the data fell within a forest of an estimated 107 trees. Further explorations into the invalidity of the independent alleles model of data coding attributed much, but not all, of the shape of the extremely unlikely, independent alleles tree to the parallel loss of plesiotypic alleles, and not the acquistion of novel alleles resulting from mutations. When the data were more appropriately evaluated using mutation coding, there was no unequivocal evidence for a punctuated equilibrium tempo of evolutionary change.
Language	English
Publishing date	2021-12-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	1462608-1
ISSN	1096-0031 ; 0748-3007
ISSN (online)	1096-0031
ISSN	0748-3007
DOI	10.1111/j.1096-0031.1998.tb00205.x
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Article: Advances in herpetological research emanating from China.

Murphy, Robert W

Dong wu xue yan jiu = Zoological research

2016 Volume 37, Issue 1, Page(s) 4–6

MeSH term(s)	Amphibians/classification ; Animals ; Biodiversity ; China ; Endangered Species ; Reptiles/classification ; Zoology
Language	English
Publishing date	2016-01-18
Publishing country	China
Document type	Journal Article
ZDB-ID	2196960-7
ISSN	0254-5853
ISSN	0254-5853
DOI	10.13918/j.issn.2095-8137.2016.1.4
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Article ; Online: A new species of the genus Oligodon Fitzinger, 1826 (Squamata: Colubridae) from Langbian Plateau, Vietnam.

Nguyen, Sang Ngoc / LE, Manh VAN / Vo, Thi-Dieu-Hien / Murphy, Robert W

Zootaxa

2022 Volume 5196, Issue 4, Page(s) 555–566

Abstract: 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 ... ...

Abstract	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 dorsal scale rows at midbody; ventrals 173-179 in males and 187-193 in females; subcaudals 58 or 59 in males and 44 or 45 in females; presubocular present; 8 supralabials, fourth and fifth entering orbit; cloacal plate undivided; 10 maxillary teeth, posterior three enlarged; vertebral stripe present; temporal streak present but faint and interrupted; long and deeply forked hemipenes, extending to 25th subcaudal, without spines and papillae; and 13-15+3-4 dorsal blotches.
MeSH term(s)	Female ; Male ; Animals ; Colubridae ; Vietnam ; Animal Structures/anatomy & histology ; Animal Distribution ; Lizards ; Phylogeny
Language	English
Publishing date	2022-10-21
Publishing country	New Zealand
Document type	Journal Article
ISSN	1175-5334
ISSN (online)	1175-5334
DOI	10.11646/zootaxa.5196.4.5
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Article ; Online: Association filtering and generative adversarial networks for predicting lncRNA-associated disease.

Zhong, Hua / Luo, Jing / Tang, Lin / Liao, Shicheng / Lu, Zhonghao / Lin, Guoliang / Murphy, Robert W / Liu, Lin

BMC bioinformatics

2023 Volume 24, Issue 1, Page(s) 234

Abstract: Background: Long non-coding RNA (lncRNA) closely associates with numerous biological processes, and with many diseases. Therefore, lncRNA-disease association prediction helps obtain relevant biological information and understand pathogenesis, and thus ... ...

Abstract	Background: Long non-coding RNA (lncRNA) closely associates with numerous biological processes, and with many diseases. Therefore, lncRNA-disease association prediction helps obtain relevant biological information and understand pathogenesis, and thus better diagnose preventable diseases. Results: Herein, we offer the LDAF_GAN method for predicting lncRNA-associated disease based on association filtering and generative adversarial networks. Experimentation used two types of data: lncRNA-disease associated data without lncRNA sequence features, and fused lncRNA sequence features. LDAF_GAN uses a generator and discriminator, and differs from the original GAN by the addition of a filtering operation and negative sampling. Filtering allows the generator output to filter out unassociated diseases before being fed into the discriminator. Thus, the results generated by the model focuses only on lncRNAs associated with disease. Negative sampling takes a portion of disease terms with 0 from the association matrix as negative samples, which are assumed to be unassociated with lncRNA. A regular term is added to the loss function to avoid producing a vector with all values of 1, which can fool the discriminator. Thus, the model requires that generated positive samples are close to 1, and negative samples are close to 0. The model achieved a superior fitting effect; LDAF_GAN had superior performance in predicting fivefold cross-validations on the two datasets with AUC values of 0.9265 and 0.9278, respectively. In the case study, LDAF_GAN predicted disease association for six lncRNAs-H19, MALAT1, XIST, ZFAS1, UCA1, and ZEB1-AS1-and with the top ten predictions of 100%, 80%, 90%, 90%, 100%, and 90%, respectively, which were reported by previous studies. Conclusion: LDAF_GAN efficiently predicts the potential association of existing lncRNAs and the potential association of new lncRNAs with diseases. The results of fivefold cross-validation, tenfold cross-validation, and case studies suggest that the model has great predictive potential for lncRNA-disease association prediction.
MeSH term(s)	RNA, Long Noncoding/genetics ; Algorithms ; Computational Biology/methods
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2023-06-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-023-05368-z
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Article ; Online: Giant salamanders: Farmed yet endangered.

Lu, Chenqi / Chai, Jing / Murphy, Robert W / Che, Jing

Science (New York, N.Y.)

2020 Volume 367, Issue 6481, Page(s) 989

MeSH term(s)	Animals ; Endangered Species ; Farms ; Urodela
Language	English
Publishing date	2020-02-27
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abb2375
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Article ; Online: A new species of Ahaetulla Link, 1807 (Squamata: Colubridae) from the Mekong Delta, Vietnam.

Lam, Ngon Quang / Thu, Tran Thi Anh / Nguyen, Luan Thanh / Murphy, Robert W / Nguyen, Sang Ngoc

Zootaxa

2021 Volume 4966, Issue 3, Page(s) 290304

Abstract: 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: ... ...

Abstract	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; body scale rows 15-15-13; ventrals 186190 in males and 182185 in females; subcaudals 143153 in males and 128 or 129 in females; 8 (rarely 9) supralabials, fourth and fifth or fourth to sixth entering orbit; 1214 maxillary teeth; hemipenis short, reaching 6th or 7th SC; cloacal plate divided; dorsum bright green; and yellow or white stripe along the lower flank. The new species differs from its congeners by an uncorrected p-distance in COI and Cytb sequences of at least 7.7% and 7.5%, respectively.
MeSH term(s)	Animal Structures ; Animals ; Colubridae/anatomy & histology ; Colubridae/classification ; Female ; Male ; Phylogeny ; Vietnam
Language	English
Publishing date	2021-05-04
Publishing country	New Zealand
Document type	Journal Article
ISSN	1175-5334
ISSN (online)	1175-5334
DOI	10.11646/zootaxa.4966.3.2
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Article ; Online: Gekko phuyenensis sp. nov. (Squamata: Gekkonidae), a new species from southern Vietnam.

Nguyen, Vu Dang Hoang / Nguyen, Luan Thanh / Orlov, Nikolai L / Murphy, Robert W / Nguyen, Sang Ngoc

Zootaxa

2021 Volume 4966, Issue 2, Page(s) 175186

Abstract: 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 ... ...

Abstract	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 90.292.8 mm; nares in contact with rostral; internasal 1; interorbitals 35 or 36; ventrals 3032; dorsal tubercle rows 9 or 10; precloacal pores 12 or 13 in males and precloacal pits 13 in female; subdigital lamellae under first finger 1821, fourth finger 19 or 20, first toe 1820, and fourth toe 2123; subcaudals median enlarged; no webbing between toes; and the absence of tubercles on hind limbs. Molecular phylogenetic analyses of mitochondrial gene COI (681 bp) using the geckos from Phu Yen and its congeners in southern Vietnam resolve the new species as the sister lineage to G. cf. grossmanni from Khanh Hoa Province. Genetic distances between G. phuyenensis sp. nov. and its congeners in southern Vietnam range from 16.924.2%. The discovery of this new species raises the number of known species of Gekko in Vietnam to 14.
MeSH term(s)	Animal Structures ; Animals ; Female ; Genes, Mitochondrial ; Lizards/anatomy & histology ; Lizards/classification ; Male ; Phylogeny ; Vietnam
Language	English
Publishing date	2021-05-03
Publishing country	New Zealand
Document type	Journal Article
ISSN	1175-5334
ISSN (online)	1175-5334
DOI	10.11646/zootaxa.4966.2.5
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Article: Comparative multi-locus assessment of modern Asian newts (

Yuan, Zhi-Yong / Wu, Yun-Ke / Yan, Fang / Murphy, Robert W / Papenfuss, Theodore J / Wake, David B / Zhang, Ya-Ping / Che, Jing

Zoological research

2022 Volume 43, Issue 5, Page(s) 706–718

Abstract: 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 ... ...

Abstract	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 environmental data to investigate shared phylogeographic patterns among three Asian-endemic newt genera,
MeSH term(s)	Animals ; Bayes Theorem ; China ; Genetic Variation ; Phylogeny ; Phylogeography ; Salamandridae/genetics
Language	English
Publishing date	2022-08-04
Publishing country	China
Document type	Journal Article
ISSN	2095-8137
ISSN	2095-8137
DOI	10.24272/j.issn.2095-8137.2022.080
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Article ; Online: Invasive Bullfrogs Maintain MHC Polymorphism Including Alleles Associated with Chytrid Fungal Infection.

LaFond, Jacob / Martin, Katherine R / Dahn, Hollis / Richmond, Jonathan Q / Murphy, Robert W / Rollinson, Njal / Savage, Anna E

Integrative and comparative biology

2022 Volume 62, Issue 2, Page(s) 262–274

Abstract: 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 ... ...

Abstract	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 major histocompatibility complex (MHC) and cytochrome b (cytb) loci from 20 populations of the American bullfrog (Rana catesbeiana) across theinvasive and native ranges in North America and quantified the presence of the pathogen Batrachochytrium dendrobatidis (Bd). Compared to native populations, invasive populations had significantly higher Bd prevalence and intensity, significantly higher pairwise MHC and cytb FST, and significantly lower cytb diversity, but maintained similar levels of MHC diversity. The two most common MHC alleles (LiCA_B and Rapi_33) were associated with a significant decreased risk of Bd infection, and we detected positive selection acting on four peptide binding residues. Phylogenetic analysis suggested invasive populations likely arose from a single founding population in the American Midwest with a possible subsequent invasion in the northwest. Overall, our study suggests that the maintenance of diversity at adaptive loci may contribute to invasion success and highlights the importance of quantifying diversity at functional loci to assess the evolutionary potential of invasive populations.
MeSH term(s)	Alleles ; Animals ; Genetic Variation ; Major Histocompatibility Complex ; Mycoses/genetics ; Mycoses/microbiology ; Mycoses/veterinary ; Phylogeny ; Polymorphism, Genetic ; Rana catesbeiana/genetics ; Rana catesbeiana/microbiology ; Selection, Genetic ; United States
Language	English
Publishing date	2022-05-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2159110-6
ISSN	1557-7023 ; 1540-7063
ISSN (online)	1557-7023
ISSN	1540-7063
DOI	10.1093/icb/icac044
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Article ; Online: Concordant species delimitation from multiple independent evidence: A case study with the Pachytriton brevipes complex (Caudata: Salamandridae).

Wu, Yunke / Murphy, Robert W

Molecular phylogenetics and evolution

2015 Volume 92, Page(s) 108–117

Abstract: Mitochondrial DNA (mtDNA) sequence data are widely used to delimit species. However, owing to its strict maternal inheritance in most species, mtDNA tracks female dispersion and dispersal only. The accuracy of mtDNA-derived species delimitation is often ... ...

Abstract	Mitochondrial DNA (mtDNA) sequence data are widely used to delimit species. However, owing to its strict maternal inheritance in most species, mtDNA tracks female dispersion and dispersal only. The accuracy of mtDNA-derived species delimitation is often not explicitly tested using other independent evidence, such as nuclear DNA (nDNA) data, morphological data, or ecological data. Because species are independent evolutionary lineages that can form testable hypotheses, we present a multi-evidence case study on species delimitation that combines statistical approaches with spatially explicit ecological analysis. Montane salamanders of the Pachytriton brevipes complex (Salamandridae) from southeastern China exhibit conservative morphology and variable color patterning that impede species diagnosis. Recent studies proposed splitting P. brevipes into four species based on deep mtDNA divergence but also found discordance between mtDNA and nDNA trees. In this study, we test evolutionary independence of these hypothesized species lineages using two coalescent-based Bayesian methods (Bayes factor and BP&P). Despite significant conflict between mtDNA gene tree and the species phylogeny, the results reinforce the inference of at least four species in the complex as opposed to the one species recognized for over 130 years. Correlative ecological niche modeling and statistical analysis of environmental data indicate that suitable habitats for each species are isolated by incompatible intervening lowland regions, so the likelihood of gene flow among species is very low, which means species lineages should maintain their evolutionary independence. We demonstrate that concordance among independent evidence confirms species status, which forms the basis for accurate assessment of regional biodiversity.
MeSH term(s)	Animals ; Bayes Theorem ; Cell Nucleus/genetics ; China ; DNA, Mitochondrial/genetics ; Ecosystem ; Gene Flow ; Phylogeny ; Salamandridae/anatomy & histology ; Salamandridae/classification ; Salamandridae/genetics
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2015-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2015.06.010
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