197 results on '"Oaks, Jamie R."'
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2. Comparison of Linked versus Unlinked Character Models for Species Tree Inference
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Cobb, Kerry, primary and Oaks, Jamie R., additional
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- 2023
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3. Marginal likelihoods in phylogenetics: a review of methods and applications
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Oaks, Jamie R., Cobb, Kerry A., Minin, Vladimir N., and Leaché, Adam D.
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Quantitative Biology - Populations and Evolution - Abstract
By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to increase in complexity to better capture micro and macroevolutionary processes. In a Bayesian framework, the marginal likelihood is how data update our prior beliefs about models, which gives us an intuitive measure of comparing model fit that is grounded in probability theory. Given the rapid increase in the number and complexity of phylogenetic models, methods for approximating marginal likelihoods are increasingly important. Here we try to provide an intuitive description of marginal likelihoods and why they are important in Bayesian model testing. We also categorize and review methods for estimating marginal likelihoods of phylogenetic models, highlighting several recent methods that provide well-behaved estimates. Furthermore, we review some empirical studies that demonstrate how marginal likelihoods can be used to learn about models of evolution from biological data. We discuss promising alternatives that can complement marginal likelihoods for Bayesian model choice, including posterior-predictive methods. Using simulations, we find one alternative method based on approximate-Bayesian computation (ABC) to be biased. We conclude by discussing the challenges of Bayesian model choice and future directions that promise to improve the approximation of marginal likelihoods and Bayesian phylogenetics as a whole., Comment: 33 pages, 3 figures
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- 2018
4. Marginal Likelihoods in Phylogenetics: A Review of Methods and Applications
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Oaks, Jamie R, Cobb, Kerry A, Minin, Vladimir N, and Leaché, Adam D
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Genetics ,Classification ,Likelihood Functions ,Phylogeny ,Marginal likelihood ,model choice ,phylogenetics ,q-bio.PE ,Evolutionary Biology - Abstract
By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to increase in complexity to better capture micro- and macroevolutionary processes. In a Bayesian framework, the marginal likelihood is how data update our prior beliefs about models, which gives us an intuitive measure of comparing model fit that is grounded in probability theory. Given the rapid increase in the number and complexity of phylogenetic models, methods for approximating marginal likelihoods are increasingly important. Here, we try to provide an intuitive description of marginal likelihoods and why they are important in Bayesian model testing. We also categorize and review methods for estimating marginal likelihoods of phylogenetic models, highlighting several recent methods that provide well-behaved estimates. Furthermore, we review some empirical studies that demonstrate how marginal likelihoods can be used to learn about models of evolution from biological data. We discuss promising alternatives that can complement marginal likelihoods for Bayesian model choice, including posterior-predictive methods. Using simulations, we find one alternative method based on approximate-Bayesian computation to be biased. We conclude by discussing the challenges of Bayesian model choice and future directions that promise to improve the approximation of marginal likelihoods and Bayesian phylogenetics as a whole.
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- 2019
5. Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data : Inferring shared demographic events is challenging
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Oaks, Jamie R., L’Bahy, Nadia, and Cobb, Kerry A.
- Published
- 2020
6. Comparative phylogeography of West African amphibians and reptiles
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Leaché, Adam D, Oaks, Jamie R., Ofori-Boateng, Caleb, and Fujita, Matthew K.
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- 2020
7. Rivers of Indochina as potential drivers of lineage diversification in the spotted flying lizard (Draco maculatus) species complex
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Klabacka, Randy L., Wood, Perry L., Jr., McGuire, Jimmy A., ., Oaks, Jamie R., Grismer, L. Lee, Grismer, Jesse L., Aowphol, Anchalee, and Sites, Jack W., Jr.
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- 2020
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8. Implications of uniformly distributed, empirically informed priors for phylogeographical model selection: A reply to Hickerson et al
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Oaks, Jamie R., Linkem, Charles W., and Sukumaran, Jeet
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Quantitative Biology - Populations and Evolution ,Statistics - Methodology - Abstract
Establishing that a set of population-splitting events occurred at the same time can be a potentially persuasive argument that a common process affected the populations. Oaks et al. (2013) assessed the ability of an approximate-Bayesian method (msBayes) to estimate such a pattern of simultaneous divergence across taxa, to which Hickerson et al. (2014) responded. Both papers agree the method is sensitive to prior assumptions and often erroneously supports shared divergences; the papers differ about the explanation and solution. Oaks et al. (2013) suggested the method's behavior is caused by the strong weight of uniform priors on divergence times leading to smaller marginal likelihoods of models with more divergence-time parameters (Hypothesis 1); they proposed alternative priors to avoid strongly weighted posteriors. Hickerson et al. (2014) suggested numerical approximation error causes msBayes analyses to be biased toward models of clustered divergences (Hypothesis 2); they proposed using narrow, empirical uniform priors. Here, we demonstrate that the approach of Hickerson et al. (2014) does not mitigate the method's tendency to erroneously support models of clustered divergences, and often excludes the true parameter values. Our results also show that the tendency of msBayes analyses to support models of shared divergences is primarily due to Hypothesis 1. This series of papers demonstrate that if our prior assumptions place too much weight in unlikely regions of parameter space such that the exact posterior supports the wrong model of evolutionary history, no amount of computation can rescue our inference. Fortunately, more flexible distributions that accommodate prior uncertainty about parameters without placing excessive weight in vast regions of parameter space with low likelihood increase the method's robustness and power to detect temporal variation in divergences., Comment: 24 pages, 4 figures, 1 table, 14 pages of supporting information with 10 supporting figures
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- 2014
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9. An Improved Approximate-Bayesian Model-choice Method for Estimating Shared Evolutionary History
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Oaks, Jamie R.
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Quantitative Biology - Populations and Evolution - Abstract
To understand biological diversification, it is important to account for large-scale processes that affect the evolutionary history of groups of co-distributed populations of organisms. Such events predict temporally clustered divergences times, a pattern that can be estimated using genetic data from co-distributed species. I introduce a new approximate-Bayesian method for comparative phylogeographical model-choice that estimates the temporal distribution of divergences across taxa from multi-locus DNA sequence data. The model is an extension of that implemented in msBayes. By reparameterizing the model, introducing more flexible priors on demographic and divergence-time parameters, and implementing a non-parametric Dirichlet-process prior over divergence models, I improved the robustness, accuracy, and power of the method for estimating shared evolutionary history across taxa. The results demonstrate the improved performance of the new method is due to (1) more appropriate priors on divergence-time and demographic parameters that avoid prohibitively small marginal likelihoods for models with more divergence events, and (2) the Dirichlet-process providing a flexible prior on divergence histories that does not strongly disfavor models with intermediate numbers of divergence events. The new method yields more robust estimates of posterior uncertainty, and thus greatly reduces the tendency to incorrectly estimate models of shared evolutionary history with strong support., Comment: 48 pages, 8 figures, 4 tables, 35 pages of supporting information with 1 supporting table and 33 supporting figures
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- 2014
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10. The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago
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Oaks, Jamie R., Siler, Cameron D., and Brown, Rafe M.
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- 2019
11. Full Bayesian Comparative Phylogeography from Genomic Data
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Oaks, Jamie R.
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- 2019
12. The Coevolution Effect as a Driver of Spillover
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Zohdy, Sarah, Schwartz, Tonia S., and Oaks, Jamie R.
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- 2019
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13. The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics
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Leaché, Adam D. and Oaks, Jamie R.
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- 2017
14. The roles of history and ecology in chloroplast phylogeographic patterns of the bird-dispersed plant parasite Phoradendron californicum (Viscaceae) in the Sonoran Desert
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Lira-Noriega, Andrés, Toro-Núñez, Oscar, Oaks, Jamie R., and Mort, Mark E.
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- 2015
15. Fossil-calibrated phylogeny and historical biogeography of Southeast Asian water monitors (Varanus salvator Complex)
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Welton, Luke J., Wood, Perry L., Jr., Oaks, Jamie R., Siler, Cameron D., and Brown, Rafe M.
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- 2014
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16. Critically endangered island endemic or peripheral population of a widespread species? Conservation genetics of Kikuchi's gecko and the global challenge of protecting peripheral oceanic island endemic vertebrates
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Siler, Cameron D., Oaks, Jamie R., Cobb, Kerry, Ota, Hidetoshi, and Brown, Rafe M.
- Published
- 2014
17. Generalizing Bayesian phylogenetics to infer shared evolutionary events
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Oaks, Jamie R., primary, Wood, Perry L., additional, Siler, Cameron D., additional, and Brown, Rafe M., additional
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- 2022
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18. EVIDENCE FOR CLIMATE-DRIVEN DIVERSIFICATION? A CAUTION FOR INTERPRETING ABC INFERENCES OF SIMULTANEOUS HISTORICAL EVENTS
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Oaks, Jamie R., Sukumaran, Jeet, Esselstyn, Jacob A., Linkem, Charles W., Siler, Cameron D., Holder, Mark T., and Brown, Rafe M.
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- 2013
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19. Evolutionary Processes of Diversification in a Model Island Archipelago
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Brown, Rafe M., Siler, Cameron D., Oliveros, Carl H., Esselstyn, Jacob A., Diesmos, Arvin C., Hosner, Peter A., Linkem, Charles W., Barley, Anthony J., Oaks, Jamie R., Sanguila, Marites B., Welton, Luke J., Blackburn, David C., Moyle, Robert G., Peterson, A. Townsend, and Alcala, Angel C.
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- 2013
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20. Did geckos ride the Palawan raft to the Philippines?
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Siler, Cameron D., Oaks, Jamie R., Welton, Luke J., Linkem, Charles W., Swab, John C., Diesmos, Arvin C., Brown, Rafe M., and Rissler, Leslie
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- 2012
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21. A TIME-CALIBRATED SPECIES TREE OF CROCODYLIA REVEALS A RECENT RADIATION OF THE TRUE CROCODILES
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Oaks, Jamie R. and Dudley, R.
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- 2011
22. Life Span of a Tropical Forest Rodent, Proechimys semispinosus
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Oaks, Jamie R., Daul, Jason M., and Adler, Gregory H.
- Published
- 2008
23. Reduced mitochondrial respiration in hybrid asexual lizards
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Klabacka, Randy Luke, primary, Parry, Hailey A., additional, Yap, Kang Nian, additional, Cook, Ryan A., additional, Herron, Victoria A., additional, Horne, L. Miles, additional, Wolak, Matthew E., additional, Maldonado, Jose A., additional, Kavazis, Andreas N., additional, Fujita, Matthew K., additional, Oaks, Jamie R., additional, and Schwartz, Tonia S., additional
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- 2022
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24. Phylogeny and biogeography of Philippine bent-toed geckos (Gekkonidae: Cyrtodactylus) contradict a prevailing model of Pleistocene diversification
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Siler, Cameron D., Oaks, Jamie R., Esselstyn, Jacob A., Diesmos, Arvin C., and Brown, Rafe M.
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- 2010
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25. Phylogenetic relationships and biogeographic range evolution in cat-eyed snakes, Boiga (Serpentes: Colubridae)
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Weinell, Jeffrey L, Barley, Anthony J, Siler, Cameron D, Orlov, Nikolai L, Ananjeva, Natalia B, Oaks, Jamie R, Burbrink, Frank T, and Brown, Rafe M
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Biodiversity ,Taxonomy - Abstract
Weinell, Jeffrey L, Barley, Anthony J, Siler, Cameron D, Orlov, Nikolai L, Ananjeva, Natalia B, Oaks, Jamie R, Burbrink, Frank T, Brown, Rafe M (2021): Phylogenetic relationships and biogeographic range evolution in cat-eyed snakes, Boiga (Serpentes: Colubridae). Zoological Journal of the Linnean Society 192 (1): 169-184, DOI: 10.1093/zoolinnean/zlaa090, URL: https://academic.oup.com/zoolinnean/article/192/1/169/5892978
- Published
- 2021
26. Generalizing Bayesian phylogenetics to infer shared evolutionary events
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Oaks, Jamie R., primary, Wood, Perry L., additional, Siler, Cameron D., additional, and Brown, Rafe M., additional
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- 2021
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27. Supplementary file 3 from Differences in quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species
- Author
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Wan, Tao, Oaks, Jamie R., Xue-Long Jiang, Huateng Huang, and L. Lacey Knowles
- Abstract
Mountains of southwest China (MSWC) is a biodiversity hotspot with highly complex and unusual terrain. However, with the majority of studies focusing on the biogeographic consequences of massive mountain building, the Quaternary legacy of biodiversity for the MSWC has long been overlooked. Here, we took a statistical comparative phylogeography approach to examine factors that shaped community-wide diversification. With data from 30 vertebrate species, the results reveal spatially concordant genetic structure, and temporally clustered co-divergence events associated with river barriers during severe glacial cycles. This indicates the importance of riverine barriers in the phylogeographic history of the MSWC vertebrate community. We conclude that the repeated glacial cycles are associated with co-divergences that are themselves structured by the heterogeneity of the montane landscape has of the MSWC. This orderly process of diversifications has profound implications for conservation by highlighting the relative independence of different geographical areas in which some, but not all species in communities have responded similarly to climate changes and calls for further comparative phylogeographic investigations to reveal the connection between biological traits and divergence pulses in this biodiversity hotspot.
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- 2021
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28. Cyrtodactylus maelanoi Grismer & Rujirawan & Termprayoon & Ampai & Yodthong & Wood & Oaks & Aowphol 2020, sp. nov
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Grismer, L. Lee, Rujirawan, Attapol, Termprayoon, Korkhwan, Ampai, Natee, Yodthong, Siriporn, Wood, Perry L., Oaks, Jamie R., and Aowphol, Anchalee
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Reptilia ,Cyrtodactylus ,Squamata ,Animalia ,Biodiversity ,Chordata ,Cyrtodactylus maelanoi ,Gekkonidae ,Taxonomy - Abstract
Cyrtodactylus maelanoi sp. nov. Mae La Noi Bent-toed Gecko (Figs. 5���7) Holotype. Adult male ZMKU R 00857 (field tag AA 03726) collected on 22 March 2017 at 2100 hrs by Piyawan Puanprapai, Attapol Rujirawan, Siriporn Yodthong, Natee Ampai, and Elyse S. Freitas from the Tha Pha Pum Subdistrict, Mae La Noi District, Mae Hong Son Province, Thailand (18.34223��N, 98.02317��E WGS; 991 m in elevation). Paratypes. The paratypes ZMKU R 00852���00856 (field tag AA 03721���25) bear the same data as the holotype. The remaining paratypes ZMKU R 00858���00860 (field tag AA 06195���97) bear the same locality data as the holotype but were collected by Attapol Rujirawan, Siriporn Yodthong, Korkwan Termprayoon, Natee Ampai on 13 June 2018. Diagnosis. Cyrtodactylus maelanoi sp. nov. differs from all species in the C. sinyineensis group by having the combination of 7���9 supralabials; six or seven infralabials; 29���37 paravertebral tubercles; 16���19 longitudinal rows of dorsal tubercles; 27���33 ventral scales ventral scales; 9���12 expanded subdigital lamellae on the fourth toe; 11���14 unmodified subdigital lamellae on the fourth toe; 22���24 total subdigital lamellae on the fourth toe; 24���28 enlarged femoral scales; a total of 8���13 pore-bearing femoral scales in males; 4���8 enlarged precloacal scales; four or five pore-bearing precloacal scales in males; three rows of enlarged post-precloacal scales; approximately five or six jagged dorsal body bands; 11 light-colored caudal bands (n=2); 11 dark-colored caudal bands (n=2); raised and strongly keeled dorsal tubercles that extend beyond base of tail; enlarged femoral and precloacal scales nearly the same size and continuous; pore-bearing femoral and precloacal scales not continuous; medial subcaudals two to three times wider than long and not extending onto lateral side of tail; iris reddish; nuchal loop lacking an anterior azygous notch, and bearing a jagged posterior border; dorsal bands not bearing paravertebral elements, wider than interspaces, bearing lightened centers, edged with white tubercles; dark markings in dorsal interspaces; dark caudal bands wider than light caudal bands; light caudal bands in adults bearing dark-colored markings; light-colored caudal bands not encircling tail; and mature regenerated tail not spotted (Table 5). Description of holotype. Adult male SVL 75.2 mm (Fig. 5); head moderate in length (HL/SVL 0.28), wide (HW/HL 0.73), flat (HD/HL 0.39), distinct from neck, triangular in dorsal profile; lores inflated, prefrontal region concave, canthus rostralis rounded; snout elongate (ES/HL 0.39), rounded in dorsal profile, broad in lateral profile; eye large (ED/HL 0.27); ear opening oval (EL/HL 0.11); eye to ear distance greater than diameter of eye; rostral rectangular, partially divided dorsally, bordered posteriorly by supranasals and one internasal, laterally by first supralabials; external nares bordered anteriorly by rostral, dorsally by supranasals, posteriorly by two postnasals, and ventrally by first supralabials; 8(R,L) rectangular supralabials extending to below midpoint of eye; 6(R,L) infralabials tapering posteriorly to commissure of jaw; scales of rostrum and lores slightly raised, larger than granular scales on top of head and occiput; scales on top of head and occiput intermixed with small tubercles; dorsal superciliaries weakly pointed and directed laterally; mental triangular, bordered laterally by first infralabials and posteriorly by large left and right trapezoidal postmentals which contact medially for 50% of their length posterior to mental; one row of enlarged chinshields, outermost row bordering first four infralabials; gular and throat scales granular, grading posteriorly into larger, subimbricate pectoral and ventral scales. Body relatively short (AG/SVL 0.39) with well-defined ventrolateral folds; dorsal scales small, raised and interspersed with large, raised, semi-regularly arranged, strongly keeled tubercles; tubercles extend from top of head onto base of tail just beyond the postcloacal swelling; tubercles on nape smaller than those on body; 30 paravertebral tubercles; approximately 17 longitudinal rows of dorsal tubercles; 28 flat, subimbricate, ventral scales larger than dorsal scales; eight enlarged precloacal scales; five pore-bearing precloacal scales not separated on the midline by a poreless scale; three rows of large, post-precloacal scales; and no deep precloacal groove or depression. Forelimbs moderate in stature, relatively short (FL/SVL 0.17); slightly raised, juxtaposed scales of forearm larger than those on body, intermixed with large tubercles; palmar scales slightly raised, juxtaposed; digits welldeveloped, relatively long, inflected at basal, interphalangeal joints; digits narrow distal to inflections; widened proximal subdigital lamellae extend onto palm; slight webbing at base of digit; claws well-developed, sheathed by a dorsal and ventral scale at base; hind limbs more robust than forelimbs, moderate in length (TBL/SVL 0.21), covered dorsally by small, raised, juxtaposed scales intermixed with large pointed tubercles and bearing flat, slightly larger imbricate scales anteriorly; ventral femoral scales flat, imbricate, much larger than dorsals; one row of 14(R)13(L) enlarged femoral scales and enlarged precloacal scales continuous; enlarged femoral scales nearly equal in size; small, postfemoral scales form an abrupt union with larger, flat ventral scales on posteroventral margin of thigh; 5,6(R,L) pore-bearing femoral scales not continuous with pore-bearing precloacal scales; subtibial scales flat, imbricate; plantar scales raised; digits relatively long, well-developed, inflected at basal, interphalangeal joints; 11(R,L) transversely expanded subdigital lamellae on fourth toe proximal to joint inflection that do not extend onto sole, 13(R,L) unmodified subdigital lamellae distal to inflection; and claws well-developed, base of claw sheathed by a dorsal and ventral scale. Tail nearly complete, gracile in proportions, 115.1 mm in length, 8.1 mm in width at base, tapering to a point, TL/SVL (1.42); dorsal scales of tail flat, forming indistinct whorls; median row of transversely expanded subcaudal scales three times as wide as long, not extending onto lateral subcaudal region; three enlarged postcloacal tubercles at base of tail on hemipenal swellings; and postcloacal scales large, flat. Color pattern (Figs. 5, 6). Dorsal ground color of head, body, limbs, and tail yellowish-brown; top of head and rostrum nearly unicolor, bearing areas of slightly darker, diffuse irregularly shaped markings; nuchal loop smooth posteriorly with two posterior projections, not divided medially; approximately five dark jagged body bands bearing lightened centers, lacking paravertebral elements, edged with whitish tubercles extend from the shoulder to the presacral region; lighter colored interspaces between bands bear darker markings; whitish tubercles scattered on flanks; sacral and postsacral bands continue onto the tail to form five black caudal bands that are wider than the five light-colored caudal bands; light-colored caudal bands bear dark markings and do not encircle tail; limbs bear distinct, dark-colored irregularly shaped markings; posterior one-third of tail regenerated with dark mottled pattern; gular scales bearing only two or three black stipples; black stippling in throat, pectoral region, and anterior portion of belly more dense; subcaudal region darkly mottled, posterior one-third grey with faint mottling. Variation. The paratypes closely resemble the holotype in dorsal banding and nuchal loop pattern (Fig. 6). The nape band are more prominent in ZMKU R 00858���00860 and ZMKU R 00855. Paratypes ZMKU R 00858���00860, 00852, 00855���00857 are darker overall. Paratypes ZMKU R 00853, 00859���00860 have regenerated tails. Paratype ZMKU R 00854 is missing the posterior one-thrid to one-half of the tail. Additional variation in meristic and mensural characters are presented in Table 6. Distribution. Cyrtodactylus maelanoi sp. nov. is known only from the type locality from the Tha Pha Pum Subdistrict, Mae La Noi District, Mae Hong Son Province, Thailand (18.34223��N, 98.02317��E WGS; 991 m in elevation; Fig. 1). Etymology. The specific epithet ��� maelanoi ��� is a toponym of the type locality Mae La Noi. The recommended vernacular name in English is Mae La Noi Bent-toed Gecko. Natural history. All lizards observed were abroad at night (Fig. 7) in the vicinity of a waterfall (Fig. 8). Lizards were found on the ground, the walls of a building, and on granite rocks and within their cracks. Lizards were also seen on tree trunks as high 70���200 cm above the ground and on a twig approximately 160 cm above the ground. These observations clearly indicate that Cyrtodactylus maelanoi sp. nov. is a habitat generalist. No hatchlings of gravid females were observed indicating that at least the period of March through June is probably outside the reproductive season of this species. characters Clade 2 Clade 1 amphipetraeus aequalis bayinnyiensis chaunghanak- waensis dammathetensis dattkyaikensis naungkayain- gensis maelanoi sp. inthanon sinyineensis taungwineensis welpyanensis doisuthep Supralabial scales (SL)mean (��SD) Range9.0 (0.00) 98.1 (0.46) 7���98.0 (0.84) 7���99.4 (0.71) 8���119.0 (0.00) 98.3 (0.58) 8 or 98.3 (0.58) 8 or 98.1 (0.60) 7���911.0 (1.00) 10���129.7 (0.57) 9 or 109.1 (0.86) 7���108.3 (0.6) 8 or 911.0 (1.0) 10���12n9375243339331433Infralabial scales (IL)Mean (��SD) Range7.0 (0.00) 76.8 (0.53) 6���86.2 (0.44) 6 or 77.9 (0.50) 7���97.7 (0.58) 7 or 86.3 (0.57) 6 or 77.0 (0.00) 76.3 (0.50) 6 or 79.3 (0.58) 9 or 108 (0.00) 87.00 (0.39) 6���87.0 (0.00) 79.5 (1.5) 8���11n9375243339331433Paravertebral tubercles (PV)Mean34.732.026.032.531.734. 034.331.1/33.730.331.7/(��SD) Range(0.50) 34 or 35(1.64) 29���36(0.71) 25���27(0.98) 31���36(1.15) 31���33(0.00) 33���35(0.58) 34 or 35(2.37) 29���37/ /(0.00) 33���35(0.84) 29���32(1.5) 30���33/n9375243339/3143/Longitudunal rows of body tubercles (LT)Mean (��SD) Range17.9 (0.78) 17���1920.6 (1.42) 18���2317.4 (01.14) 16���1919.5 (1.47) 17���2214.3 (1.15) 13���1519.0 (1.00) 18���2017.3 (1.54) 16���1815.5 (0.87) 16���1919. 0 (1.00) 18���2015 (0.00) 1518.7 (0.61) 18���2016.0 (0.00) 1619.7 (0.58) 19 or 20n9375243339331433Ventral scales (VS)Mean (��SD) Range28.3 (0.71) 28���3024.5 (1.68) 22���3125.6 (1.52) 24���2825.4 (1.10) 23���2726.7 (1.53) 25���2825.3 (0.58) 25 or 2627.0 (0.00) 2728.4 (1.94) 27���3330.7 (2.89) 29���3428 (0.00) 27���2932.3 (2.02) 30���3629.3 (1.20) 28���3032.0 (3.00) 29���35n9375243339331433nov ......continued on the next page ......continued on the next page ......continued on the next page ......continued on the next page ......continued on the next page ......continued on the next page ......continued on the next page ......continued on the next page Comparisons. Cyrtodactylus maelanoi sp. nov. (n=9) differs from all other species of the C. sinyineensis based on various combinations of character states (Table 5). In clade 1, it differs from C. inthanon, C. sinyineensis, and C. taungwineensis in having significantly fewer supralabials and from these species plus C. welpyanensis in having significantly fewer infralabials (Fig. 4; Table 4). It differs further from C. sinyineensis, C. taungwineensis, and C. welpyanensis having significantly fewer precloacal scales; from C. sinyineensis it differs significantly in having fewer enlarged femoral scales; it differs further from C. taungwineensis by having significantly fewer ventral scales (Fig. 4; Table 4). Cyrtodactylus maelanoi sp. nov. may differ further from its sister species C. inthanon in having 24���28 enlarged femoral scales versus 29���32 in C. inthanon and they plot completely separate in the PCA and DAPC analyses (Fig. 3). Increases in sample sizes may indicate that some of these character differences are not statistically significant whereas other differences may be statistically significant. Differences in color pattern among all species of the C. sinyineensis group are listed in Table 5., Published as part of Grismer, L. Lee, Rujirawan, Attapol, Termprayoon, Korkhwan, Ampai, Natee, Yodthong, Siriporn, Wood, Perry L., Oaks, Jamie R. & Aowphol, Anchalee, 2020, A new species of Cyrtodactylus Gray (Squamata; Gekkonidae) from the Thai Highlands with a discussion on the evolution of habitat preference, pp. 401-427 in Zootaxa 4852 (4) on pages 410-424, DOI: 10.11646/zootaxa.4852.4.1, http://zenodo.org/record/4410011
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- 2020
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29. A new species of Cyrtodactylus Gray (Squamata; Gekkonidae) from the Thai Highlands with a discussion on the evolution of habitat preference
- Author
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Grismer, L. Lee, Rujirawan, Attapol, Termprayoon, Korkhwan, Ampai, Natee, Yodthong, Siriporn, Wood, Perry L., Oaks, Jamie R., and Aowphol, Anchalee
- Subjects
Reptilia ,Squamata ,Animalia ,Biodiversity ,Chordata ,Gekkonidae ,Taxonomy - Abstract
Grismer, L. Lee, Rujirawan, Attapol, Termprayoon, Korkhwan, Ampai, Natee, Yodthong, Siriporn, Wood, Perry L., Oaks, Jamie R., Aowphol, Anchalee (2020): A new species of Cyrtodactylus Gray (Squamata; Gekkonidae) from the Thai Highlands with a discussion on the evolution of habitat preference. Zootaxa 4852 (4): 401-427, DOI: https://doi.org/10.11646/zootaxa.4852.4.1
- Published
- 2020
30. Hemiphyllodactylus kyaiktiyoensis Grismer & Wood & Quah & Thura & Oaks & Lin 2020, sp. nov
- Author
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Grismer, L. Lee, Wood, Perry L., Quah, Evan S. H., Thura, Myint Kyaw, Oaks, Jamie R., and Lin, Aung
- Subjects
Reptilia ,Hemiphyllodactylus ,Squamata ,Animalia ,Hemiphyllodactylus kyaiktiyoensis ,Biodiversity ,Chordata ,Gekkonidae ,Taxonomy - Abstract
Hemiphyllodactylus kyaiktiyoensis sp. nov. Kyaiktiyo Mountain Slender Gecko (Figs. 7, 9) Holotype. Adult female (LSUHC 14032) collected on 4 November 2018 at 1900 hrs by Evan S. H. Quah, L. Lee Grismer, Perry L. Wood Jr., Myint Kyaw Thura, Jamie R. Oaks, and Aung Lin along a trail leading down the northwest facing flank of the mountain from the Golden Rock Pagoda, Mon State, Myanmar (17.47840°N 97.10042°E WGS; 1057 m in elevation). Paratypes. Female paratypes (LSUHC 14030–31, 14033–34) bear the same collection data as the holotype. Diagnosis. Hemiphyllodactylus kyaiktiyoensis sp. nov. can be separated from all other species of Hemiphyllodactylus by possessing the unique combination of having a maximum SVL of 43.4 mm; 8–10 chin scales; enlarged postmentals; five circumnasal scales; 3–5 intersupranasals (=postrostrals); 7–10 supralabials; eight or nine infralabials; 12–16 longitudinally arranged dorsal scales at midbody contained within one eye diameter and eight or nine ventral scales; four subdigital lamellae on the first finger and four or five on first toe; no plate-like subcaudal scales; adult females not yellow; a dark postorbital stripe extending to at least base of neck; dorsolateral light-colored spots on trunk; no dark, dorsolateral stripe on trunk; faint, dark, ventrolateral stripe on trunk; no dark-colored pattern on trunk; wide, light-brown, nearly unicolor, vertebral region on trunk; beige, postsacral marking bearing anteriorly projecting arms; and caecum and gonads unpigmented. These characters are scored across all Burmese species in Tables 3 and 6 and from all other species of Hemiphyllodactylus from southern China and western Thailand (clades 3 and 4 in Grismer et al. [2017: Table 3]). Description of holotype Adult female SVL 43.4 mm; head triangular in dorsal profile, depressed, distinct from neck; lores flat; rostrum moderate in length (SN/SVL 0.11); prefrontal region weakly concave; canthus rostralis smoothly rounded, barely discernable; snout moderate, rounded in dorsal profile; eye large; ear opening elliptical, small; eye to ear distance greater than diameter of eye; rostral wider than high, bordered posteriorly by large supranasals; three equally sized intersupranasals (=postnasals); external nares bordered anteriorly by rostral, dorsally by supranasal, posteriorly by two postnasals, ventrally by first supralabial (=circumnasals); nine (R, L) rectangular supralabials tapering to below posterior margin of eye; 8 (R, L) rectangular infralabials tapering to below posterior margin of eye; scales of rostrum, lores, top of head, and occiput small, granular, those of rostrum largest, slightly raised; dorsal superciliaries flat, mostly square, subimbricate, largest anteriorly; mental triangular, bordered laterally by first infralabials and posteriorly by two rectangular postmentals; each postmental in contact with first infralabial and bordered laterally by slightly smaller sublabial; 10 chin scales; gular scales small, subimbricate, grading posteriorly into slightly larger, subimbricate throat and even larger pectoral scales which grade into slightly larger, subimbricate ventrals. Body somewhat elongate (AG/SVL 0.54), dorsoventrally compressed; ventrolateral folds absent; dorsal scales small, granular, 13 dorsal scales at midbody contained within one eye diameter; ventral scales flat, subimbricate much larger than dorsal scales, eight ventral scales contained within one eye diameter; precloacal scales larger than abdominal scales; no pore-bearing femoroprecloacal scales; single enlarged tubercle on lateral margin of tail base; forelimbs short, robust in stature, covered with flat, subimbricate scales dorsally and ventrally; palmar scales flat, subimbricate; all digits except digit I well-developed; digit I vestigial, clawless; distal subdigital lamellae of digits II–V undivided, angular, U-shaped, lamellae proximal to these transversely expanded; distal lamellar formula of digits II–V 3-3-4-3 (R, L); four transversely expanded lamellae on digit I; claws on digits II–V well developed, unsheathed; distal portions of digits strongly curved, terminal joint free, arising from central portion of lamellar pad; hind limbs short, more robust than forelimbs, covered with raised, juxtaposed scales dorsally and by larger, flat, subimbricate scales anteriorly and ventrally; plantar scales slightly raised, subimbricate; all digits except digit I well-developed; digit I vestigial, clawless; distal subdigital lamellae of digits II–V undivided, angular, and Ushaped, lamellae proximal to these transversely expanded; distal lamellar formula of digits II–V 3-4-4-4 (R, L); five transversely expanded lamellae on digit I; claws on digits II–V well-developed, unsheathed; distal portions of digits strongly curved, terminal joint free, arising from central portion of lamellar pad; caudal scales occurring in whorls; dorsal caudal scales of original tail larger than dorsal body scales, flat, subcycloid, subimbricate; ventrolateral caudals enlarged, weakly flared giving a fringe-like appearance punctuated every five or six scales by even larger, raised scales; subcaudals flat slightly larger than dorsal caudals, not plate-like; posterior one-half of tail regenerated; dorsal caudals of regenerated portion smaller, more irregular in shape; other caudal scales generally same shape as those in original tail. Morphometric data are presented in Table 9. Coloration in life (Fig. 7). All Hemiphyllodactylus are capable of considerable change in the intensity and boldness of their coloration and pattern. The description below is of that when the holotype was photographed the morning after capture, approximately 12 hours after the time of collection when in its light-phase. Ground color of top of head, body, limbs, and tail dull-yellow or straw; top of head overlain with a dense dark-brown mottling giving top of head a brownish appearance; brown, semi-reticulate pattern on top of head; broad, dark, diffuse pre- and postorbital stripe extends from external nares, through eye to forelimb, preorbital portion very faint; wide, nearly immaculate, light-brown stripe with crenulated margins extends from nape to base of tail, nearly covering entire dorsum; invaginations of crenulated margins contain a diffuse, light-colored spot that collectively appear as regularly spaced, dorsolateral spots along trunk; faint, dark, ventrolateral stripe on trunk; immaculate, beige, postsacral marking bears light-colored, anteriorly projecting arms; flanks faintly mottled with diffuse brown speckling; limbs bearing irregularly shaped, diffuse, brown bands and markings; base of toes bearing a faintly orange spot; gular region mottled with brown and faint stippling in scales; pigmentation density in scales decreases posteriorly with the abdomen being generally beige with faint stippling; original portion of tail bearing four faint, irregularly shaped, brown bands and heavily mottled interspaces; enlarged scales of ventrolateral fringe highlighted in white; subcaudal region densely stippled; regenerated portion of tail brownish with faint, dark markings. Variation (Figs. 7, 9). The color pattern of the paratypes (LSUHC 14030–31, 14033–34) generally match that of the holotype. The dark, dorsal patterns of LSUHC 14031 and 14033 are slightly bolder. LSUHC 14030 has a more lightly colored dorsal pattern overall and the dorsolateral trunk spots are more obvious. Variation in scales counts, mensural data, and additional minor aspects in coloration are presented in Table 9. Distribution. Hemiphyllodactylus kyaiktiyoensis sp. nov. is known only from the type locality on Kyaiktiyo Mountain in Mon State, Myanmar but is expected to occur in other, nearby upland areas (Fig. 1). Natural History. All individuals of the type series were found on the brick wall of a house at night beneath a neon light approximately 2.5 meters above the ground in disturbed hill forest (Fig. 10). No other geckos were found on the wall but Hemidactylus garnotii, Hemidactylus brookii, Gehyra mutilata, and Cyrtodactylus aequalis were abundant on all other nearby vegetation and human-made structures. Specimens LSUHC 14032–34 were gravid with two eggs indicating the month of November falls within the reproductive season of this species. Although no males were found, we cannot determine if this species is parthenogenetic or not. Etymology. The specific epithet is a toponym referring to the type locality of Kyaiktiyo Mountain, Mon State, Myanmar. Comparisons. The molecular analyses indicate that Hemiphyllodactylus kyaiktiyoensis sp. nov. is a genetically distinct member of the south lineage and is the sister species to H. pinlaungensis sp. nov. (Fig. 1) from which it bears an uncorrected pairwise sequence divergence of 9.5% (Table 10). Hemiphyllodactylus kyaiktiyoensis sp. nov. differs significantly from H. pinlaungensis sp. nov. in having a lower mean value of CS (9.2 vs 11.2, p = 0.014) and a lower adjusted mean value of SN (1.242 vs 1.363) p = 0.018, respectively; Table 6, Fig. 3). It differs further from H. pinlaungensis sp. nov. by having a significantly different centroid position based on the factor loadings of the PC1–3 (p = 0.002; Fig. 3). This latter metric can not be considered a diagnostic character but serves as a measure of the quantitative difference between these two species in multivariate space. Its differences from H. zwegabinensis sp. nov. are listed above in the comparisons section for that species.
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31. Hemiphyllodactylus pinlaungensis Grismer & Wood & Quah & Thura & Oaks & Lin 2020, sp. nov
- Author
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Grismer, L. Lee, Wood, Perry L., Quah, Evan S. H., Thura, Myint Kyaw, Oaks, Jamie R., and Lin, Aung
- Subjects
Reptilia ,Hemiphyllodactylus ,Hemiphyllodactylus pinlaungensis ,Squamata ,Animalia ,Biodiversity ,Chordata ,Gekkonidae ,Taxonomy - Abstract
Hemiphyllodactylus pinlaungensis sp. nov. Pinlaung Slender Gecko (Figs. 11, 12) Holotype. Adult male (LSUHC 14274) collected on 12 November 2018 at 1900 hrs by Jamie R. Oaks, L. Lee Grismer, Perry L. Wood Jr., Myint Kyaw Thura, Evan S. H. Quah, and Aung Lin from Pinlaung City, Shan State, Myanmar (20.12869°N 96.78464°E WGS; 1498 m in elevation). Paratypes. Paratypes (LSUHC 14257, 14259–73, 14275–77) bear the same collection data as the holotype. Additional specimens. Additional specimens (LSUHC 14301–05) were collected from Wingabar Cave approximately 7 km southwest of Pinlaung City, Shan State, Myanamar (20.06936°N 96.76988°E WGS; 1464 m in elevation) by Jamie R. Oaks, L. Lee Grismer, Perry L. Wood Jr., Myint Kyaw Thura, Evan S. H. Quah, and Aung Lin on 13 November 2018. Diagnosis. Hemiphyllodactylus pinlaungensis sp. nov. can be separated from all other species of Hemiphyllodactylus by possessing the unique combination of having a maximum SVL of 43.0 mm; 9–14 chin scales; enlarged postmentals; five or six circumnasal scales; 2–5 intersupranasals (=postrostrals); 7–10 supralabials; 8–11 infralabi- als; 12–19 longitudinally arranged dorsal scales at midbody contained within one eye diameter and 7–12 ventral scales; 17–24 pore-bearing femoroprecloacal scales in males; three or four subdigital lamellae on first finger and first toe; no plate-like subcaudal scales; adult females not yellow; a dark postorbital stripe extending to at least base of neck; dorsolateral light-colored spots on trunk variable; no dark, dorsolateral stripe on trunk; dark ventrolateral stripe on trunk; dark paravertebral markings on trunk; light-colored postsacral marking bearing anteriorly projecting arms; and caecum and gonads unpigmented. These characters are scored across all Burmese species in Tables 3 and 6 and from all other species of Hemiphyllodactylus from southern China and western Thailand (clades 3 and 4 in Grismer et al. (2017: Table 3)). Description of holotype Adult male SVL 38.9 mm; head triangular in dorsal profile, depressed, distinct from neck; lores flat; rostrum moderate in length (SN/SVL 0.10); prefrontal region weakly concave; canthus rostralis smoothly rounded, barely discernable; snout moderate, rounded in dorsal profile; eye large; ear opening circular, small; eye to ear distance greater than diameter of eye; rostral wider than high, bordered posteriorly by large supranasals; five equally sized intersupranasals (=postnasals); external nares bordered anteriorly by rostral, dorsally by supranasal, posteriorly by two postnasals, ventrally by first supralabial (=circumnasals); 10 (R, L) rectangular supralabials tapering to below posterior margin of eye; 8 (R, L) rectangular infralabials tapering to below posterior margin of eye; scales of rostrum, lores, top of head, and occiput small, granular, raised, those of rostrum largest; dorsal superciliaries flat, mostly square, subimbricate, largest anteriorly; mental triangular, bordered laterally by first infralabials, posteriorly by two trapizoidal postmentals; each postmental in contact with first infralabial, bordered laterally by slightly smaller sublabial; 10 chin scales; gular scales small, subimbricate to slightly raised, grading posteriorly into slightly larger, subimbricate throat and larger pectoral scales which grade into slightly larger, subimbricate ventrals. Body somewhat elongate (AG/SVL 0.48), dorsoventrally compressed; ventrolateral folds absent; dorsal scales small, granular, 14 dorsal scales at midbody contained within one eye diameter; ventral scales flat, subimbricate much larger than dorsal scales, eight ventral scales contained within one eye diameter; precloacal scales larger than abdominal scales; 19 pore-bearing femoroprecloacal scales; single enlarged tubercle on lateral margin of tail base; forelimbs short, robust in stature, covered with flat, subimbricate scales dorsally and ventrally; palmar scales flat, subimbricate; all digits except digit I well-developed; digit I vestigial, clawless; distal subdigital lamellae of digits II–V undivided, angular, U-shaped, lamellae proximal to these transversely expanded; distal lamellar formula of digits II–V 3-4-4-3 (R, L); three transversely expanded lamellae on digit I; claws on digits II–V well developed, unsheathed; distal portions of digits strongly curved, terminal joint free, arising from central portion of lamellar pad; hind limbs short, more robust than forelimbs, covered with raised, juxtaposed scales dorsally and by larger, flat, subimbricate scales anteriorly and ventrally; plantar scales slightly raised, subimbricate; all digits except digit I well-developed; digit I vestigial, clawless; distal subdigital lamellae of digits II–V undivided, angular, and Ushaped, lamellae proximal to these transversely expanded; distal lamellar formula of digits II–V 3-4-4-4 (R, L); three transversely expanded lamellae on digit I; claws on digits II–V well-developed, unsheathed; distal portions of digits strongly curved, terminal joint free, arising from central portion of lamellar pad; caudal scales not occurring in distinct whorls; dorsal caudal scales of original tail larger than dorsal body scales, flat, subcycloid, subimbricate; ventrolateral caudals enlarged, weakly flared giving a weak fringe-like appearance punctated every 4–6 scales by slightly larger, raised scales; subcaudals flat, slightly larger than dorsal caudals, not plate-like. Morphometric data are presented in Table 11. .....Continued next page .....Continued next page .....Continued next page .....Continued next page Coloration in life. All Hemiphyllodactylus are capable of considerable change in the intensity and boldness of their coloration and pattern. The description below is of that when the holotype was photographed the morning after capture, approximately 12 hours after the time of collection when in its light-phase. Ground color of top of head, body, limbs, and tail straw-colored but heavily mottled with dark-brown markings; top of head overlain with a lightcolored mottling and small, dark-brown reticulations on occiput; broad, faint, diffuse pre- and postorbital stripe extends from external nares, through eye to forelimb, preorbital portion very faint; dorsolateral row of faint, diffuse, dark, paravertebral markings extend from nape to base of tail, countershaded posteriorly by diffuse light-colored spots composing a dorsolateral row; faint, wide dark, ventrolateral stripe on trunk; beige, postsacral marking bears light-colored, anteriorly projecting arms; flanks faintly mottled with diffuse, brown speckling; limbs bearing faint, dark, irregularly shaped markings; base of toes bearing a single faint, orange spot; gular region mottled with brown, dense stippling in most scales; stippling density increases posteriorly with the abdomen being generally darker, especially laterally; original tail bearing 10 faint, irregularly shaped, brown bands and heavily mottled interspaces; enlarged scales of ventrolateral fringe highlighted in white; subcaudal region densely stippled. Variation (Figs. 11, 12). Given the large sample size (25) across all ages classes and both sexes coupled with the ability of this species to change the intensity and boldness of is color pattern, dorsal color pattern characteristics vary considerably ranging from nearly unicolor gray-brown (Fig. 11A) to boldly contrasted patterns being offset by lightly colored areas (Figs. 11B, D). Other specimens have dorsal patterns that are more lightly colored overall and overlain with relatively faint, diffuse darker markings (Figs. 11C, E). The single hatchling had a nearly uniform gray dorsal coloration and pattern (Fig. 11F). Caudal pattern of original tails is especially variable, ranging from lightyellow to dull-white with bold, dark-colored bands (Figs. 11B, D) to having wide, faint, diffuse bands (Fig.11C) or thin, dark, dorsal, transverse markings (Fig. 11E). There are no consistent differences in color pattern variation between individuals from the Pinlaung City (n=20) population and those from the Wingabar Cave population (n=5). Variation in scales counts, mensural data, and additional minor aspects in coloration are presented in Table 11. Distribution. Hemiphyllodactylus pinlaungensis sp. nov. is known from the type locality of Pinlaung City and from Wingabar Cave approximately 7 km to the southwest, Shan State and is expected to occur in other nearby areas (Fig. 1). Natural History. During the evening from 1800–2400 hrs, we observed dozens of individuals on the cement and brick walls of nearly every building on the outskirts of the city but none in the surrounding upland forest (Fig. 12). Many of the females were gravid with two eggs and we also found hatchlings (SVL Etymology. The specific epithet is a toponym referring to the type locality of Pinlaung City, Shan State, Myanmar. Comparisons. The molecular analyses indicate that Hemiphyllodactylus pinlaungensis sp. nov. is a genetically distinct member of the south lineage and is the sister species to H. kyaiktiyoensis sp. nov. (Fig. 1) from which it bears an uncorrected pairwise sequence divergence of 9.5% (Table 10). Its differences from H. kyaiktiyoensis sp. nov. and H. zwegabinensis sp. nov. are listed in the comparisons sections for those species.
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- 2020
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32. Hemiphyllodactylus zwegabinensis Grismer & Wood & Quah & Thura & Oaks & Lin 2020, sp. nov
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Grismer, L. Lee, Wood, Perry L., Quah, Evan S. H., Thura, Myint Kyaw, Oaks, Jamie R., and Lin, Aung
- Subjects
Reptilia ,Hemiphyllodactylus ,Squamata ,Animalia ,Biodiversity ,Hemiphyllodactylus zwegabinensis ,Chordata ,Gekkonidae ,Taxonomy - Abstract
Hemiphyllodactylus zwegabinensis sp. nov. Zwegabin Mountain Slender Gecko (Figs. 7A, 8) Holotype. Adult female (LSUHC 14184) collected on 8 August 2019 at 1830 hrs by L. Lee Grismer, Evan S. H. Quah, Perry L. Wood Jr., Myint Kyaw Thura, Jamie R. Oaks, and Aung Lin at the top of Zwegabin Mountain, Kayin State, Myanmar (16.82407°N 97.66810°E WGS; 710 m in elevation). Diagnosis. Hemiphyllodactylus zwegabinensis sp. nov. can be separated from all other species of Hemiphyllodactylus by possessing the unique combination of having a maximum SVL of 36.9 mm; 12 chin scales; enlarged postmentals; five circumnasal scales; five intersupranasals (=postrostrals); nine supralabials; 10 infralabials; 16 longitudinally arranged dorsal scales at midbody contained within one eye diameter and seven ventral scales; varied digital formulae on hands and feet; four subdigital lamellae on the first finger and toe; no pore-bearing, femoroprecloacal scales; no plate-like subcaudal scales; adult females not yellow; a dark postorbital stripe extending to at least base of neck; dorsolateral light-colored spots on trunk; no dark dorsolateral or ventrolateral stripe on trunk; dark paravertebral markings on trunk; light-colored postsacral marking bearing anteriorly projecting arms; and caecum and gonads unpigmented. These characters are scored across all Burmese species in Tables 3 and 6 and from all other species of Hemiphyllodactylus from southern China and western Thailand (clades 3 and 4 in Grismer et al. (2017: Table 3)). Description of holotype. Adult female SVL 36.9 mm; head triangular in dorsal profile, depressed, distinct from neck; lores flat; rostrum moderate in length (SN/SVL 0.09); prefrontal region weakly concave; canthus rostralis smoothly rounded, barely discernable; snout moderate, rounded in dorsal profile; eye large; ear opening elliptical, small; eye to ear distance greater than diameter of eye; rostral wider than high, bordered posteriorly by large supranasals; five equally sized intersupranasals (=postnasals); external nares bordered anteriorly by rostral, dorsally by supranasal, posteriorly by two postnasals, ventrally by first supralabial (=circumnasals); 9, 10 (R, L) rectangular supralabials tapering to below posterior margin of eye; 10, 10 (R, L) rectangular infralabials tapering to below posterior margin of eye; scales of rostrum, lores, top of head, and occiput small, raised, those of rostrum largest; dorsal superciliaries flat, mostly square, subimbricate, largest anteriorly; mental triangular, bordered laterally by first infralabials and posteriorly by two differently sized, square-shaped postmentals; each postmental in contact with first infralabial and bordered laterally by a smaller sublabial; 12 chin scales; gular scales small, subimbricate, grading posteriorly into slightly larger, subimbricate throat and even larger pectoral scales which grade into slightly larger, subimbricate ventrals. Body somewhat elongate (AG/SVL 0.51), dorsoventrally compressed; ventrolateral folds absent; dorsal scales small, granular, 16 dorsal scales at midbody contained within one eye diameter; ventral scales flat, subimbricate much larger than dorsal scales, seven ventral scales contained within one eye diameter; precloacal scales larger than abdominal scales; no pore-bearing femoroprecloacal scales; single enlarged tubercle on lateral margin of tail base; forelimbs short, robust in stature, covered with flat, subimbricate scales dorsally and ventrally; palmar scales slightly raised, subimbricate; all digits except digit I well-developed; digit I vestigial, clawless; distal subdigital lamellae of digits II–V undivided, angular and U-shaped, lamellae proximal to these transversely expanded; distal lamellar formula of digits II–V 4-4-4-4 (R, L); four transversely expanded lamellae on digit I; claws on digits II–V well developed, unsheathed; distal portions of digits strongly curved, terminal joint free, arising from central portion of lamellar pad; hind limbs short, more robust than forelimbs, covered with slightly raised, juxtaposed scales dorsally and by larger, flat subimbricate scales anteriorly and ventrally; plantar scales slightly raised, subimbricate; all digits except digit I well-developed; digit I vestigial, clawless; distal subdigital lamellae of digits II–V undivided, angular and U-shaped, lamellae proximal to these transversely expanded; distal lamellar formula of digits II–V 4-5-5-4 (R, L); four transversely expanded lamellae on digit I; claws on digits II–V well-developed, unsheathed; distal portions of digits strongly curved, terminal joint free, arising from central portion of lamellar pad; tail original, complete; caudal scales occurring in whorls; dorsal caudal scales larger than dorsal body scales, flat, subcycloid, subimbricate; ventrolateral caudals slightly enlarged, weakly flared anteriorly giving a fringe-like appearance; subcaudals flat, slightly larger than dorsal caudals, not plate-like. Morphometric data are presented in Table 9. ....Continued next page Coloration in life (Fig. 7). All Hemiphyllodactylus are capable of considerable change in the intensity and boldness of their coloration and pattern. The description below is of that when the holotype was photographed the morning after capture, approximately 12 hours after the time of collection when in its light-phase. Ground color of top of head, body, and limbs, light-brown and densely mottled with darker markings; top of head overlain with dark, semi-reticulate pattern; broad, dark, diffuse pre- and postorbital stripe extends from the external nares, through the eye to forelimb insertion; pairs of diffuse, dark, paravertebral markings counter-shaded posteriorly with diffuse white markings extend from nape to base of tail transforming into a distinct black, post-sacral marking; lightcolored counter shaded areas appear as dorsolateral spots along the trunk; faint yellow post-sacral marking bears light-colored anteriorly projecting arms (most obvious on left side); dorsum and flanks heavily mottled with faint, dark, diffuse speckling; limbs bearing irregularly shaped diffuse dark markings and bands; gular region generally immaculate, except for darker lateral areas, scales faintly stippled, and pigmentation density increases posteriorly with abdomen being generally gray; ground color of dorsal caudal region dull-yellow, bearing three faint diffuse bands anteriorly that do not encircle the tail and irregular dark mottling posteriorly; median subcaudal region heavily stippled. Distribution. Hemiphyllodactylus zwegabinenis sp. nov. is known only from the type locality of Zwegabin Mountain, Kayin State (Fig. 1). Natural History. The holotype was collected on a metal building in stunted, wind-blown, primary forest at the crest of Zwegabin Mountain (Fig. 8). the south lineage. Bold values are intraspecific values. Etymology. The specific epithet is a toponym referring to the type locality of Zwegabin Mountain. Comparisons. The molecular analyses indicate that Hemiphyllodactylus zwegabinensis sp. nov. is a genetically distinct member of the south lineage and is the sister species to a clade composed of the sister species H. kyaiktiyoensis sp. nov., and H. pinlaungensis sp. nov. (Fig. 1) from which it bears an uncorrected pairwise sequence divergence of 13.7% and 14.1%, respectively (Table 10). Hemiphyllodactylus zwegabinensis sp. nov. differs from H. pinlaungensis sp. nov. and H. kyaiktiyoensis sp. nov. by having significantly different centroid position based on the factor loadings of the PC1–3 (p = 0.002 and 0.022, respectively). Hemiphyllodactylus zwegabinensis sp. nov. differs from H. kyaiktiyoensis sp. nov. by having 12 as opposed to 8–10 chin scales (CS), 10 as opposed to eight or nine infralabials, seven as opposed to eight or nine ventral scales (VS) (Fig. 3, Table 6), and lacking as opposed to having a nearly dorsum-wide, brown vertebral stripe (Fig. 7). Hemiphyllodactylus zwegabinensis sp. nov. differs from H. pinlaungensis sp. nov. by having significantly shorter adjusted SN (1.065 vs 1.363, p = 0.005; Fig. 3, Table 6).
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- 2020
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33. Hemiphyllodactylus ngwelwini Grismer & Wood & Quah & Thura & Oaks & Lin 2020, sp. nov
- Author
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Grismer, L. Lee, Wood, Perry L., Quah, Evan S. H., Thura, Myint Kyaw, Oaks, Jamie R., and Lin, Aung
- Subjects
Reptilia ,Hemiphyllodactylus ngwelwini ,Hemiphyllodactylus ,Squamata ,Animalia ,Biodiversity ,Chordata ,Gekkonidae ,Taxonomy - Abstract
Hemiphyllodactylus ngwelwini sp. nov. Ngwe Lwin’s Slender Gecko (Figs. 4, 5) Holotype. Adult male (LSUHC 14473) collected on 2 August 2019 at 1955 hrs by L. Lee Grismer, Perry L. Wood Jr., Myint Kyaw Thura, and Aung Lin at the Thayeumin Cave, State, Myanmar (20.72288°N 96.58994°E WGS; 1057 m in elevation). Paratypes. Females and juvenile LSUHC 14474–76 bear the same collection data as the holotype. Females LSUHC 14328–29 and male 14330 were collected from Pwe Hla Village, Shan State (20.84125°N 96.69030°E WGS; 1416 m in elevation) by L. Lee Grismer, Perry L. Wood, Jr, Evan S. H. Quah, Myint Kyaw Thura, Jamie R. Oaks, and Aung Lin on 14 November 2018 and female LSUHC 14489 bears the same collecting locality but was collected by L. Lee Grismer, Perry L. Wood Jr., Myint Kyaw Thura, and Aung Lin on 3 August 2019. Female LSUHC 14326 and male 14327 from the Myintmahati Cave, Shan State (20.59082°N 96.61198°E WGS; 1326 m in elevation) were collected by L. Lee Grismer, Perry L. Wood, Jr, Evan S. H. Quah, Myint Kyaw Thura, Jamie R. Oaks, and Aung Lin on 15 November 2018. Diagnosis. Hemiphyllodactylus ngwelwini sp. nov. can be separated from all other species of Hemiphyllodactylus by possessing the unique combination of having a maximum SVL of 40.2 mm; 9–13 chin scales; enlarged postmentals; five circumnasal scales; 1–3 intersupranasals (=postrostrals); 8–11 supralabials; 8–10 infralabials; 11–14 longitudinally arranged dorsal scales at midbody contained within one eye diameter and seven or eight ventral scales; four subdigital lamellae on the first finger and toe; 15–22 continuous, pore-bearing, femoroprecloacal scales in males; no plate-like subcaudal scales; adult females variably yellow; a dark postorbital stripe extending to at least base of neck; dorsolateral light-colored spots usually present on trunk; no dark, dorsolateral or ventrolateral stripe on trunk; dark zig-zag of paravertebral markings on trunk variable; light-colored postsacral marking variably bearing anteriorly projecting arms; and caecum and gonads unpigmented. These characters are scored across all Burmese species in Tables 3 and 6 and from all other species of Hemiphyllodactylus from southern China and western Thailand (clades 3 and 4 in Grismer et al. (2017: Table 3)). Description of holotype. Adult male, SVL 34.4 mm; head triangular in dorsal profile, depressed, distinct from neck; lores flat; rostrum moderate in length (SN/SVL 0.10); prefrontal region weakly concave; canthus rostralis smoothly rounded, barely discernible; snout moderate, rounded in dorsal profile; eye large; ear opening elliptical, small; eye to ear distance greater than diameter of eye; rostral wider than high, bordered posteriorly by large supra- nasals; two differently sized intersupranasals (=postnasals); external nares bordered anteriorly by rostral, dorsally by supranasal, posteriorly by two postnasals, ventrally by first supralabial (=circumnasals); eight (R, L) rectangular supralabials tapering to below posterior margin of eye; 9, 10 (R, L) rectangular infralabials tapering to below posterior margin of eye; scales of rostrum, lores, top of head, and occiput small, granular, those of rostrum largest and slightly raised; dorsal superciliaries flat, mostly square, subimbricate, largest anteriorly; mental triangular, bordered laterally by first infralabials, posteriorly by two large nearly square postmentals; each postmental in contact with first infralabial, bordered laterally by single slightly enlarged sublabial; 10 chin scales; gular scales small, subimbricate, grading posteriorly into slightly larger, subimbricate throat and even larger pectoral scales which grade into slightly larger, subimbricate ventrals. Body somewhat elongate (AG/SVL 0.49), dorsoventrally compressed; ventrolateral folds absent; dorsal scales small, granular, 12 dorsal scales at midbody contained within one eye diameter; ventral scales flat, subimbricate much larger than dorsal scales, eight ventral scales contained within one eye diameter; precloacal scales slightly larger than abdominal scales; pore-bearing precloacal scales continuous with pore-bearing femoral scales, totaling 21 pore-bearing femoroprecloacal scales; single enlarged tubercle on anterior margin of hemipenial swelling; forelimbs short, robust in stature, covered with flat, subimbricate scales dorsally and ventrally; palmar scales flat, subimbricate; all digits except digit I well-developed; digit I vestigial, clawless; distal subdigital lamellae of digits II–V undivided, angular and U-shaped, lamellae proximal to these transversely expanded; distal lamellar formula of digits II–V 3-3-3-3 (R, L); four transversely expanded lamellae on digit I; claws on digits II–V well developed, unsheathed; distal portions of digits strongly curved, terminal joint free, arising from central portion of lamellar pad; hind limbs short, more robust than forelimbs, covered with flat, juxtaposed scales dorsally and larger, flat subimbricate scales ventrally; plantar scales low, flat, subimbricate; all digits except digit I well-developed; digit I vestigial, clawless; distal subdigital lamellae of digits II–V undivided, angular and U-shaped, lamellae proximal to these transversely expanded; distal lamellar formula of digits II–V 3-3-3-3 (R, L); four transversely expanded lamellae on digit I; claws on digits II–V well-developed, unsheathed; distal portions of digits strongly curved, terminal joint free, arising from central portion of lamellar pad; caudal scales not occurring in whorls; dorsal caudal scales of original tail larger than dorsal body scales, flat, subcycloid, subimbricate; subcaudals slightly larger than dorsal caudals, not plate-like. Raw and ratiometric mensural data are presented in Table 7. ....Continued next page Coloration in life (Fig. 4). All Hemiphyllodactylus are capable of considerable change in the intensity and boldness of their coloration and pattern. The description below was taken when the holotype was photographed the morning after capture, approximately 12 hours following the time of collection while during its light-phase. Ground color of top of head, body, and limbs, gray and densely mottled with darker markings; top of head overlain with dark, semi-reticulate pattern; broad, dark, diffuse pre- and postorbital stripe extends from the external nares, through eye to just posterior of forelimb insertion on the body; pairs of diffuse, dark, paravertebral markings counter-shaded posteriorly with diffuse white spots extend from nape to base of tail transforming into a distinct, dark (nearly black), post-sacral band; immaculate, beige post-sacral marking immediately posterior to black post-sacral band not bearing light-colored, anteriorly projecting arms; dorsum and flanks faintly mottled with diffuse speckling; limbs bearing irregularly shaped, diffuse, dark markings; original tail bearing eight dark bands; gular region generally immaculate, except for darker lateral areas and faint stippling in scales; pigmentation density increases posteriorly with abdomen being generally gray; ground color of dorsal caudal region beige, bearing nine black diffuse bands not encircling tail; median subcaudal region faintly orange, generally immaculate. Variation (Figs. 4, 5). The color patterns of the paratypes generally match that of the holotype and no interpopulational differences were observed (Table 6). The dark, dorsal pattern of LSUHC 14326, 14328, 14330, 14489 is not as bold as that of the holotype. LSUHC 14476 is a juvenile with a broken tail. The tails of LSUHC 14326–28, 14330, and 14489 are regenerated and generally unicolor gray. Variation in scales counts, mensural data, and additional minor aspects in coloration are presented in Table 7. Distribution. Hemiphyllodactylus ngwelwini sp. nov. is known from three localities across a distance of approximately 29 km from Pwe Hla Village in the north to the Thayeumin and Myintmahati caves in the south, Shan State (Fig. 1). Natural History. All individuals from Pwe Hla Village were found on man-made structures in highly disturbed forest. LSUHC 14328–29 and LSUHC 14489 were collected on the walls of cement water tanks and LSUHC 14330 was collected from the underside of a wooden roof from a nearby rest shelter along the road. Both specimens from the Myintmahati Cave population (LSUHC 14326–27) were collected on cement structures immediately outside of a limestone cave in highly disturbed forest. LSUHC 14473 (the holotype) and LSUHC 14474–76 from the Thayeumin Cave population were found outside the limestone cave on corrugated tin shacks, cement buildings, and other man-made structures (Fig. 6) between a rice paddy and an isolated tract of highly disturbed forest. Etymology. The specific epithet recognizes and honors Mr. Ngwe Lwin, northern Program Manager of Fauna and Flora International in Myanmar. Mr. Ngwe Lwin has been supportive and invaluably instrumental in facilitating our field work in Myanmar since October of 2017. Comparisons. The molecular analyses indicate that Hemiphyllodactylus ngwelwini sp. nov. is a genetically distinct member of the north lineage composed of three, putatively, interbreeding populations being that the intrapopulational uncorrected pairwise sequence divergence across 29 km is only 1.0% and that individuals from the three populations are polyphyletic with respect to one another (Fig. 1, Table 8). Hemiphyllodactylus ngwelwini sp. nov. is the sister species to a clade composed of H. ywanganensis and the sister species H. uga, and H. linnwayensis (Fig. 1) from which it bears an uncorrected pairwise sequence divergence of 8.4% from H. linnwayensis, 9.0% from H. uga, and 8.5% from H. ywanganensis (Table 8). H. ngwelwini sp. nov. differs significantly from H. linnwayensis, H. montawaensis, and H. tonywhitteni in mean values of CS (10.8 vs 5.0, p = 7.42 -06; 10.8 vs 6.3, p = 4.93 -05; and 10.8 vs. 6.6, p = 5.14 -05; respectively; Table 3); differs significantly from H. tonywhitteni in mean values of DS (12.7 vs 14.8, p = 0.014; Table 3); and from H. montawaensis it differs significantly in adjusted mean values of HL (1.985 vs 2.852, p = 0.021; Fig. 2, Table 3). Hemiphyllodactylus ngwelwini sp. nov. differs from H. uga and H. ywanganensis (n = 2) by having four subdigital lamelae on the first finger as opposed to two or three in H. uga and three in H. ywanganensis and four subdigital lamelae on the first toe as opposed to two or three in the latter two species. However, the sample sizes of the latter two species (n =4 and n = 2, respectively) are so small that these values are likely to change with the addition of more samples. Owing to the high intraspecific variability of color pattern characters in H. ngwelwini sp. nov. (Figs. 4, 5), no interspecific differences between it and other members of the north lineage were found.
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34. Cyrtodactylus evanquahi Wood Jr & Grismer & Muin & Anuar & Oaks & Sites Jr 2020, sp. nov
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Wood Jr, Perry L., Grismer, L. Lee, Muin, Mohd Abdul, Anuar, Shahrul, Oaks, Jamie R., and Sites Jr, Jack W.
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Reptilia ,Cyrtodactylus ,Squamata ,Animalia ,Biodiversity ,Cyrtodactylus evanquahi ,Chordata ,Gekkonidae ,Taxonomy - Abstract
Cyrtodactylus evanquahi sp. nov. English: Evan Quah���s banded Bent-toed Gecko Malay: Cicak Jari-bengkok Evan Quah (Figs. 5 and 6) Holotype. Adult male, BYU 53435 collected on 13 August 2016 by Perry L. Wood, Jr. and Evan S. H. Quah from Gunung Baling, Kedah, Peninsular Malaysia (5.684989 N, 100.912590 E; 226 m). Paratypes. Adult female, BYU 53436 and juvenile BYU 53437 collected on 14 August 2016 by Evan S. H. Quah and Perry L. Wood, Jr. both specimens bear the same collection data as the holotype. Diagnosis. Cyrtodactylus evanquahi sp. nov. can be differentiated from all other species of Cyrtodactylus by having a combination of the following characters: maximum SVL of approximately 96 mm; nine or 10 supralabials; nine or 10 infralabials; prominent tuberculation on body; no tubercles on ventral surface of forelimbs, gular region, in ventrolateral body folds, or anterior one-third of tail; 31���34 paravertebral tubercles; 18���23 longitudinal tubercle rows; 29���33 ventral scales; 22 or 23 subdigital lamellae on fourth toe; 32���36 femoro-precloacal pores; shallow precloacal groove in males; six or seven dark dorsal body bands; body bands much narrower than interspaces; faint rostral chevron; body bands and nuchal loop edged with a thin white, tubercle-bearing line; dorsum lacking scattered pattern of white tubercles; no banding on base of thigh; 9���11 dark caudal bands on original tail; white caudal bands generally not immaculate; hatchlings and juveniles bearing white tail tips; and adult posterior caudal region white. All these characters are scored across all species of the C. pulchellus complex in Table 5. TABLE 5. Diagnostic characters differentiating the 17 species of the Cyrtodactylus pulchellus complex. W=weak; M=moderate; S=strong; /=data unavailable. Some information was collected from the following literature (Grismer & Ahmad 2008; Grismer et al. 2012, 2014d, 2016b; Sumontha et al. 2012; Quah et al. 2019). TABLE 5. (Continued) Description of the Holotype. Adult male, 85 mm SVL; head large, moderate in length (HL/SVL 0.29), wide (HW/HL 0.65), slightly flattened (HD/HL 0.39), distinct from neck, triangular in dorsal profile; lores concave anteriorly, inflated posteriorly; frontal and prefrontal regions deeply concave; canthus rostralis rounded anteriorly; snout elongate (ES/HL 0.43), rounded in dorsal profile, laterally constricted; eye large (ED/HL 0.21); ear opening elliptical, taller than wide, moderate in size (EL/HL 0.03), obliquely oriented; eye to ear distance greater than diameter of eye; rostral rectangular, divided dorsally by an inverted Y-shaped furrow, bordered posteriorly by left and right supranasals, and one medial postrostrals (=internasals), bordered laterally by first supralabials; external nares bordered anteriorly by rostral, dorsally by large supranasal and smaller postrostral, posteriorly by two postnasals, ventrally by first supralabial; 9(R, L) rectangular supralabials extending to just beyond upturn of labial margin, tapering abruptly below midpoint of eye; 9(R,L) infralabials tapering in size posteriorly; scales on rostrum and lores weakly raised, larger than granular scales on top of head and occiput, those on posterior portion of canthus rostralis boney frontal ridges bordering orbit confluent with boney, transverse, parietal ridge; dorsal superciliaries elongate, smooth, largest anteriorly; mental triangular, bordered laterally by first infralabials and posteriorly by left and right, rectangular postmentals which contact medially for 70% of their length; single row of slightly enlarged, elongate chinshields extending posteriorly to seventh infralabials; small, granular to flat gular scales grading posteriorly into larger, flat, smooth, imbricate, pectoral and ventral scales. Body relatively short (AG/SVL 0.43) with well-defined, non-tuberculate, ventrolateral folds; dorsal scales small, granular, interspersed with low, regularly arranged, keeled tubercles, smaller intervening tubercles occasionally present; tubercles extend from top of head to caudal constriction and onto anterior one-fifth of tail; tubercles on occiput and nape small, those on body largest; approximately 18 longitudinal rows of tubercles at midbody; 33 paravertebral tubercles; 33 flat imbricate ventral scales between ventrolateral body folds; ventral scales larger than dorsal scales; precloacal scales large, smooth; shallow precloacal groove. Forelimbs moderate in stature, relatively short (FL/SVL 0.16); scales on dorsal surfaces of forelimbs, small, juxtaposed, intermixed with large tubercles in close contact with one another; scales of ventral surface of forearm flat, subimbricate, tubercles absent; palmar scales weakly rounded; digits well-developed, inflected at basal, interphalangeal joints; subdigital lamellae rectangular proximal to joint inflection, only slightly expanded distal to inflection; digits more narrow distal to joints; claws well-developed, sheathed by a dorsal and ventral scale; hind limbs more robust than forelimbs, moderate in length (TBL/SVL 0.20), larger tubercles on dorsal surface of legs separated by smaller subimbricate scales; ventral scales of thigh flat, smooth, imbricate, larger than dorsal granular scales; ventral, tibial scales flat, smooth, imbricate; single row of greatly enlarged, flat, rectangular, imbricate, femoroprecloacal scales extend nearly from knee to knee through precloacal region where they are continuous with slightly larger; those on the occiput intermixed with small tubercles; posterior interorbital region tuberculate; large, enlarged, pore-bearing precloacal scales; 36 contiguous, pore-bearing precloacal scales forming an inverted T bearing a shallow, precloacal groove in which 11 pore-bearing scales are found (six on left, five on right); postfemoral scales immediately posterior to enlarged scale row small, nearly granular, forming an abrupt union with postfemoral scales on posteroventral margin of thigh; plantar scales low, slightly raised, slightly round; digits well-developed, inflected at basal, interphalangeal joints; subdigital lamellae proximal to joint inflection rectangular, only slightly expanded distal to inflection; digits more narrow distal to joints; claws well-developed, sheathed by a dorsal and ventral scale; 22(R) 21(L) subdigital lamellae on 4th toe. Original tail 199 mm in length, 7.2 mm in width at base, tapering to a point; dorsal scales of tail flat, squarish; subcaudal region bearing large median row of transverse scales; shallow caudal furrow; base of the tail bearding hemipenial swellings; three small, postcloacal tubercles on each hemipenial swelling; postcloacal scales smooth, flat, large, imbricate. Coloration in life. Dorsal ground color of head, body, limbs, and base of tail, light brownish grey, immaculate; no V-shaped line on the rostrum; moderate, dark-brown nuchal loop edged anteriorly and posteriorly by thin, whitish cream line bearing tubercles; six dark-brown body bands between nuchal loop and hind limb insertions edged anteriorly and posteriorly by thin whitish cream lines bearing tubercles; body bands slightly thinner than interspaces; no markings on posterior margin of thigh; ventral surface of head, body, and limbs beige, immaculate except for black stipples in each scale; tail bearing eleven dark bands separated by ten, narrower, beige (anteriorly) to white (posteriorly) bands; subcaudal region tan (Figs 5 and 6). Variation. The paratypes closely resemble the holotype in all aspects of color and pattern except that the female paratype (BYU 53436) has a darker dorsal ground color, two incomplete dark dorsal bands, and nearly immaculate white bands on the tail (Figs 5 and 6). Additional color pattern and morphological differences are listed in Table 5. Distribution. Cyrtodactylus evanquahi sp. nov. is known only from Gunung Baling, Kedah, Peninsular Malaysia (Fig. 1). It is expected to be found at other limestone forested areas near the Gunung Baling karst formation. Etymology. The specific epithet honors Dr. Evan S. H. Quah, who suggested the urgency to document the herpetofaunal diversity of Gunung Baling, Kedah, which is under constant threat from two cement companies that are actively mining the limestone. He also participated in the only herpetological survey of the area. Dr. Quah is an extremely productive contributor to the study of herpetology in Malaysia and is a champion for conservation of the region. Natural History. All specimens were collected at night between 2000���2400 hrs at the type locality in primary limestone forest habitat (Fig. 7). The adult male (BYU 53435) was found on a root at the base of the karst formation. The adult female (BYU 53436) was found on a thin sapling approximately 1.5 m off the ground. The juvenile female (BYU 53437) was found on a sapling close to the karst. None of the specimens were found directly on the karst and all were found on vegetation, so we hypothesize that these are a limestone forest dwelling species and facultative karst-dwellers. The only adult female collected was not gravid so there are no data on the reproductive biology of this species. TABLE 6. Characters and measurements of the type series of Cyrtodactylus evanquahi sp. nov. from Gunung Baling, Kedah Peninsular Malaysia. M=male, F=female, J=juvenile, /=data unavailable, R=regenerated, B=broken. W=weak, P=prominent. Other abbreviations are listed in the Materials and Methods. Comparisons. Cyrtodactylus evanquahi sp. nov. differs from all other species in the C. pulchellus complex by having prominent tuberculation, more dark body bands, and a smaller maximum SVL (Table 5). It is further differentiated from all other species by having a combination of prominent tuberculation on the body; no tubercles on the ventral surface of the forelimbs, gular region, or in the ventrolateral folds; 31���34 paravetebral dorsal tubercles; 18���23 longitudinal rows of tubercles; 29���33 ventral scales; 22���23 subdigital lamellae on the fourth toe; 32���36 fem- oroprecloacl pores; a shallow precloacal groove in males; body bands and nuchal loop edged with a thin white line bearing tubercles; no scattered white sports on the dorsum; six or seven dark body bands thinner than interspaces; 9���11 dark caudal bands on original tail; bands on the original tail separated by not imperfect white caudal bands (Table 4). Additional comparisons between C. evanquahi sp. nov. and other members of the C. pulchellus complex can be found in Table 4. Within the C. pulchellus complex, C. evanquahi sp. nov. is the sister species to C. pulchellus and can be further differentiated from it by having prominent tuberculation as opposed to moderate���moderate+; shallow precloacal groove in males opposed to a deep groove; having more dark dorsal body bands (six or seven vs. four); having thinner dark body bands; hatchlings and juveniles with white tail tips as opposed to no white tail tips; white caudal bands in adults not immaculate; adults having a posterior caudal region white (Table 5). Conservation and Threats. Based on the what we know about the limited distribution of this species and the fact that the type locality has cement quarries on either side of it (Figs. 8���9), it is likely that the continued mining of limestone will result in the extinction of this species if this species does not occur in other localities. Gunung Baling is also a popular hiking destination and the increased traffic of tourists also pose a threat to habitat. For example, there have been multiple human induced fires that inflicted considerable damage to the area. We suggest that this species be listed as ���Vulnerable��� in accordance with the formulaic conservation status assessment criterion of the International Union for Conservation of Nature (IUCN 2019), based on its small population size and the threat of nearby habitat destruction from mining and quarrying., Published as part of Wood Jr, Perry L., Grismer, L. Lee, Muin, Mohd Abdul, Anuar, Shahrul, Oaks, Jamie R. & Sites Jr, Jack W., 2020, A new potentially endangered limestone-associated Bent-toed Gecko of the Cyrtodactylus pulchellus (Squamata: Gekkonidae) complex from northern Peninsular Malaysia, pp. 437-460 in Zootaxa 4751 (3) on pages 448-455, DOI: 10.11646/zootaxa.4751.3.2, http://zenodo.org/record/3714651, {"references":["Grismer, L. L. & Ahmad, N. (2008) A new insular species of Cyrtodactylus (Squamata: Gekkonidae) from the Langkawi Archipelago, Kedah, Peninsular Malaysia. Zootaxa, (1924), 53 - 68. https: // doi. org / 10.11646 / zootaxa. 1924.1.3","Grismer, L. L., Wood Jr., P. L., Quah, E. S., Anuar, S., Muin, M. A., Sumontha, M., Ahmad, N., Bauer, A. M., Wangkulangkul, S. & Grismer, J. L. (2012) A phylogeny and taxonomy of the Thai-Malay Peninsula Bent-toed Geckos of the Cyrtodactylus pulchellus complex (Squamata: Gekkonidae): combined morphological and molecular analyses with descriptions of seven new species. Zootaxa, 3520 (3), 1 - 55. https: // doi. org / 10.11646 / zootaxa. 3520.1.1","Grismer, L. L., Wood Jr., P. L., Shahrul, A., Quah, E. S., Muin, M. A., Mohamed, M. & Onn, C. K. (2014 d) The phylogenetic relationships of three new species of the Cyrtodactylus pulchellus complex (Squamata: Gekkonidae) from poorly explored regions in northeastern peninsular malaysia. Zootaxa, 3786 (3), 359 - 381. http: // dx. doi. org / 10.11646 / zootaxa. 3786.3.6","Grismer, L. L., Wood Jr., P. L., Anuar, S., Grismer, M. S., Murdoch, M. L., Muin, M. A., Davis, H. R. & Cobos, A. J. (2016 b) Two new Bent-toed Geckos of the Cyrtodactylus pulchellus complex from Peninsular Malaysia and multiple instances of convergent adaptation to limestone forest ecosystems. Zootaxa, 4105 (5), 401 - 429. https: // doi. org / 10.11646 / zootaxa. 4105.5.1","Sumontha, M., Pauwels, O. S., Kunya, K., Nitikul, A., Samphanthamit, P. & Grismer, L. L. (2012) A new forest-dwelling gecko from Phuket Island, southern Thailand, related to Cyrtodactylus macrotuberculatus (Squamata: Gekkonidae). Zootaxa, 3522 (1), 61 - 72. https: // doi. org / 10.11646 / zootaxa. 3522.1.4","Quah, E. S., Grismer, L. L., Wood Jr., P. L. & Shahrul, A. (2019) The discovery and description of a new species of Bent-toed Gecko of the Cyrtodactylus pulchellus complex (Squamata: Gekkonidae) from the Langkawi Archipelago, Kedah, Peninsular Malaysia. Zootaxa, 4668 (1), 51 - 75. https: // doi. org / 10.11646 / zootaxa. 4668.1.3","IUCN (2019) IUCN International Union for Conservation of Nature. Available from: https: // www. iucnredlist. org / (accessed 1 November 2019)"]}
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35. A new potentially endangered limestone-associated Bent-toed Gecko of the Cyrtodactylus pulchellus (Squamata: Gekkonidae) complex from northern Peninsular Malaysia
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Wood Jr, Perry L., Grismer, L. Lee, Muin, Mohd Abdul, Anuar, Shahrul, Oaks, Jamie R., and Sites Jr, Jack W.
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Reptilia ,Squamata ,Animalia ,Biodiversity ,Chordata ,Gekkonidae ,Taxonomy - Abstract
Wood Jr, Perry L., Grismer, L. Lee, Muin, Mohd Abdul, Anuar, Shahrul, Oaks, Jamie R., Sites Jr, Jack W. (2020): A new potentially endangered limestone-associated Bent-toed Gecko of the Cyrtodactylus pulchellus (Squamata: Gekkonidae) complex from northern Peninsular Malaysia. Zootaxa 4751 (3): 437-460, DOI: https://doi.org/10.11646/zootaxa.4751.3.2
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36. Supplementary file 2 from Differences in quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species
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Wan, Tao, Oaks, Jamie R., Xue-Long Jiang, Huateng Huang, and L. Lacey Knowles
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Mountains of southwest China (MSWC) is a biodiversity hotspot with highly complex and unusual terrain. However, with the majority of studies focusing on the biogeographic consequences of massive mountain building, the Quaternary legacy of biodiversity for the MSWC has long been overlooked. Here, we took a statistical comparative phylogeography approach to examine factors that shaped community-wide diversification. With data from 30 vertebrate species, the results reveal spatially concordant genetic structure, and temporally clustered co-divergence events associated with river barriers during severe glacial cycles. This indicates the importance of riverine barriers in the phylogeographic history of the MSWC vertebrate community. We conclude that the repeated glacial cycles are associated with co-divergences that are themselves structured by the heterogeneity of the montane landscape has of the MSWC. This orderly process of diversifications has profound implications for conservation by highlighting the relative independence of different geographical areas in which some, but not all species in communities have responded similarly to climate changes and calls for further comparative phylogeographic investigations to reveal the connection between biological traits and divergence pulses in this biodiversity hotspot.
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37. Differences in Quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species
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Wan, Tao, primary, Oaks, Jamie R., additional, Jiang, Xue-Long, additional, Huang, Huateng, additional, and Knowles, L. Lacey, additional
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- 2021
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38. Integrative taxonomic and geographic variation analyses in Cyrtodactylus aequalis (Squamata: Gekkonidae) from southern Myanmar (Burma): one species, two different stories
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Lee Grismer, L., primary, Perry, L. Wood, additional, Grismer, Marta S., additional, Quah, Evan S.H., additional, Thura, Myint Kyaw, additional, Oaks, Jamie R., additional, Lin, Aung, additional, and Lim, Diana Y., additional
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39. A new species of Cyrtodactylus Gray (Squamata; Gekkonidae) from the Thai Highlands with a discussion on the evolution of habitat preference
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GRISMER, L. LEE, primary, RUJIRAWAN, ATTAPOL, additional, TERMPRAYOON, KORKHWAN, additional, AMPAI, NATEE, additional, YODTHONG, SIRIPORN, additional, WOOD, PERRY L. JR, additional, OAKS, JAMIE R., additional, and AOWPHOL, ANCHALEE, additional
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40. Phylogenetic relationships and biogeographic range evolution in cat-eyed snakes, Boiga (Serpentes: Colubridae)
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Weinell, Jeffrey L, primary, Barley, Anthony J, additional, Siler, Cameron D, additional, Orlov, Nikolai L, additional, Ananjeva, Natalia B, additional, Oaks, Jamie R, additional, Burbrink, Frank T, additional, and Brown, Rafe M, additional
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41. A new insular species of the Cyrtodactylus intermedius (Squamata: Gekkonidae) group from Cambodia with a discussion of habitat preference and ecomorphology
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GRISMER, L. LEE, primary, ONN, CHAN KIN, additional, OAKS, JAMIE R., additional, NEANG, THY, additional, SOKUN, LANG, additional, MURDOCH, MATTHEW L., additional, STUART, BRYAN L., additional, and GRISMER, JESSE L., additional
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42. Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs ( Rhacophorus )
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O’Connell, Kyle A., primary, Oaks, Jamie R., additional, Hamidy, Amir, additional, Shaney, Kyle J., additional, Kurniawan, Nia, additional, Smith, Eric N., additional, and Fujita, Matthew K., additional
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43. Patterns of gene evolution following duplications and speciations in vertebrates
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David, Kyle T., primary, Oaks, Jamie R., additional, and Halanych, Kenneth M., additional
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44. Four new Burmese species of Hemiphyllodactylus Bleeker (Squamata: Gekkonidae) from distantly related parapatric clades from the Shan Plateau and Salween Basin
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GRISMER, L. LEE, primary, WOOD, PERRY L. JR., additional, QUAH, EVAN S. H., additional, THURA, MYINT KYAW, additional, OAKS, JAMIE R., additional, and LIN, AUNG, additional
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45. A new potentially endangered limestone-associated Bent-toed Gecko of the Cyrtodactylus pulchellus (Squamata: Gekkonidae) complex from northern Peninsular Malaysia
- Author
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WOOD, PERRY L. JR., primary, GRISMER, L. LEE, additional, MUIN, MOHD ABDUL, additional, ANUAR, SHAHRUL, additional, and OAKS, JAMIE R., additional
- Published
- 2020
- Full Text
- View/download PDF
46. The why, when, and how of computing in biology classrooms
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Wright, April M., primary, Schwartz, Rachel S., additional, Oaks, Jamie R., additional, Newman, Catherine E., additional, and Flanagan, Sarah P., additional
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- 2020
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47. Neglected Quaternary legacy on biodiversity in the Mountains of Southwest China
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Wan, Tao, primary, Huang, Huateng, additional, Oaks, Jamie R., additional, Jiang, Xuelong, additional, and Knowles, L. Lacey, additional
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- 2020
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48. Two new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from a karstic archipelago in the Salween Basin of southern Myanmar (Burma)
- Author
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GRISMER, L. LEE, primary, WOOD, PERRY L. JR., additional, QUAH, EVAN S. H., additional, GRISMER, MARTA S., additional, THURA, MYINT KYAW, additional, OAKS, JAMIE R., additional, and LIN, AUNG, additional
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- 2020
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49. Congruent demographic responses to Pleistocene geological processes in Sumatran parachuting frogs: a comparison of target-capture and ddRADseq for population genomic analyses
- Author
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O’Connell, Kyle A., Oaks, Jamie R., Hamidy, Amir, Kurniawan, Nia, Smith, Eric N., and Fujita, Matthew K.
- Abstract
Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super-volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co-distributed species of parachuting frogs (Genus Rhacophorus ) on Sumatra. We generate target-capture data (∼950 loci and ∼440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction-site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modeling, and to estimate the temporal clustering of size change events using a full-likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that these northern populations exhibit a signal of contraction around the time of the eruption (∼80 kya). However, we infer a stronger signal of expansion in southern populations around ∼400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, this suggests that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was more greatly impacted by mid-Pleistocene forest expansion, supporting local rather than regional effects of the Toba eruption.
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- 2019
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50. Discovery of the westernmost population of the genus Ansonia Stoliczka (Anura, Bufonidae) with the description of a new species from the Shan Plateau of eastern Myanmar
- Author
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Quah, Evan S. H., Grismer, L. Lee, Wood, Perry L., Thura, Myint Kyaw, Oaks, Jamie R., and Lin, Aung
- Subjects
Amphibia ,Animalia ,Biodiversity ,Anura ,Chordata ,Bufonidae ,Taxonomy - Abstract
Quah, Evan S. H., Grismer, L. Lee, Wood, Perry L., Thura, Myint Kyaw, Oaks, Jamie R., Lin, Aung (2019): Discovery of the westernmost population of the genus Ansonia Stoliczka (Anura, Bufonidae) with the description of a new species from the Shan Plateau of eastern Myanmar. Zootaxa 4656 (3): 545-571, DOI: https://doi.org/10.11646/zootaxa.4656.3.11
- Published
- 2019
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