Cryptic diversity and population genetic structure in the rare, endemic, forest-obligate, slender geckos of the Philippines

Molecular Phylogenetics and Evolution

Volumn 70, Issue 1, 2014, Pages 204-209

  Siler, Cameron D ^a,b   Alex Dececchi, T ^b   Merkord, Chris L ^b   Davis, Drew R ^b   Christiani, Tony J ^b   Brown, Rafe M ^c  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b University of South Dakota   (United States)

^c UNIVERSITY OF KANSAS   (United States)

Author keywords

Conservation; Deforestation; Endemicity; Enigmatic taxa; Lepidodactylus; Pseudogekko

Indexed keywords

GEKKONIDAE; LEPIDODACTYLUS; SQUAMATA;

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; CLASSIFICATION; CONSERVATION; DEFORESTATION; DNA SEQUENCE; ENDEMIC DISEASE; ENIGMATIC TAXA; GENETIC VARIABILITY; GENETICS; LEPIDODACTYLUS; LIZARD; PHILIPPINES; PHYLOGENY; POPULATION GENETICS; PSEUDOGEKKO; TREE;

CONSERVATION; DEFORESTATION; ENDEMICITY; ENIGMATIC TAXA; LEPIDODACTYLUS; PSEUDOGEKKO;

ANIMALS; BAYES THEOREM; DNA, MITOCHONDRIAL; GENETIC VARIATION; GENETICS, POPULATION; LIZARDS; PHILIPPINES; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TREES;

EID: 84885705256     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2013.09.014     Document Type: Article

References (42)

1. Brown R.M., Diesmos A.C. Application of lineage-based species concepts to oceanic island frog populations: the effects of differing taxonomic philosophies on the estimation of Philippine biodiversity. Silliman J. 2002, 42:133-162.
2. Brown R.M., Diesmos A.C. Philippines, biology. Encyclopedia of Islands 2009, 723-732. University of California Press, Berkeley. R. Gillespie, D. Clague (Eds.).
3. Brown R.M., Siler C.D., Das I., Min Y. Testing the phylogenetic affinities of Southeast Asia's rarest geckos: flap-legged geckos (Luperosaurus), flying geckos (Ptychozoon) and their relationship to the pan-Asian genus Gekko. Mol. Phylogenet. Evol. 2012, 63:915-921.
4. Brown R.M., Siler C.D., Grismer L.L., Das I., McGuire J.A. Phylogeny and cryptic diversification in Southeast Asian flying geckos. Mol. Phylogenet. Evol. 2012, 65:351-361.
5. Brown R.M., Siler C.D., Oliveros C.H., Diesmos A.C., Alcala A.C. A new Gekko from Sibuyan Island, Central Philippines. Herpetologica 2011, 67:460-476.
6. Brown R.M., Siler C.D., Oliveros C.H., Welton L.J., Rock A., Swab J., Van Weerd M., van Beijnen J., Jose E., Rodriguez D., Jose E., Diesmos A.C. The amphibians and reptiles of Luzon Island, Philippines, VIII: the herpetofauna of Cagayan and Isabela Provinces, Northern Sierra Madre Mountain Range. Zookeys 2013, 266:1-120.
7. Brown W.C. The status of Pseudogekko shebae and observations on the geckos of the Solomon Islands. Breviora 1964, 204:1-8.
8. Brown W.C., Alcala A.C. Philippine Lizards of the Family Gekkonidae 1978, Silliman University Press, Dumaguete City.
9. Bryant D., Moulton V. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 2004, 21:255-265.
10. Catibog-Sinha C.S., Heaney L.R. Philippine Biodiversity: Principles and Practice 2006, Haribon Foundation for the Conservation of Natural Resources Inc., Quezon City.
11. Earl D.A., vonHoldt B.M. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 2012, 4:359-361.
12. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
13. Evanno G., Regnaut S., Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 2005, 14:2611-2620.
14. Flecks M., Weinsheimer F., Böhme W., Chenga J., Lötters S., Rödder D. Watching extinction happen: the dramatic population decline of the critically endangered Tanzanian Turquoise Dwarf Gecko, Lygodactylus williamsi. Salamandra 2012, 48:12-20.
15. Gamble T., Bauer A.M., Colli G.R., Greenbaum E., Jackman T.R., Vitt L.J., Simons A.M. Coming to America: multiple origins of New World geckos. J. Evolution. Biol. 2011, 24:231-244.
16. Gamble T., Colli G.R., Rodrigues M.T., Werneck F.P., Simons A.M. Phylogeny and cryptic diversity in geckos (Phyllopezus; Phyllodactylidae; Gekkota) from South America's open biomes. Mol. Phylogenet. Evol. 2012, 62:943-953.
17. Heaney L.R., Regalado J.C. Vanishing Treasures of the Philippine Rain Forest 1998, The Field Museum, Chicago, Illinois.
18. Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23:245-267.
19. IUCN, 2012. IUCN Red List of Threatened Species. Version 2011.3.
20. Jackman T.R., Bauer A.M., Greenbaum A.M., Glaw F., Vences M. Molecular phylogenetic relationships among species of the Malagasy-Comoran gecko genus Paroedura (Squamata: Gekkonidae). Mol. Phylogenet. Evol. 2008, 46:74-81.
21. Kluge A.G. Phylogenetic relationships of the gekkonid lizard genera Lepidodactylus Fitzinger, Hemiphyllodactylus Bleeker, and Pseudogekko Taylor. Philipp. J. Sci. 1968, 95:331-352.
22. Lasco R.D., Pulhin F.B. Philippine Forestry and CO2 Sequestration: opportunities for Mitigating Climate Change 1998, Environmental Forestry Programme (ENFOR), UPLB College of Forestry and Natural Resources, Laguna, Philippines, 24 pp.
23. th century. J. Trop. For. Sci. 2001, 13:652-670.
24. Linkem C.W., Siler C.D., Diesmos A.C., Sy E., Brown R.M. A new species of Gekko (Squamata: Gekkonidae) from Central Luzon Island, Philippines. Zootaxa 2010, 2396:37-49.
25. Liu D.S., Iverson L.R., Brown S. Rates and patterns of deforestation in the Philippines: application of geographic information system analysis. Forest Ecol. Manage. 1993, 57:1-16.
26. Marshall D.C. Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees. Syst. Biol. 2010, 59:108-117.
27. PhilBREO, 2013. Philippines Biodiversity Research and Education Outreach. <> (accessed 15.03.13). http://philbreo.lifedesks.org/.
28. Posada D. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
29. Pritchard J.K., Stephens M., Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000, 155:945-959.
30. Rambaut, A., Drummond, A.J., 2007. Tracer v1.4. <>. http://beast.bio.ed.ac.uk/Tracer.
31. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
32. Rosenberg N.A. DISTRUCT: a program for the graphical display of population structure. Mol. Ecol. Notes 2004, 4:137-138.
33. Siler C.D., Oaks J.R., Esselstyn J.A., Diesmos A.C., Brown R.M. Phylogeny and biogeography of Philippine bent-toed geckos (Gekkonidae: Cyrtodactylus) contradicts a prevailing model of Pleistocene diversification. Mol. Phylogenet. Evol. 2010, 55:699-710.
34. Siler C.D., Oaks J.R., Welton L.J., Linkem C.W., Swab J.C., Diesmos A.C., Brown R.M. Did geckos ride the Palawan raft to the Philippines?. J. Biogeogr. 2012, 39:1217-1234.
35. Siler C.D., Jones R.M., Diesmos A.C., Diesmos M.L., Brown R.M. Phylogeny-based species delimitation in Philippine slender skinks (Reptilia: Squamata: Scincidae) III: taxonomic revision of the Brachymeles gracilis Complex, with descriptions of three new species. Herpetol. Monogr. 2012, 26:135-172.
36. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
37. Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 2008, 57:758-771.
38. Stephens M., Donnelly P. A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am. J. Hum. Genet. 2003, 73:1162-1169.
39. Taylor E.H. New species of Philippine lizards. Phil. J. Sci. 1915, 10:89-108.
40. Taylor E.H. Additions to the herpetological fauna of the Philippines islands, I. Phil. J. Sci. 1922, 21:161-206.
41. Welton L.J., Siler C.D., Linkem C.W., Diesmos A.C., Brown R.M. Philippine bent-toed geckos of the Cyrtodactylus agusanensis complex: multilocus phylogeny, morphological diversity, and description of three new species. Herpetol. Monogr. 2010, 24:55-85.
42. Wilgenbusch, J.C., Warren, D.L., Swofford, D.L., 2004. AWTY: A System for Graphical Exploration of MCMC Convergence in Bayesian Phylogenetic Inference. <>. http://ceb.csit.fsu.edu/awty.