Diversity and endemism of Murinae rodents in Thai limestone karsts

References

• Agapow , P. M. , Bininda-Emonds , O. R.P. , Crandall , K. A. , Gittleman , J. L. , Mace , G. M. , Marshall , J. C. and Purvis , A. 2004 . The impact of species concept on biodiversity studies . Quarterly Review of Biology , 79 : 161 – 179 . doi: 10.1086/383542
   PubMed Web of Science ®Google Scholar
• Aguilar , J. P. and Michaux , J. 1996 . The beginning of the age of Murinae (Mammalia: Rodentia) in southern France . Acta Zoologica Cracoviensia , 39 : 35 – 45 .
   Google Scholar
• Aplin , K. P. , Brown , P. R. , Jacobs , J. , Krebs , C. J. and Singleton , G. R. 2003 . Field Methods for Rodent Studies in Asia and the Indo-Pacific , Canberra : ACIAR .
   Google Scholar
• Aplin , K. P. , Suzuki , H. , Chinen , A. A. , Chesser , R. T. , Ten Have , J. , Donnellan , S. C. , Austin , J. , Frost , A. , Gonzalez , J. P. , Herbreteau , V. , Catzeflis , F. , Soubrier , J. , Fang , Y. P. , Robins , J. , Matisoo-Smith , E. , Bastos , A. D.S. , Maryanto , I. , Sinaga , M. H. , Denys , C. , Van Den Bussche , R. A. , Conroy , C. , Rowe , K. and Cooper , A. 2011 . Multiple geographic origins of commensalism and complex dispersal history of black rats . Public Library of Science ONE , 6 : e26357
   Google Scholar
• ASEAN , CFB . 2010 . ASEAN Biodiversity Outlook ASEAN Centre for Biodiversity, Philippines
   Google Scholar
• Baker , R. J. and Bradley , R. D. 2006 . Speciation in mammals and the genetic species concept . Journal of Mammalogy , 87 : 643 – 662 . doi: 10.1644/06-MAMM-F-038R2.1
   PubMed Web of Science ®Google Scholar
• Bastos , A. , Nair , D. , Taylor , P. , Brettschneider , H. , Kirsten , F. , Mostert , E. , Von Maltitz , E. , Lamb , J. , Van Hooft , P. , Belmain , S. , Contrafatto , G. , Downs , S. and Chimimba , C. 2011 . Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in South Africa . BioMed Central Genetics , 12 : 26 doi: 10.1186/1471-2156-12-26
   Web of Science ®Google Scholar
• Bickford , D. , Lohman , D. J. , Sodhi , N. S. , Ng , P. K.L. , Meier , R. , Winker , K. , Ingram , K. K. and Das , I. 2007 . Cryptic species as a window on diversity and conservation . Trends in Ecology and Evolution , 22 : 148 – 155 . doi: 10.1016/j.tree.2006.11.004
   PubMed Web of Science ®Google Scholar
• Bradley , R. D. and Baker , R. J. 2001 . A test of the genetic species concept: cytochrome-b sequences and mammals . Journal of Mammalogy , 82 : 960 – 973 . doi: 10.1644/1545-1542(2001)082<0960:ATOTGS>2.0.CO;2
   Web of Science ®Google Scholar
• Chaimanee , Y. and Jaeger , J.-J. 2001 . Evolution of Rattus (mammalia, Rodentia) during the plio-pleistocene in Thailand . Historical Biology , 15 : 181 – 191 . doi: 10.1080/10292380109380590
   Google Scholar
• Charuppat , T. 1998 . Forest Situation of Thailand in the Past 37 Years (1961–1998) , Thailand : Forest Resources Assessment Div. Forest Research Office. Royal Forest Department .
   Google Scholar
• Clements , R. , Sodhi , N. S. , Schilthuizen , M. and Ng , P. K.L. 2006 . Limestone karsts of southeast Asia: imperiled arks of biodiversity . Bioscience , 56 : 733 – 742 . doi: 10.1641/0006-3568(2006)56[733:LKOSAI]2.0.CO;2
   Web of Science ®Google Scholar
• Corbet , G. and Hill , J. 1992 . The Mammals of the Indomalayan Region: A Systematic Review , Oxford, UK : Oxford University Press .
   Google Scholar
• Day , M. and Urich , P. 2000 . An assessment of protected karst landscapes in Southeast Asia . Cave and Karst Science , 27 : 61 – 70 .
   Google Scholar
• De Queiroz , K. 2005 . Different species problems and their resolution . Bioessays , 27 : 1263 – 1269 . doi: 10.1002/bies.20325
   PubMed Web of Science ®Google Scholar
• De Queiroz , K. 2007 . Species concepts and species delimitation . Systematic Biology , 56 : 879 – 886 . doi: 10.1080/10635150701701083
   PubMed Web of Science ®Google Scholar
• Drummond , A. J. and Rambaut , A. 2007 . BEAST: Bayesian evolutionary analysis by sampling trees . BioMed Central Evolutionary Biology , 7 : 214 doi: 10.1186/1471-2148-7-214
   PubMed Web of Science ®Google Scholar
• Drummond , A. J. , Ho , S. Y.W. , Phillips , M. J. and Rambaut , A. 2006 . Relaxed phylogenetics and dating with confidence . Public Library of Science Biology , 4 : 699 – 710 .
   Google Scholar
• Dupuy , S. , Herbreteau , V. , Feyfant , T. , Morand , S. and Tran , A. 2012 . “ Land-cover dynamics in Southeast Asia: contribution of object-oriented techniques for change detection ” . In 4th GEOBIA. 217 – 222 . Rio de Janeiro, Brazil
   Google Scholar
• ESCAP . 2001 . Atlas of Mineral resources of the ESCAP region, Volume 16, Mineral Resources of Thailand , New York : United Nations .
   Google Scholar
• Excoffier , L. , Laval , G. and Schneider , S. 2005 . Arlequin (version 3.0): an integrated software package for population genetics data analysis . Evolutionary Bioinformatics , 1 : 47 – 50 .
   PubMed Web of Science ®Google Scholar
• Fontaneto , D. , Herniou , E. A. , Boschetti , C. , Caprioli , M. , Melone , G. , Ricci , C. and Barraclough , T. G. 2007 . Independently evolving species in asexual bdelloid rotifers . Public Library of Science Biology , 5 : 914 – 921 .
   Google Scholar
• Francis , C. M. 2008 . A Field Guide to the Mammals of South-East Asia , London, UK : New Holland .
   Google Scholar
• Furey , N. M. , Mackie , I. J. and Racey , P. A. 2010 . Bat diversity in Vietnamese limestone karst areas and the implications of forest degradation . Biodiversity and Conservation , 19 : 1821 – 1838 . doi: 10.1007/s10531-010-9806-0
   Web of Science ®Google Scholar
• Gilbert , M. T.P. , Bandelt , H. J. , Hofreiter , M. and Barnes , I. 2005 . Assessing ancient DNA studies . Trends in Ecology and Evolution , 20 : 541 – 544 . doi: 10.1016/j.tree.2005.07.005
   PubMed Web of Science ®Google Scholar
• Gillieson , D. 2005 . “ Karsts of Southeast Asia ” . In The Physical Geography of Southeast Asia , Edited by: Gupta , A. 157 – 176 . Oxford, UK : Oxford University Press .
   Google Scholar
• Guindon , S. , Dufayard , J. F. , Lefort , V. , Anisimova , M. , Hordijk , W. and Gascuel , O . 2010 . New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 . Systematic Biology , 59 : 307 – 321 . doi: 10.1093/sysbio/syq010
   PubMed Web of Science ®Google Scholar
• Hall , T. A. 1999 . BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT . Nucleic Acids Symposium Series , 41 : 95 – 98 .
   Google Scholar
• Hausdorf , B. 2011 . Progress toward a general species concept . Evolution , 65 : 923 – 931 . doi: 10.1111/j.1558-5646.2011.01231.x
   PubMed Web of Science ®Google Scholar
• Hebert , P. D.N. , Penton , E. H. , Burns , J. M. , Janzen , D. H. and Hallwachs , W. 2004 . Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator . Proceedings of the National Academy of Sciences USA , 101 : 14812 – 14817 . doi: 10.1073/pnas.0406166101
   PubMed Web of Science ®Google Scholar
• Huchon , D. , Chevret , P. , Jordan , U. , Kilpatrick , C. W. , Ranwez , V. , Jenkins , P. D. , Brosius , J. and Schmitz , J. 2007 . Multiple molecular evidences for a living mammalian fossil . Proceedings of the National Academy of Sciences USA , 104 : 7495 – 7499 . doi: 10.1073/pnas.0701289104
   PubMed Web of Science ®Google Scholar
• Hughes , J. B. , Round , P. D. and Woodruff , D. S. 2003 . The Indochinese-Sundaic faunal transition at the Isthmus of Kra: an analysis of resident forest bird species distributions . Journal of Biogeography , 30 : 569 – 580 . doi: 10.1046/j.1365-2699.2003.00847.x
   Web of Science ®Google Scholar
• Irwin , D. M. , Kocher , T. D. and Wilson , A. C. 1991 . Evolution of the cytochrome b gene of mammals . Journal of Molecular Evolution , 32 : 128 – 144 . doi: 10.1007/BF02515385
   PubMed Web of Science ®Google Scholar
• Jacobs , L. L. and Flynn , L. J. 2005 . “ Of mice … again: the Siwalik rodent record, murine distribution, and molecular clocks ” . In Interpreting the Past: Essays on Human, Primate and Mammal Evolution , Edited by: Lieberman , D. , Smith , R. and Kelley , J. 63 – 80 . Leiden, The Netherlands : Brill Academic .
   Google Scholar
• Jenkins , P. D. , Kilpatrick , C. W. , Robinson , M. F. and Timmins , R. J. 2005 . Morphological and molecular investigations of a new family, genus and species of rodent (Mammalia: Rodentia: Hystricognatha) from Lao PDR . Systematics and Biodiversity , 2 : 419 – 454 . doi: 10.1017/S1477200004001549
   Google Scholar
• Kloss , C. B. 1915 . Zoogeographical divisions for Siam . Journal of the Natural History Society of Siam , 1 : 250 – 251 .
   Google Scholar
• Kloss , C. B. 1929 . The zoo-geographical boundaries between Asia and Australia and some Oriental sub-regions . Bulletin of the Raffles Museum , 2 : 1 – 10 .
   Google Scholar
• Lack , J. B. , Greene , D. U. , Conroy , C. J. , Hamilton , M. J. , Braun , J. K. , Mares , M. A. and Van Den Bussche , R. A. 2012 . Invasion facilitates hybridization with introgression in the Rattus rattus species complex . Molecular Ecology , 21 : 3545 – 3561 . doi: 10.1111/j.1365-294X.2012.05620.x
   PubMed Web of Science ®Google Scholar
• Latinne , A. , Waengsothorn , S. , Herbreteau , V. and Michaux , J. R. 2011 . Evidence of complex phylogeographic structure for the threatened rodent Leopoldamys neilli, in Southeast Asia . Conservation Genetics , 12 : 1495 – 1511 . doi: 10.1007/s10592-011-0248-3
   Web of Science ®Google Scholar
• Latinne , A. , Waengsothorn , S. , Rojanadilok , P. , Eiamampai , K. , Sribuarod , K. and Michaux , J. R. 2012 . Combined mitochondrial and nuclear markers revealed a deep vicariant history for Leopoldamys neilli, a cave-dwelling rodent of Thailand . Public Library of Science ONE , 7 : e47670
   Google Scholar
• Lecompte , E. , Aplin , K. , Denys , C. , Catzeflis , F. , Chades , M. and Chevret , P. 2008 . Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily . BioMed Central Evolutionary Biology , 8 : 199 doi: 10.1186/1471-2148-8-199
   PubMed Web of Science ®Google Scholar
• Lekagul , B. and Mcneely , J. A. 1988 . Mammals of Thailand , Bangkok : White Lotus Press .
   Google Scholar
• Librado , P. and Rozas , J. 2009 . DnaSP v5: a software for comprehensive analysis of DNA polymorphism data . Bioinformatics , 25 : 1451 – 1452 . doi: 10.1093/bioinformatics/btp187
   PubMed Web of Science ®Google Scholar
• Lunde , D. P. and Aplin , K. 2008a . Leopoldamys neilli . IUCN 2012. IUCN Red List of Threatened Species. Version 2012.1. IUCN, Cambridge, UK.
   Google Scholar
• Lunde , D. P. and Aplin , K. 2008b . Niviventer hinpoon . IUCN 2012. IUCN Red List of Threatened Species. Version 2012.1. IUCN, Cambridge, UK
   Google Scholar
• Michaux , J. , Aguilar , J. P. , Montuire , S. , Wolff , A. and Legendre , S. 1997 . Les Murinae (Rodentia, Mammalia) neogenes du Sud de la France: Evolution et paleoenvironnements . Geobios , 30 : 379 – 385 . doi: 10.1016/S0016-6995(97)80042-3
   Google Scholar
• Monaghan , M. T. , Wild , R. , Elliot , M. , Fujisawa , T. , Balke , M. , Inward , D. J.G. , Lees , D. C. , Ranaivosolo , R. , Eggleton , P. , Barraclough , T. G. and Vogler , A. P. 2009 . Accelerated species inventory on Madagascar using coalescent-based models of species delineation . Systematic Biology , 58 : 298 – 311 . doi: 10.1093/sysbio/syp027
   PubMed Web of Science ®Google Scholar
• Musser , G. G. and Carleton , M. 2005 . “ Superfamily Muroidea ” . In Mammal Species of the World: A Taxonomic and Geographic Reference , Edited by: Wilson , D. E. and Reeder , D. M. 894 – 1531 . Baltimore, USA : Johns Hopkins University Press .
   Google Scholar
• Musser , G. G. , Smith , A. L. , Robinson , M. F. and Lunde , D. P. 2005 . Description of a new genus and species rodent (Murinae, Muridae, Rodentia) from Khammouan Limestone National Biodiversity Conservation Area in Lao PDR . American Museum Novitates , 3497 : 1 – 31 . doi: 10.1206/0003-0082(2005)497[0001:DOANGA]2.0.CO;2
   Web of Science ®Google Scholar
• Musser , G. G. , Lunde , D. P. and Son , N. T. 2006 . Description of a new genus and species of rodent (Murinae, Muridae, Rodentia) from the tower karst region of northeastern Vietnam . American Museum Novitates , 3517 : 1 – 41 . doi: 10.1206/0003-0082(2006)3517[1:DOANGA]2.0.CO;2
   Google Scholar
• Myers , N. , Mittermeier , R. A. , Mittermeier , C. G. , Da Fonseca , G. A.B. and Kent , J. 2000 . Biodiversity hotspots for conservation priorities . Nature , 403 : 853 – 858 . doi: 10.1038/35002501
   PubMed Web of Science ®Google Scholar
• Pages , M. , Chaval , Y. , Herbreteau , V. , Waengsothorn , S. , Cosson , J. F. , Hugot , J. P. , Morand , S. and Michaux , J. 2010 . Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries . BioMed Central Evolutionary Biology , 10 : 184 doi: 10.1186/1471-2148-10-184
   PubMed Web of Science ®Google Scholar
• Pages , M. , Corbet , G. , Orth , A. , Volobouev , V. , Michaux , J. and Catzeflis , F. 2011 . Morphological, chromosomal, and genic differences between sympatric Rattus rattus and Rattus satarae in South India . Journal of Mammalogy , 92 : 659 – 670 . doi: 10.1644/10-MAMM-A-033.1
   Web of Science ®Google Scholar
• Pages , M. , Bazin , E. , Galan , M. , Chaval , Y. , Claude , J. , Herbreteau , V. , Michaux , J. R. , Piry , S. , Morand , S. and Cosson , J. F. 2012 . Cytonuclear discordance among Southeast Asian black rats (Rattus rattus complex) . Molecular Ecology , 22 : 1019 – 1034 . doi: 10.1111/mec.12149
   PubMed Web of Science ®Google Scholar
• Papadopoulou , A. , Monaghan , M. T. , Barraclough , T. G. and Vogler , A. P. 2009 . Sampling error does not invalidate the Yule-Coalescent model for species delimitation. A response to Lohse (2009) . Systematic Biology , 58 : 442 – 444 . doi: 10.1093/sysbio/syp038
   Web of Science ®Google Scholar
• Pons , J. , Barraclough , T. G. , Gomez-Zurita , J. , Cardoso , A. , Duran , D. P. , Hazell , S. , Kamoun , S. , Sumlin , W. D. and Vogler , A. P. 2006 . Sequence-based species delimitation for the DNA taxonomy of undescribed insects . Systematic Biology , 55 : 595 – 609 . doi: 10.1080/10635150600852011
   PubMed Web of Science ®Google Scholar
• Posada , D. and Crandall , K. A. 1998 . MODELTEST: testing the model of DNA substitution . Bioinformatics , 14 : 817 – 818 . doi: 10.1093/bioinformatics/14.9.817
   PubMed Web of Science ®Google Scholar
• Rambaut , A. and Drummond , A. J. 2007 . Tracer v1.4 (http://beast.bio.ed.ac.uk/Tracer, accessed 19 June 2013)
   Google Scholar
• Robins , J. H. , Hingston , M. , Matisoo-Smith , E. and Ross , H. A. 2007 . Identifying Rattus species using mitochondrial DNA . Molecular Ecology Notes , 7 : 717 – 729 . doi: 10.1111/j.1471-8286.2007.01752.x
   Web of Science ®Google Scholar
• Ronquist , F. and Huelsenbeck , J. P. 2003 . MrBayes 3: Bayesian phylogenetic inference under mixed models . Bioinformatics , 19 : 1572 – 1574 . doi: 10.1093/bioinformatics/btg180
   PubMed Web of Science ®Google Scholar
• Rowe , K. C. , Aplin , K. P. , Baverstock , P. R. and Moritz , C. 2011 . Recent and rapid speciation with limited morphological disparity in the genus Rattus . Systematic Biology , 60 : 188 – 203 . doi: 10.1093/sysbio/syq092
   PubMed Web of Science ®Google Scholar
• Sarkar , I. N. , Planet , P. J. and Desalle , R. 2008 . CAOS software for use in character-based DNA barcoding . Molecular Ecology Resources , 8 : 1256 – 1259 . doi: 10.1111/j.1755-0998.2008.02235.x
   PubMed Web of Science ®Google Scholar
• Sauer , J. and Hausdorf , B. 2012 . A comparison of DNA-based methods for delimiting species in a Cretan land snail radiation reveals shortcomings of exclusively molecular taxonomy . Cladistics , 28 : 300 – 316 . doi: 10.1111/j.1096-0031.2011.00382.x
   Web of Science ®Google Scholar
• Shi , L. 2010 . “ The mineral industry of Thailand ” . In 2008 Minerals Yearbook, Thailand , USA : U.S. Geological Survey .
   Google Scholar
• Simms , M. J. 2005 . “ Sedimentary processes, karsts and palaeokarst ” . In Encyclopedia of Geology , Edited by: Selley , R. C. , Cocks , L. R.M. and Plimer , I. R. 678 – 687 . Oxford, UK : Elsevier .
   Google Scholar
• Swofford , D. L. 1998 . PAUP*. Phylogenetic Analysis using Parsimony, (*and other Methods), version 4 , Sunderland , MA, USA : Sinauer Associates .
   Google Scholar
• Tamura , K. , Dudley , J. , Nei , M. and Kumar , S. 2007 . MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0 . Molecular Biology and Evolution , 24 : 1596 – 1599 . doi: 10.1093/molbev/msm092
   PubMed Web of Science ®Google Scholar
• Teletchea , F. , Bernillon , J. , Duffraisse , M. , Laudet , V. and Hanni , C. 2008 . Molecular identification of vertebrate species by oligonucleotide microarray in food and forensic samples . Journal of Applied Ecology , 45 : 967 – 975 . doi: 10.1111/j.1365-2664.2007.01415.x
   Web of Science ®Google Scholar
• Vermeulen , J. J. and Whitten , T. 1999 . Biodiversity and Cultural Property in the Management of Limestone Resources – Lessons from East Asia , Washington, DC, USA : World Bank .
   Google Scholar
• Waengsothorn , S. , Nabhitabhata , J. and Moochan , T. 2007 . The ecological distribution of Thai endemic rodents with a new distributional range of Niviventer hinpoon . Thailand Natural History Museum Journal , 2 : 31 – 42 .
   Google Scholar
• Waengsothorn , S. , Kenthao , A. , Latinne , A. and Hugot , J. P. 2009 . Rodents within the Centre for Thai National Reference Collections (CTNRC), past, present and future . Kasetsart Journal Natural Sciences , 43 : 118 – 124 .
   Google Scholar
• Wells , D. R. 1976 . “ Resident birds ” . In The Birds of the Malay Peninsula , Edited by: Medway , L. and Wells , D. R. Vol. V: , 1 – 33 . London, UK : Whiterby .
   Google Scholar
• Winkler , A. J. 2002 . Neogene paleobiogeography and East African paleoenvironments: contributions from the Tugen Hills rodents and lagomorphs . Journal of Human Evolution , 42 : 237 – 256 . doi: 10.1006/jhev.2001.0501
   PubMed Web of Science ®Google Scholar
• Woodruff , D. S. and Turner , L. M. 2009 . The Indochinese-Sundaic zoogeographic transition: a description and analysis of terrestrial mammal species distributions . Journal of Biogeography , 36 : 803 – 821 . doi: 10.1111/j.1365-2699.2008.02071.x
   Web of Science ®Google Scholar
• WORLD BANK . 2004 . Thailand Environment Monitor 2004, Biodiversity Conservation , Washington, DC, USA : World Bank .
   Google Scholar