A phylogeographic study of the endemic rodent Eliurus carletoni (Rodentia: Nesomyinae) in an ecological transition zone of Northern Madagascar.

We conducted a mitochondrial phylogeographic study of the endemic dry forest rodent Eliurus carletoni (Rodentia: Nesomyinae) in an ecological transition zone of northern Madagascar (Loky-Manambato) and 2 surrounding regions (Ankarana and Analamerana). The main goal was to assess the evolutionary consequences on this taxon of the complex landscape features and Quaternary ecological vicissitudes. Three haplogroups were identified from the 215 specimens obtained from 15 populations. High levels of genetic diversity and significant genetic differentiation among populations were observed. The different geographical subdivisions of the study area by regions, by river catchment zones, and the physical distance between populations are not correlated with genetic patterns. In contrast, population structure is mostly explained by the geographic distribution of the samples among existing forest blocks. E. carletoni experienced a genetic bottleneck between 18 750 and 7500 years BP, which correlates with periods when moister climates existed on the island. Overall, our data suggest that the complex genetic patterns of E. carletoni can be explained by Quaternary climatic vicissitudes that resulted in habitat fluctuations between dry and humid forests, as well as subsequent human-induced fragmentation of forest habitat.

[1]  Jason L. Brown,et al.  Integrating statistical genetic and geospatial methods brings new power to phylogeography. , 2011, Molecular phylogenetics and evolution.

[2]  S. Goodman,et al.  Phylogeny and species boundaries of the endemic species complex, Eliurus antsingy and E. carletoni (Rodentia: Muroidea: Nesomyidae), in Madagascar using mitochondrial and nuclear DNA sequence data. , 2010, Molecular phylogenetics and evolution.

[3]  L. Chikhi,et al.  Landscape genetics of an endangered lemur (Propithecus tattersalli) within its entire fragmented range , 2010, Molecular ecology.

[4]  Benjamin M. Fitzpatrick.  Power and sample size for nested analysis of molecular variance , 2009, Molecular ecology.

[5]  M. Vences,et al.  Madagascar as a model region of species diversification. , 2009, Trends in ecology & evolution.

[6]  Pablo Librado,et al.  DnaSP v5: a software for comprehensive analysis of DNA polymorphism data , 2009, Bioinform..

[7]  吕一旭 Yixu Lu.  引言 (Introduction) , 2009, Provincial China.

[8]  M. Nachman,et al.  Inferring the history of speciation in house mice from autosomal, X‐linked, Y‐linked and mitochondrial genes , 2008, Molecular ecology.

[9]  P. Arctander,et al.  Mitochondrial DNA diversity and population structure of a forest-dependent rodent, Praomys taitae (Rodentia: Muridae) Heller 1911, in the fragmented forest patches of Taita Hills, Kenya , 2008 .

[10]  A. Drummond,et al.  Bayesian inference of population size history from multiple loci , 2008, BMC Evolutionary Biology.

[11]  J. Rougemont,et al.  A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.

[12]  L. Beheregaray.  Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere , 2008, Molecular ecology.

[13]  N. Howell,et al.  Molecular clock debate: Time dependency of molecular rate estimates for mtDNA: this is not the time for wishful thinking , 2008, Heredity.

[14]  A. Navarro,et al.  Statistical Power Analysis of Neutrality Tests Under Demographic Expansions, Contractions and Bottlenecks With Recombination , 2008, Genetics.

[15]  Steven J. Phillips,et al.  Aligning Conservation Priorities Across Taxa in Madagascar with High-Resolution Planning Tools , 2008, Science.

[16]  D. Rakotondravony,et al.  Growth of the tufted-tailed rat. , 2007, Integrative zoology.

[17]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[18]  M. Nei,et al.  MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. , 2007, Molecular biology and evolution.

[19]  S. Ho,et al.  Evidence for time dependency of molecular rate estimates. , 2007, Systematic biology.

[20]  M. Milinkovitch,et al.  Estimating population parameters using the structured serial coalescent with Bayesian MCMC inference when some demes are hidden. , 2007 .

[21]  Tony O’Hagan.  Bayes factors , 2006 .

[22]  S. Goodman,et al.  Biogeographic Evolution of Madagascar's Microendemic Biota , 2006, Science.

[23]  Peter Beerli,et al.  Comparison of Bayesian and maximum-likelihood inference of population genetic parameters , 2006, Bioinform..

[24]  O. Pybus,et al.  Bayesian coalescent inference of past population dynamics from molecular sequences. , 2005, Molecular biology and evolution.

[25]  S. Kelley,et al.  Isolation by distance, web service , 2005, BMC Genetics.

[26]  J. Searle,et al.  Mitochondrial DNA variation in the western house mouse (Mus musculus domesticus) close to its site of origin: studies in Turkey , 2005 .

[27]  H. Hauffe,et al.  Geographical distance and physical barriers shape the genetic structure of Eurasian red squirrels (Sciurus vulgaris) in the Italian Alps , 2005, Molecular ecology.

[28]  S. Schneider,et al.  Arlequin (version 3.0): An integrated software package for population genetics data analysis , 2005, Evolutionary bioinformatics online.

[29]  Henry T. Wright,et al.  A chronology for late prehistoric Madagascar. , 2004, Journal of human evolution.

[30]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[31]  N. Solomon.  A REEXAMINATION OF FACTORS INFLUENCING PHILOPATRY IN RODENTS , 2003 .

[32]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[33]  J. Rozas,et al.  Statistical properties of new neutrality tests against population growth. , 2002, Molecular biology and evolution.

[34]  David Posada,et al.  PHYLOGEOGRAPHIC HISTORY OF THE LAND SNAIL CANDIDULA UNIFASCIATA (HELICELLINAE, STYLOMMATOPHORA): FRAGMENTATION, CORRIDOR MIGRATION, AND SECONDARY CONTACT , 2002, Evolution; international journal of organic evolution.

[35]  John P. Huelsenbeck,et al.  MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..

[36]  M. Suchard,et al.  Bayesian selection of continuous-time Markov chain evolutionary models. , 2001, Molecular biology and evolution.

[37]  K. Crandall,et al.  TCS: a computer program to estimate gene genealogies , 2000, Molecular ecology.

[38]  R. Hudson,et al.  A new statistic for detecting genetic differentiation. , 2000, Genetics.

[39]  P. Tucker,et al.  Molecular Phylogeny and Biogeography of the Native Rodents of Madagascar (Muridae: Nesomyinae): A Test of the Single‐Origin Hypothesis , 1999, Cladistics : the international journal of the Willi Hennig Society.

[40]  F. Gasse,et al.  A 40,000-yr Pollen and Diatom Record from Lake Tritrivakely, Madagascar, in the Southern Tropics , 1998, Quaternary Research.

[41]  Y. Fu,et al.  Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. , 1997, Genetics.

[42]  F. Rousset.  Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. , 1997, Genetics.

[43]  Katsumi Matsumotot,et al.  Late Holocene environments at Lake Mitsinjo, northwestern Madagascar , 1994 .

[44]  C. Jones,et al.  Mitochondrial DNA sequence diversity and the colonization of Scandinavia by house mice from East Holstein , 1993 .

[45]  M. Nei,et al.  Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. , 1993, Molecular biology and evolution.

[46]  C. Sing,et al.  A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. , 1992, Genetics.

[47]  L. Excoffier,et al.  Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. , 1992, Genetics.

[48]  F. Tajima.  Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. , 1989, Genetics.

[49]  M. Nei.  Molecular Evolutionary Genetics , 1987 .

[50]  E. Bermingham,et al.  Molecular zoogeography of freshwater fishes in the southeastern United States. , 1986, Genetics.

[51]  H. Akaike.  A new look at the statistical model identification , 1974 .

[52]  S. Wright,et al.  Isolation by Distance. , 1943, Genetics.

[53]  Bryan C. Carstens,et al.  Phylogeography's past, present, and future: 10 years after Avise, 2000. , 2010, Molecular phylogenetics and evolution.

[54]  S. Goodman,et al.  A new species of Eliurus Milne Edwards, 1885 (Rodentia: Nesomyinae) from the Réserve Spéciale d'Ankarana, northern Madagascar , 2005 .

[55]  Michel Veuille,et al.  Power of Neutrality Tests to Detect Bottlenecks and Hitchhiking , 2003, Journal of Molecular Evolution.

[56]  Nicolas Ray,et al.  A GIS-based vegetation map of the world at the Last Glacial Maximum (25,000-15,000 BP) , 2001 .

[57]  David Posada,et al.  MODELTEST: testing the model of DNA substitution , 1998, Bioinform..

[58]  C. Moritz,et al.  Genetic effects of forest fragmentation on a rainforest restricted lizard (Scincidae: Gnypetoscincus queenslandiae) , 1998 .

[59]  L. Ferry,et al.  Fleuves et rivières de Madagascar = Ony sy renirano eto Madagasikara , 1993 .