Pleistocene climatic fluctuations explain the disjunct distribution and complex phylogeographic structure of the Southern Red-backed Salamander, Plethodon serratus

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• 作者：Benjamin D. Thesing ; Richard D. Noyes ; David E. Starkey…
• 关键词：Allopatric speciation ; Biogeography ; Climate change ; Cryptic species ; Lineage diversification ; Ecological niche modeling
• 刊名：Evolutionary Ecology
• 出版年：2016
• 出版时间：February 2016
• 年：2016
• 卷：30
• 期：1
• 页码：89-104
• 全文大小：1,107 KB
• 参考文献：Adams DC (2007) Organization of Plethodon salamander communities: guild-based community assembly. Ecology 88:1292–1299CrossRef PubMed
  Allen RT (1990) Insect endemism in the Interior Highlands of North America. Fla Entomol 73:539–569CrossRef
  Arévalo E, Davis SK, Sites JW Jr (1994) Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynosomatidae) in Central Mexico. Syst Biol 43:387–418CrossRef
  Axelrod DI (1985) Rise of the grassland biome, central North America. Bot Rev 51:163–201CrossRef
  Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA, Alekseyenko AV (2012) Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol Biol Evol 29:2157–2167PubMedCentral CrossRef PubMed
  Baele G, Lok W, Li S, Drummond AJ, Suchard MA, Lemey P (2013) Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics. Mol Biol Evol 30:239–243PubMedCentral CrossRef PubMed
  Barve N, Barve V, Jiménez-Valverde A, Lira-Noriega A, Maher SP, Peterson AT, Soberón J, Villalobos F (2011) The crucial role of the accessible area in ecological niche modeling and species distribution modeling. Ecol Model 222:1810–1819CrossRef
  Bayer CSO, Sackman AM, Bezold K, Cabe PR, Marsh DM (2012) Conservation genetics of an endemic mountaintop salamander with an extremely limited range. Conserv Genet 13:443–454CrossRef
  Bennett KD (1990) Milankovitch cycles and their effects on species in ecological and evolutionary time. Paleobiology 16:11–21
  Bond JE, Stockman AK (2008) An integrative method for delimiting cohesion species: finding the population-species interface in a group of Californian trapdoor spiders with extreme genetic divergence and geographic structuring. Syst Biol 57:628–646CrossRef PubMed
  Brown JH, Stevens GC, Kaufman DM (1996) The geographic range: size, shape, boundaries, and internal structure. Annu Rev Ecol Syst 27:597–623CrossRef
  Chase JM, Leibold MA (2003) Ecological niches: linking classical and contemporary approaches. University of Chicago Press, ChicagoCrossRef
  Costa GC, Wolfe CA, Shepard DB, Caldwell JP, Vitt LJ (2008) Detecting the influence of climatic variables on species distributions: a test using GIS niche-based models along a steep longitudinal environmental gradient. J Biogeogr 35:637–646CrossRef
  Crandall KA, Templeton AR (1999) The zoogeography and centers of origin of the crayfish subgenus Procericambarus (Decapoda: Cambaridae). Evolution 53:123–134CrossRef
  Crandall KA, Bininda-Emonds ORP, Mace GM, Wayne RK (2000) Considering evolutionary processes in conservation biology. Trends Ecol Evol 15:290–295CrossRef PubMed
  Crawford JA, Peterman WE (2013) Biomass and habitat partitioning of Desmognathus on wet rock faces in southern Appalachian Mountains. J Herpetol 47:580–584CrossRef
  Davis MB (1983) Quaternary history of deciduous forests of eastern North America and Europe. Ann Mo Bot Gard 70:550–563CrossRef
  Dowling H (1956) Geographic relations of Ozarkian amphibians and reptiles. Southwest Nat 1:174–189CrossRef
  Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214PubMedCentral CrossRef PubMed
  Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4:699–710CrossRef
  Edwards SV (2009) Is a new and general theory of molecular systematics emerging? Evolution 63:1–19CrossRef PubMed
  Edwards SV, Beerli P (2000) Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839–1854PubMed
  Elith J, Leathwick JR (2009) Species distribution models: ecological explanation and prediction across space and time. Annu Rev Ecol Evol Syst 40:677–697CrossRef
  Elith J, Phillips SJ, Hastie T, Dudík M, Chee YE, Yates CJ (2011) A statistical explanation of MaxEnt for ecologists. Divers Distrib 17:43–57CrossRef
  Feder ME (1983) Integrating the ecology and physiology of plethodontid salamanders. Herpetologica 39:291–310
  Fraser DJ, Bernatchez L (2001) Adaptive evolutionary conservation: towards a unified concept for defining conservation units. Mol Ecol 10:2741–2752CrossRef PubMed
  Frost DR (2015) Amphibian Species of the World: an online reference. Version 6.0. American Museum of Natural History, New York. http://​research.​amnh.​org/​vz/​herpetology/​amphibia/​ . Accessed 8 July 2015
  Gaston KJ (2003) The structure and dynamics of geographic ranges. Oxford University Press, Oxford
  Grundstein A (2009) Evaluation of climate change over the continental United States using a moisture index. Clim Change 93:103–115CrossRef
  Hairston NG (1951) Interspecies competition and its probable influence upon the vertical distribution of Appalachian salamanders in the genus Plethodon. Ecology 32:266–274CrossRef
  Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biol J Linn Soc 58:247–276CrossRef
  Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature 405:907–913CrossRef PubMed
  Hewitt GM (2004) Genetic consequences of climatic oscillations in the Quaternary. Philos Trans R Soc B 359:183–195CrossRef
  Highton R (1995) Speciation in eastern North-American salamanders of the genus Plethodon. Annu Rev Ecol Syst 26:579–600CrossRef
  Highton R, Webster TP (1976) Geographic protein variation and divergence in populations of the salamander Plethodon cinereus. Evolution 30:33–45CrossRef
  Highton R, Hastings AP, Palmer C, Watts R, Hass CA, Culver M, Arnold SJ (2012) Concurrent speciation in the eastern woodland salamanders (Genus Plethodon): DNA sequences of the complete albumin nuclear and partial mitochondrial 12s genes. Mol Phylogenet Evol 63:278–290CrossRef PubMed
  Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A (2005) Very high resolution interpolated climate surfaces for global land areas. Int J Climatol 25:1965–1978CrossRef
  Jackson ST, Webb RS, Anderson KH, Overpeck JT, Webb T III, Williams JH, Hansen BCS (2000) Vegetation and environment in eastern North America during the last glacial maximum. Quat Sci Rev 19:489–508CrossRef
  Jaeger RG (1971) Competitive exclusion as a factor influencing the distributions of two species of terrestrial salamanders. Ecology 52:632–637CrossRef
  Jansson R, Dynesius M (2002) The fate of clades in a world of recurrent climatic change: Milankovitch oscillations and evolution. Annu Rev Ecol Syst 33:741–777CrossRef
  Jones MT, Voss SR, Ptacek MB, Weisrock DW, Tonkyn DW (2006) River drainages and phylogeography: an evolutionary significant lineage of shovel-nosed salamander (Desmognathus marmoratus) in the southern Appalachians. Mol Phylogenet Evol 38:280–287CrossRef PubMed
  Kass RE, Raftery AE (1995) Bayes factors. J Am Stat Assoc 90:773–795CrossRef
  Kohn MJ, Fremd TJ (2008) Miocene tectonics and climate forcing of biodiversity, western United States. Geology 36:783–786CrossRef
  Kozak KH, Wiens JJ (2006) Does niche conservatism promote speciation? A case study in North American salamanders. Evolution 60:2604–2621CrossRef PubMed
  Kozak KH, Wiens JJ (2010) Niche conservatism drives elevational diversity patterns in Appalachian salamanders. Am Nat 176:40–54CrossRef PubMed
  Kozak KH, Wiens JJ (2012) Phylogeny, ecology, and the origins of climate-richness relationships. Ecology 93:S167–S181CrossRef
  Kozak KH, Blaine RA, Larson A (2006a) Gene lineages and eastern North American paleodrainage basins: phylogeography and speciation in salamanders of the Eurycea bislineata species complex. Mol Ecol 15:191–207CrossRef PubMed
  Kozak KH, Weisrock DW, Larson A (2006b) Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon). Proc R Soc B 273:539–546PubMedCentral CrossRef PubMed
  Kozak KH, Graham CH, Wiens JJ (2008) Integrating GIS-based environmental data into evolutionary biology. Trends Ecol Evol 23:141–148CrossRef PubMed
  Kozak KH, Mendyk RW, Wiens JJ (2009) Can parallel diversification occur in sympatry? Repeated patterns of body-size evolution in coexisting clades of North American salamanders. Evolution 63:1769–1784CrossRef PubMed
  Kürschner WM, Kvacek Z, Dilcher DL (2008) The impact of Miocene atmospheric carbon dioxide fluctuations on climate and the evolution of terrestrial ecosystems. Proc Natl Acad Sci USA 105:449–453PubMedCentral CrossRef PubMed
  Lanfear R, Calcott B, Ho SYW, Guindon S (2012) PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analysis. Mol Biol Evol 29:1695–1701CrossRef PubMed
  Liu C, Berry PM, Dawson TP, Pearson RG (2005) Selecting thresholds of occurrence in the prediction of species distributions. Ecography 28:385–393CrossRef
  MacArthur RH (1984) Geographical ecology: patterns in the distribution of species. Princeton University Press, Princeton
  Mayden RL (1985) Biogeography of Ouachita Highland fishes. Southwest Nat 30:195–211CrossRef
  Mayden RL (1988) Vicariance biogeography, parsimony, and evolution in North American freshwater fishes. Syst Zool 37:329–355CrossRef
  Moritz C (1994) Defining ‘evolutionarily significant units’ for conservation. Trends Ecol Evol 9:373–375CrossRef PubMed
  Morrone JJ (2009) Evolutionary biogeography: an integrative approach with case studies. Columbia University Press, New York
  Mueller RL, Macey JR, Jaekel M, Wake DB, Boore JL (2004) Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proc Natl Acad Sci USA 101:13820–13825PubMedCentral CrossRef PubMed
  Near TJ, Keck BP (2005) Dispersal, vicariance, and timing of diversification in Nothonotus darters. Mol Ecol 14:3485–3496CrossRef PubMed
  Near TJ, Page LM, Mayden RL (2001) Intraspecific phylogeography of Percina evides (Percidae: Etheostomatinae): an additional test of the Central Highlands pre-Pleistocene vicariance hypothesis. Mol Ecol 10:2235–2240CrossRef PubMed
  Peterson AT (2001) Predicting species’ geographic distributions based on ecological niche modeling. Condor 103:599–605CrossRef
  Peterson AT, Soberón J, Pearson RG, Anderson RP, Martínez-Meyer E, Nakamura M, Araújo MB (2011) Ecological niches and geographic distributions. Princeton University Press, Princeton
  Petit JR, Jouzel J, Raynaud D, Barkov NI, Barnola JM, Basile I, Bender M, Chappellaz J, Davis M, Delaygue G, Delmotte M, Kotlyakov VM, Legrand M, Lipenkov VY, Lorius C, Pépin L, Ritz C, Saltzman E, Stievenard M (1999) Climate and atmospheric history of the past 420,000 years from Vostok ice core, Antarctica. Nature 399:429–436CrossRef
  Petranka JW (1998) Salamanders of the United States and Canada. Smithsonian Institution Press, Washington, DC
  Petranka JW, Murray SS (2001) Effectiveness of removal sampling for determining salamander density and biomass: a case study in an Appalachian streamside community. J Herpetol 35:36–44CrossRef
  Phillips SJ, Dudík M (2008) Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography 31:161–175CrossRef
  Phillips SJ, Anderson RP, Schapire RE (2006) Maximum entropy modeling of species geographic distributions. Ecol Model 190:231–259CrossRef
  Pyron RA, Burbrink FT (2010) Hard and soft allopatry: physically and ecologically mediated modes of geographic speciation. J Biogeogr 37:2005–2015
  Rader RB, Belk MC, Shiozawa DK, Crandall KA (2005) Empirical tests for ecological exchangeability. Anim Conserv 8:239–247CrossRef
  Rambaut A, Drummond AJ (2009) Tracer v.1.6. http://​beast.​bio.​ed.​ac.​uk/​Tracer
  Rissler LJ, Smith WH (2010) Mapping amphibian contact zones and phylogeographic break hotspots across the United States. Mol Ecol 19:5404–5416CrossRef PubMed
  Semlitsch RD, O’Donnell KM, Thompson FR III (2014) Abundance, biomass production, nutrient content, and the possible role of terrestrial salamanders in Missouri Ozark forest ecosystems. Can J Zool 92:997–1004CrossRef
  Shepard DB, Burbrink FT (2008) Lineage diversification and historical demography of a sky island salamander, Plethodon ouachitae, from the Interior Highlands. Mol Ecol 17:5315–5335CrossRef PubMed
  Shepard DB, Burbrink FT (2009) Phylogeographic and demographic effects of Pleistocene climatic fluctuations in a montane salamander, Plethodon fourchensis. Mol Ecol 18:2243–2262CrossRef PubMed
  Shepard DB, Burbrink FT (2011) Local-scale environmental variation generates highly divergent lineages associated with stream drainages in a terrestrial salamander, Plethodon caddoensis. Mol Phylogenet Evol 59:399–411CrossRef PubMed
  Sites JW Jr, Morando M, Highton R, Huber F, Jung RE (2004) Phylogenetic relationships of the endangered Shenandoah Salamander (Plethodon shenandoah) and other salamanders of the Plethodon cinereus group (Caudata: Plethodontidae). J Herpetol 38:96–105CrossRef
  Soltis DE, Morris AB, McLachlan JS, Manos PS, Soltis PS (2006) Comparative phylogeography of unglaciated eastern North America. Mol Ecol 15:4261–4293CrossRef PubMed
  Spotila JR (1972) Temperature and water in the ecology of lungless salamanders. Ecol Monogr 42:95–125CrossRef
  Stockman AK, Bond JE (2007) Delimiting cohesion species: extreme population structuring and the role of ecological interchangeability. Mol Ecol 16:3374–3392CrossRef PubMed
  Strange RM, Burr BM (1997) Intraspecific phylogeography of North American highland fishes: a test of the Pleistocene vicariance hypothesis. Evolution 51:885–897CrossRef
  Swenson NG, Howard DJ (2005) Clustering of contact zones, hybrid zones, and phylogeographic breaks in North America. Am Nat 166:581–591CrossRef PubMed
  Swets JA (1988) Measuring the accuracy of diagnostic systems. Science 240:1285–1293CrossRef PubMed
  Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739PubMedCentral CrossRef PubMed
  Wake DB (2009) What salamanders have taught us about evolution. Annu Rev Ecol Evol Syst 40:333–352CrossRef
  Watts WA (1980) The Late Quaternary vegetation history of the southeastern United States. Annu Rev Ecol Syst 11:387–409CrossRef
  Webb T III, Bartlein PJ (1992) Global changes during the last 3 million years: climatic controls and biotic responses. Annu Rev Ecol Syst 23:141–173CrossRef
  Weisrock DW, Larson A (2006) Testing hypotheses of speciation in the Plethodon jordani species complex with allozymes and mitochondrial DNA sequences. Biol J Linn Soc 89:25–51CrossRef
  Werle E, Schneider C, Renner M, Völker M, Fiehn W (1994) Convenient single-step, one tube purification of PCR products for direct sequencing. Nucl Acids Res 22:4354–4355PubMedCentral CrossRef PubMed
  Wiens JJ (2004) Speciation and ecology revisited: phylogenetic niche conservatism and the origin of species. Evolution 58:193–197CrossRef PubMed
  Wiens JJ, Graham CH (2005) Niche conservatism: integrating evolution, ecology, and conservation biology. Annu Rev Ecol Evol Syst 36:519–539CrossRef
  Wiens JJ, Engstrom TN, Chippendale PT (2006) Rapid diversification, incomplete isolation, and the “speciation clock” in North American salamanders (Genus: Plethodon): testing the hybrid swarm hypothesis of rapid radiation. Evolution 60:2585–2603PubMed
  Zachos J, Pagani M, Sloan L, Thomas E, Billups K (2001) Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292:686–693CrossRef PubMed
  
• 作者单位：Benjamin D. Thesing (1)
  Richard D. Noyes (1)
  David E. Starkey (1) (2)
  Donald B. Shepard (1)
  
  1. Department of Biology, University of Central Arkansas, 201 Donaghey Ave., LSC 180, Conway, AR, 72035, USA
  2. Department of Biology, University of the Incarnate Word, 4301 Broadway, San Antonio, TX, 78209, USA
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Evolutionary Biology
  Plant Sciences
  Human Genetics
  
• 出版者：Springer Netherlands
• ISSN：1573-8477

文摘

The southeastern United States (U.S.) has experienced dynamic climatic changes over the past several million years that have impacted species distributions. In many cases, contiguous ranges were fragmented and a lack of gene flow between allopatric populations led to genetic divergence and speciation. The Southern Red-backed Salamander, Plethodon serratus, inhabits four widely disjunct regions of the southeastern U.S.: the southern Appalachian Mountains, the Ozark Plateau, the Ouachita Mountains, and the Southern Tertiary Uplands of central Louisiana. We integrated phylogenetic analysis of mitochondrial DNA sequences (1399 base pairs) with ecological niche modeling to test the hypothesis that climate fluctuations during the Pleistocene drove the isolation and divergence of disjunct populations of P. serratus. Appalachian, Ozark, and Louisiana populations each formed well-supported clades in our phylogeny. Ouachita Mountain populations sorted into two geographically distinct clades; one Ouachita clade was sister to the Louisiana clade whereas the other Ouachita clade grouped with the Appalachian and Ozark clades but relationships were unresolved. Plethodon serratus diverged from its sister taxon, P. sherando, ~5.4 million years ago (Ma), and lineage diversification within P. serratus occurred ~1.9–0.6 Ma (Pleistocene). Ecological niche models showed that the four geographic isolates of P. serratus are currently separated by unsuitable habitat, but the species was likely more continuously distributed during the colder climates of the Pleistocene. Our results support the hypothesis that climate-induced environmental changes during the Pleistocene played a dominant role in driving isolation and divergence of disjunct populations of P. serratus. Keywords Allopatric speciation Biogeography Climate change Cryptic species Lineage diversification Ecological niche modeling