351
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Zhou WW, Wen Y, Fu J, Xu YB, Jin JQ, Ding L, Min MS, Che J, Zhang YP. Speciation in the Rana chensinensis species complex and its relationship to the uplift of the Qinghai-Tibetan Plateau. Mol Ecol 2012; 21:960-73. [PMID: 22221323 DOI: 10.1111/j.1365-294x.2011.05411.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Speciation remains a fundamental issue in biology. Herein, we report an investigation into speciation in the Rana chensinensis species complex using DNA sequence data from one mitochondrial and five nuclear genes. A phylogenetic analysis of the data revealed four major clades in the complex, and each of them was found to likely represent a species, including one cryptic species. Ecological niche models were generated from 19 climatic variables for three of the four major clades, which were represented by widespread sampling, including R. chensinensis, Rana kukunoris and the potential cryptic species. Each clade is associated with a unique ecological unit, and this indicates that ecological divergence probably drove speciation. Ecological divergence is likely related to the late Cenozoic orogenesis of the Qinghai-Tibetan Plateau. In addition, gene flow between species was detected but only in peripheral portions of the ranges of the four major clades, thus likely had little influence on the speciation processes. Discordances between mitochondrial and nuclear genes were also found; the nominal species, R. chensinensis, contains multiple maternal clades, suggesting potential mitochondrial introgression between R. chensinensis and R. kukunoris.
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Affiliation(s)
- Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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352
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Species designation of the Bruneau Dune tiger beetle (Cicindela waynei) is supported by phylogenetic analysis of mitochondrial DNA sequence data. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0295-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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353
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Tonione MA, Reeder N, Moritz CC. High genetic diversity despite the potential for stepping-stone colonizations in an invasive species of gecko on Moorea, French Polynesia. PLoS One 2011; 6:e26874. [PMID: 22073211 PMCID: PMC3206873 DOI: 10.1371/journal.pone.0026874] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 10/05/2011] [Indexed: 11/30/2022] Open
Abstract
Invasive species often have reduced genetic diversity, but the opposite can be true if there have been multiple introductions and genetic admixture. Reduced diversity is most likely soon after establishment, in remote locations, when there is lower propagule pressure and with stepping-stone colonizations. The common house gecko (Hemidactylus frenatus) was introduced to Moorea, French Polynesia in the remote eastern Pacific within the last two decades and accordingly is expected to exhibit low diversity. In contrast, we show that H. frenatus on Moorea has exceptionally high genetic diversity, similar to that near the native range in Asia and much higher than reported for other Pacific island reptiles. The high diversity in this recently founded population likely reflects extensive genetic admixture in source population(s) and a life history that promotes retention of diversity. These observations point to the importance of understanding range-wide dynamics of genetic admixture in highly invasive species.
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Affiliation(s)
- Maria A Tonione
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America.
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354
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Niemiller ML, Near TJ, Fitzpatrick BM. Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae). Evolution 2011; 66:846-866. [PMID: 22380444 DOI: 10.1111/j.1558-5646.2011.01480.x] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A major challenge facing biodiversity conservation and management is that a significant portion of species diversity remains undiscovered or undescribed. This is particularly evident in subterranean animals in which species delimitation based on morphology is difficult because differentiation is often obscured by phenotypic convergence. Multilocus genetic data constitute a valuable source of information for species delimitation in such organisms, but until recently, few methods were available to objectively test species delimitation hypotheses using genetic data. Here, we use recently developed methods for discovering and testing species boundaries and relationships using a multilocus dataset in a widely distributed subterranean teleost fish, Typhlichthys subterraneus, endemic to Eastern North America. We provide evidence that species diversity in T. subterraneus is currently underestimated and that the picture of a single, widely distributed species is not supported. Rather, several morphologically cryptic lineages comprise the diversity in this clade, including support for the recognition of T. eigenmanni. The high number of cryptic species in Typhlichthys highlights the utility of multilocus genetic data in delimiting species, particularly in lineages that exhibit slight morphological disparity, such as subterranean organisms. However, results depend on sampling of individuals and loci; this issue needs further study.
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Affiliation(s)
- Matthew L Niemiller
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, Tennessee 37996Department of Ecology and Evolutionary Biology, Yale University, 370 ESC, New Haven, Connecticut 06520 E-mail:
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, Tennessee 37996Department of Ecology and Evolutionary Biology, Yale University, 370 ESC, New Haven, Connecticut 06520 E-mail:
| | - Benjamin M Fitzpatrick
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, Tennessee 37996Department of Ecology and Evolutionary Biology, Yale University, 370 ESC, New Haven, Connecticut 06520 E-mail:
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355
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Burbrink FT, Yao H, Ingrasci M, Bryson RW, Guiher TJ, Ruane S. Speciation at the Mogollon Rim in the Arizona Mountain Kingsnake (Lampropeltis pyromelana). Mol Phylogenet Evol 2011; 60:445-54. [DOI: 10.1016/j.ympev.2011.05.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 05/06/2011] [Accepted: 05/13/2011] [Indexed: 10/18/2022]
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356
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Leavitt SD, Johnson LA, Goward T, St. Clair LL. Species delimitation in taxonomically difficult lichen-forming fungi: An example from morphologically and chemically diverse Xanthoparmelia (Parmeliaceae) in North America. Mol Phylogenet Evol 2011; 60:317-32. [DOI: 10.1016/j.ympev.2011.05.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 05/13/2011] [Accepted: 05/16/2011] [Indexed: 01/03/2023]
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357
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Zhang C, Zhang DX, Zhu T, Yang Z. Evaluation of a Bayesian Coalescent Method of Species Delimitation. Syst Biol 2011; 60:747-61. [PMID: 21876212 DOI: 10.1093/sysbio/syr071] [Citation(s) in RCA: 214] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Chi Zhang
- Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Xing Zhang
- Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianqi Zhu
- School of Mathematical Sciences, Peking University, Beijing 100871, China
| | - Ziheng Yang
- Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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358
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Uncovering cryptic species diversity of a termite community in a West African savanna. Mol Phylogenet Evol 2011; 61:964-9. [PMID: 21896335 DOI: 10.1016/j.ympev.2011.08.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 08/11/2011] [Accepted: 08/16/2011] [Indexed: 11/22/2022]
Abstract
To uncover the termite species diversity of a natural African savanna ecosystem, we combined morphological analyses and sequencing of three gene fragments (cytochrome oxidase I, cytochrome oxidase II and 28SrDNA, total length about 2450 bp) to infer putative species from phylogenetic trees. We identified 18 putative species clusters with high support values and which we retrieved consistently. Samples from two genera (Ancistrotermes and Microcerotermes) were excluded from the mitochondrial phylogenetic analyses as they might represent nuclear mitochondrial sequences (NUMTs). In total, our data suggest a species richness of at least 20 species, all but one belonging to the Termitidae (higher termites), and among them the fungus-growing Macrotermitinae were most prevalent with at least nine putative species. Within the fungus-growers the most species-rich genus was Microtermes and its four putative species were all cryptic species. Their abundance in the samples suggests that they play an important ecological role which is completely unstudied also due to the lack of reliable identification means. Our study shows that morphological traits are unreliable means of species identification for several termite taxa. Yet reliable and consistent identification is necessary for studying the functional role of termites in ecosystem and global processes.
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359
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Salicini I, Ibáñez C, Juste J. Multilocus phylogeny and species delimitation within the Natterer's bat species complex in the Western Palearctic. Mol Phylogenet Evol 2011; 61:888-98. [PMID: 21872668 DOI: 10.1016/j.ympev.2011.08.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 06/17/2011] [Accepted: 08/05/2011] [Indexed: 10/17/2022]
Abstract
Delimiting species is a crucial issue for many biological disciplines and is of primary importance for designing effective conservation plans. Traditional taxonomy based on morphological characters can be misled by the presence of phenotypic plesiomorphism or adaptative convergence. The use of multiple locus genetic data appears thus as a powerful tool for recognizing species boundaries. In this study, we used six nuclear introns and two mitochondrial markers to conduct a phylogenetic study of the Myotis nattereri species complex in the Western Palearctic. We combined tree-based and non-tree-based analyses, and also used concatenated phylogenetic methods of the separated nuclear and mitochondrial dataset as well as a recent coalescence-based multilocus approach. The strong concordance between the results of the analyses conducted confirms that M. nattereri is a paraphyletic group that is composed of four well-differentiated lineages in the study area. In the framework of the unified species concept, these four clades can be confidently considered as four valid species. This recognition of new cryptic species in the Western Mediterranean region shows that the biodiversity of this well-studied area is still not fully understood.
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Affiliation(s)
- I Salicini
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Seville, Spain.
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360
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Complex patterns of speciation in cosmopolitan “rock posy” lichens – Discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota). Mol Phylogenet Evol 2011; 59:587-602. [DOI: 10.1016/j.ympev.2011.03.020] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 12/16/2010] [Accepted: 03/17/2011] [Indexed: 11/19/2022]
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361
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Powell JR. Accounting for uncertainty in species delineation during the analysis of environmental DNA sequence data. Methods Ecol Evol 2011. [DOI: 10.1111/j.2041-210x.2011.00122.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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362
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Smith BT, Escalante P, Hernández Baños BE, Navarro-Sigüenza AG, Rohwer S, Klicka J. The role of historical and contemporary processes on phylogeographic structure and genetic diversity in the Northern Cardinal, Cardinalis cardinalis. BMC Evol Biol 2011; 11:136. [PMID: 21599972 PMCID: PMC3112092 DOI: 10.1186/1471-2148-11-136] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Accepted: 05/20/2011] [Indexed: 11/21/2022] Open
Abstract
Background Earth history events such as climate change are believed to have played a major role in shaping patterns of genetic structure and diversity in species. However, there is a lag between the time of historical events and the collection of present-day samples that are used to infer contemporary population structure. During this lag phase contemporary processes such as dispersal or non-random mating can erase or reinforce population differences generated by historical events. In this study we evaluate the role of both historical and contemporary processes on the phylogeography of a widespread North American songbird, the Northern Cardinal, Cardinalis cardinalis. Results Phylogenetic analysis revealed deep mtDNA structure with six lineages across the species' range. Ecological niche models supported the same geographic breaks revealed by the mtDNA. A paleoecological niche model for the Last Glacial Maximum indicated that cardinals underwent a dramatic range reduction in eastern North America, whereas their ranges were more stable in México. In eastern North America cardinals expanded out of glacial refugia, but we found no signature of decreased genetic diversity in areas colonized after the Last Glacial Maximum. Present-day demographic data suggested that population growth across the expansion cline is positively correlated with latitude. We propose that there was no loss of genetic diversity in areas colonized after the Last Glacial Maximum because recent high-levels of gene flow across the region have homogenized genetic diversity in eastern North America. Conclusion We show that both deep historical events as well as demographic processes that occurred following these events are critical in shaping genetic pattern and diversity in C. cardinalis. The general implication of our results is that patterns of genetic diversity are best understood when information on species history, ecology, and demography are considered simultaneously.
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363
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BARRETT CRAIGF, FREUDENSTEIN JOHNV. An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid. Mol Ecol 2011; 20:2771-86. [DOI: 10.1111/j.1365-294x.2011.05124.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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364
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Phylogenetic structure and species boundaries in the mountain pitviper Ovophis monticola (Serpentes: Viperidae: Crotalinae) in Asia. Mol Phylogenet Evol 2011; 59:444-57. [DOI: 10.1016/j.ympev.2011.02.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 02/04/2011] [Accepted: 02/05/2011] [Indexed: 11/23/2022]
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365
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Bauer AM, Parham JF, Brown RM, Stuart BL, Grismer L, Papenfuss TJ, Böhme W, Savage JM, Carranza S, Grismer JL, Wagner P, Schmitz A, Ananjeva NB, Inger RF. Availability of new Bayesian-delimited gecko names and the importance of character-based species descriptions. Proc Biol Sci 2011; 278:490-2; discussion 493-5. [PMID: 20961901 PMCID: PMC3025678 DOI: 10.1098/rspb.2010.1330] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Accepted: 07/27/2010] [Indexed: 11/12/2022] Open
Affiliation(s)
- Aaron M. Bauer
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA
| | - James F. Parham
- Alabama Museum of Natural History, University of Alabama, Box 870340, Tuscaloosa, AL 35487, USA
| | - Rafe M. Brown
- Natural History Museum and Biodiversity Research Center and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Blvd, Dyche Hall, University of Kansas, Lawrence, KS 66045, USA
| | - Bryan L. Stuart
- North Carolina Museum of Natural Sciences, 11 West Jones Street, Raleigh, NC 27601, USA
| | - Lee Grismer
- Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, CA 92515, USA
| | | | - Wolfgang Böhme
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Jay M. Savage
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Jesse L. Grismer
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA
- Natural History Museum and Biodiversity Research Center and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Blvd, Dyche Hall, University of Kansas, Lawrence, KS 66045, USA
| | - Philipp Wagner
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Andreas Schmitz
- Department of Herpetology and Ichthyology, Muséum d'Histoire Naturelle, C.P. 6434, CH-1211, Genèva 6, Switzerland
| | - Natalia B. Ananjeva
- Division of Herpetology and Ornithology, Zoological Institute, Russian Academy of Sciences, Universitetskaya nab.,1, St Petersburg 199034, Russia
| | - Robert F. Inger
- Division of Amphibians and Reptiles, The Field Museum of Natural History, Chicago, IL, USA
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366
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Fujita MK, Leaché AD. A coalescent perspective on delimiting and naming species: a reply to Bauer
et al. Proc Biol Sci 2010. [DOI: 10.1098/rspb.2010.1864] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Matthew K. Fujita
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Adam D. Leaché
- Burke Museum and Department of Biology, University of Washington, Seattle, WA 98195, USA
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367
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South Asia supports a major endemic radiation of Hemidactylus geckos. Mol Phylogenet Evol 2010; 57:343-52. [PMID: 20601010 DOI: 10.1016/j.ympev.2010.06.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 06/20/2010] [Accepted: 06/21/2010] [Indexed: 11/21/2022]
Abstract
Hemidactylus geckos are a species-rich component of many tropical lizard assemblages. We sampled deeply among tropical Asian, and especially South Asian, taxa and used a multi-gene approach to establish the affinities of Indian and Sri Lankan Hemidactylus and to evaluate the monophyly of previously proposed taxa within the genus. There is only weak support for the monophyly of tropical Asian Hemidactylus as a whole, but two strongly supported subclades were retrieved: the bowringii group is a predominantly East Asian clade that reaches South Asia only peripherally; the brookii group is a morphologically diverse clade that represents a previously unrecognized, species-rich (25 species), chiefly South Asian radiation. Deep genetic divergences support the specific recognition of three Sri Lankan taxa previously regarded as subspecies of mainland forms and validate H. subtriedrus as a species distinct from H. triedrus. Unlike several other vertebrate groups, Sri Lankan Hemidactylus do not represent a single insular radiation. Rather, each of six Sri Lankan species reached the island independently from different continental sources. There have been extensive Quaternary land connections between India and Sri Lanka but sister-species pairs of Hemidactylus on the two land masses diverged from one another much earlier, probably in the mid-Miocene.
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