801
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Burton RS, Pereira RJ, Barreto FS. Cytonuclear Genomic Interactions and Hybrid Breakdown. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135758] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ronald S. Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202; , ,
| | - Ricardo J. Pereira
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202; , ,
| | - Felipe S. Barreto
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202; , ,
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802
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Cordero D, Peña JB, Saavedra C. Phylogeographic analysis of introns and mitochondrial DNA in the clam Ruditapes decussatus uncovers the effects of Pleistocene glaciations and endogenous barriers to gene flow. Mol Phylogenet Evol 2013; 71:274-87. [PMID: 24269315 DOI: 10.1016/j.ympev.2013.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 10/30/2013] [Accepted: 11/06/2013] [Indexed: 12/22/2022]
Abstract
Studies on the phylogeography of species inhabiting the Mediterranean and the nearby coasts of the NE Atlantic Ocean (MEDAT) have found subdivision and/or phylogeographic structure in one or more of the Atlantic, western Mediterranean and eastern Mediterranean basins. This structure has been explained as the result of past population fragmentation caused by Pleistocene sea level changes and current patterns of marine circulation. However, the increasing use of nuclear markers has revealed that these two factors alone are not enough to explain the phylogeographic patterns, and an additional role has been suggested for endogenous barriers to gene flow or natural selection. In this article we examined the role of these factors in Ruditapes decussatus, a commercial clam species native to MEDAT. A genetic analysis of 11 populations was carried out by examining 6 introns with a PCR-RFLP technique. We found subdivision in three regions: Atlantic (ATL), western Mediterranean plus Tunisia (WMED), and Aegean and Adriatic seas (AEGAD). Two introns (Ech and Tbp) showed alleles that were restricted to AEGAD. Sequencing a subsample of individuals for these introns indicated that AEGAD-specific alleles were separate clades, thus revealing a phylogeographic brake at the WMED-AEGAD boundary. Sequencing of the mitochondrial COI locus confirmed this phylogeographic break. Dating of the AEGAD mitochondrial haplotypes and nuclear alleles with a Bayesian MCMC method revealed that they shared common ancestors in the Pleistocene. These results can be explained in the framework of Pleistocene sea level drops and patterns of gene flow in MEDAT. An additional observation was a lack of differentiation at COI between the ATL and WMED, in sharp contrast with 4 introns that showed clear genetic subdivision. Neutrality tests did not support the hypothesis of a selective sweep acting on mtDNA to explain the contrasting levels of differentiation between mitochondrial and nuclear markers across the ATL-WMED transition, and we argue that the difference between markers is best explained by the existence of an endogenous genetic barrier, rather than by a physical barrier to larval migration alone.
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Affiliation(s)
- David Cordero
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, 12595 Ribera de Cabanes (Castellón), Spain
| | - Juan B Peña
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, 12595 Ribera de Cabanes (Castellón), Spain
| | - Carlos Saavedra
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, 12595 Ribera de Cabanes (Castellón), Spain.
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803
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Haye PA, Muñoz-Herrera NC. Isolation with differentiation followed by expansion with admixture in the tunicate Pyura chilensis. BMC Evol Biol 2013; 13:252. [PMID: 24238017 PMCID: PMC3840596 DOI: 10.1186/1471-2148-13-252] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 10/29/2013] [Indexed: 11/21/2022] Open
Abstract
Background Pyura chilensis, a tunicate commercially exploited as food resource in Chile, is subject to management strategies, including restocking. The goal of this study was to examine the genetic structure of P. chilensis using information from a mitochondrial gene (Cytochrome Oxidase I, COI) and a nuclear gene (Elongation 1 alpha, EF1a), to characterize the geographic distribution of genetic diversity and differentiation, and to identify the main processes that have shaped it. We analyzed 268 and 208 sequences of COI and EF1a, respectively, from samples of eight local populations covering ca. 1800 km. Results For Pyura chilensis, partial sequences of the gene COI revealed three highly supported haplogroups that diverged 260000 to 470000 years ago. Two haplogroups currently are widely distributed and sympatric, while one is dominant only in Los Molinos (LM, 39°50′S). The two widespread COI haplogroups underwent a geographic expansion during an interglacial period of the Late Pleistocene ca. 100000 years ago. The nuclear gene was less divergent and did not resolve the COI haplogroups. Bayesian clustering of the nuclear gene’s SNPs revealed that individuals from the two widespread COI haplogroups were mostly assigned to two of the three detected clusters and had a marked degree of admixture. The third cluster predominated in LM and showed low admixture. Haplotypic diversity of both genes was very high, there was no isolation by distance, and most localities were genetically undifferentiated; only LM was consistently differentiated with both genes analyzed. Conclusions Pyura chilensis has less genetic structure than expected given its life history, which could be a consequence of dispersal on ship hulls. The only differentiated local population analyzed was LM. Coincidentally, it is the one furthest away from main maritime routes along the coast of Chile. The use of mitochondrial and nuclear markers allowed detection of divergent mitochondrial haplogroups in P. chilensis, two of which revealed nuclear admixture. The genetic structure of P. chilensis has likely been shaped by Pleistocene’s climatic effect on sea level leading to population contraction with isolation, followed by geographic range expansions with concomitant secondary contact and admixture.
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Affiliation(s)
- Pilar A Haye
- Laboratorio de Diversidad Molecular, Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Casilla 117, Coquimbo, Chile.
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804
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Zhang L, An B, Backström N, Liu N. Phylogeography-Based Delimitation of Subspecies Boundaries in the Common Pheasant (Phasianus colchicus). Biochem Genet 2013; 52:38-51. [DOI: 10.1007/s10528-013-9626-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 07/31/2013] [Indexed: 11/28/2022]
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805
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Segatto ALA, Cazé ALR, Turchetto C, Klahre U, Kuhlemeier C, Bonatto SL, Freitas LB. Nuclear and plastid markers reveal the persistence of genetic identity: a new perspective on the evolutionary history of Petunia exserta. Mol Phylogenet Evol 2013; 70:504-12. [PMID: 24161675 DOI: 10.1016/j.ympev.2013.10.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/27/2013] [Accepted: 10/11/2013] [Indexed: 12/01/2022]
Abstract
Recently divergent species that can hybridize are ideal models for investigating the genetic exchanges that can occur while preserving the species boundaries. Petunia exserta is an endemic species from a very limited and specific area that grows exclusively in rocky shelters. These shaded spots are an inhospitable habitat for all other Petunia species, including the closely related and widely distributed species P. axillaris. Individuals with intermediate morphologic characteristics have been found near the rocky shelters and were believed to be putative hybrids between P. exserta and P. axillaris, suggesting a situation where Petunia exserta is losing its genetic identity. In the current study, we analyzed the plastid intergenic spacers trnS/trnG and trnH/psbA and six nuclear CAPS markers in a large sampling design of both species to understand the evolutionary process occurring in this biological system. Bayesian clustering methods, cpDNA haplotype networks, genetic diversity statistics, and coalescence-based analyses support a scenario where hybridization occurs while two genetic clusters corresponding to two species are maintained. Our results reinforce the importance of coupling differentially inherited markers with an extensive geographic sample to assess the evolutionary dynamics of recently diverged species that can hybridize.
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Affiliation(s)
- Ana Lúcia Anversa Segatto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
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806
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High cryptic diversity across the global range of the migratory planktonic copepods Pleuromamma piseki and P. gracilis. PLoS One 2013; 8:e77011. [PMID: 24167556 PMCID: PMC3805563 DOI: 10.1371/journal.pone.0077011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/28/2013] [Indexed: 11/25/2022] Open
Abstract
Although holoplankton are ocean drifters and exhibit high dispersal potential, a number of studies on single species are finding highly divergent genetic clades. These cryptic species complexes are important to discover and describe, as identification of common marine species is fundamental to understanding ecosystem dynamics. Here we investigate the global diversity within Pleuromamma piseki and P. gracilis, two dominant members of the migratory zooplankton assemblage in subtropical and tropical waters worldwide. Using DNA sequence data from the mitochondrial gene cytochrome c oxidase subunit II (mtCOII) from 522 specimens collected across the Pacific, Atlantic and Indian Oceans, we discover twelve well-resolved genetically distinct clades in this species complex (Bayesian posterior probabilities >0.7; 6.3–17% genetic divergence between clades). The morphologically described species P. piseki and P. gracilis did not form monophyletic groups, rather they were distributed throughout the phylogeny and sometimes co-occurred within well-resolved clades: this result suggests that morphological characters currently used for taxonomic identification of P. gracilis and P. piseki may be inaccurate as indicators of species’ boundaries. Cryptic clades within the species complex ranged from being common to rare, and from cosmopolitan to highly restricted in distribution across the global ocean. These novel lineages appear to be ecologically divergent, with distinct biogeographic distributions across varied pelagic habitats. We hypothesize that these mtDNA lineages are distinct species and suggest that resolving their systematic status is important, given the ecological significance of the genus Pleuromamma in subtropical-tropical waters worldwide.
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807
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Petrou EL, Seeb JE, Hauser L, Witteveen MJ, Templin WD, Seeb LW. Fine-scale sampling reveals distinct isolation by distance patterns in chum salmon (Oncorhynchus keta) populations occupying a glacially dynamic environment. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0534-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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808
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Hulsey CD, García-de-León FJ. Introgressive hybridization in a trophically polymorphic cichlid. Ecol Evol 2013; 3:4536-47. [PMID: 24340193 PMCID: PMC3856752 DOI: 10.1002/ece3.841] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 09/10/2013] [Accepted: 09/17/2013] [Indexed: 11/09/2022] Open
Abstract
Trophically polymorphic species could represent lineages that are rapidly diverging along an ecological axis or could phenotypically mark the collapse of species through introgressive hybridization. We investigated patterns of introgression between the trophically polymorphic cichlid fish Herichthys minckleyi and its relative H. cyanoguttatus using a combination of population genetics and species tree analyses. We first examined the distribution of mitochondrial haplotypes within the alternative H. minckleyi pharyngeal jaw morphotypes that are endemic to the small desert valley of Cuatro Ciénegas. We recovered two clusters of mitochondrial haplotypes. The first contained a number of slightly differentiated cytochrome b (cytb) haplotypes that showed some phylogeographic signal and were present in both jaw morphotypes. The other haplotype was monomorphic, highly differentiated from the other cluster, present in equal frequencies in the morphotypes, and identical to H. cyanoguttatus haplotypes found outside Cuatro Ciénegas. Then, we investigated whether H. minckleyi individuals with the H. cyanoguttatus cytb were more evolutionarily similar to H. cyanoguttatus or other H. minckleyi using a species tree analysis of 84 nuclear loci. Both H. minckleyi pharyngeal morphotypes, regardless of their cytb haplotype, were quite distinct from H. cyanoguttatus. However, hybridization could be blurring subdivision within H. minckleyi as the alternative jaw morphotypes were not genetically distinct from one another. Accounting for introgression from H. cyanoguttatus will be essential to understand the evolution of the trophically polymorphic cichlid H. minckleyi.
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Affiliation(s)
- C Darrin Hulsey
- Department of Ecology and Evolutionary Biology, University of Tennessee 569 Dabney Hall, Knoxville, Tennessee, 37996
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809
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Singhal S, Moritz C. Reproductive isolation between phylogeographic lineages scales with divergence. Proc Biol Sci 2013; 280:20132246. [PMID: 24107536 DOI: 10.1098/rspb.2013.2246] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogeographic studies frequently reveal multiple morphologically cryptic lineages within species. What is not yet clear is whether such lineages represent nascent species or evolutionary ephemera. To address this question, we compare five contact zones, each of which occurs between ecomorphologically cryptic lineages of skinks from the rainforests of the Australian Wet Tropics. Although the contacts probably formed concurrently in response to Holocene expansion from glacial refugia, we estimate that the divergence times (τ) of the lineage pairs range from 3.1 to 11.5 Ma. Multi-locus analyses of the contact zones yielded estimates of reproductive isolation that are tightly correlated with divergence time and, for lineages with older divergence times (τ > 5 Myr), substantial. These results show that phylogeographic splits of increasing depth represent stages along the speciation continuum, even in the absence of overt change in ecologically relevant morphology.
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Affiliation(s)
- Sonal Singhal
- Museum of Vertebrate Zoology, University of California, , 3101 Valley Life Sciences Building, Berkeley, CA 94720-3160, USA, Department of Integrative Biology, University of California, , 1005 Valley Life Sciences Building, Berkeley, CA 94720-3140, USA, Research School of Biology, The Australian National University, , Building 116, Acton, Australian Capital Territory 0200, Australia
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810
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Pons JM, Sonsthagen S, Dove C, Crochet PA. Extensive mitochondrial introgression in North American Great Black-backed Gulls (Larus marinus) from the American Herring Gull (Larus smithsonianus) with little nuclear DNA impact. Heredity (Edinb) 2013; 112:226-39. [PMID: 24105440 DOI: 10.1038/hdy.2013.98] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 07/31/2013] [Accepted: 08/15/2013] [Indexed: 11/09/2022] Open
Abstract
Recent genetic studies have shown that introgression rates among loci may greatly vary according to their location in the genome. In particular, several cases of mito-nuclear discordances have been reported for a wide range of organisms. In the present study, we examine the causes of discordance between mitochondrial (mtDNA) and nuclear DNA introgression detected in North American populations of the Great Black-backed Gull (Larus marinus), a Holarctic species, from the Nearctic North American Herring Gull (Larus smithsonianus). Our results show that extensive unidirectional mtDNA introgression from Larus smithsonianus into Larus marinus in North America cannot be explained by ancestral polymorphism but most likely results from ancient hybridization events occurring when Larus marinus invaded the North America. Conversely, our nuclear DNA results based on 12 microsatellites detected very little introgression from Larus smithsonianus into North American Larus marinus. We discuss these results in the framework of demographic and selective mechanisms that have been postulated to explain mito-nuclear discrepancies. We were unable to demonstrate selection as the main cause of mito-nuclear introgression discordance but cannot dismiss the possible role of selection in the observed pattern. Among demographic explanations, only drift in small populations and bias in mate choice in an invasive context may explain our results. As it is often difficult to demonstrate that selection may be the main factor driving the introgression of mitochondrial DNA in natural populations, we advocate that evaluating alternative demographic neutral hypotheses may help to indirectly support or reject hypotheses invoking selective processes.
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Affiliation(s)
- J-M Pons
- 1] UMR7205 Origine, Structure et Evolution de la Biodiversité, Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Paris, France [2] Service de Systématique Moléculaire, UMS 2700, Muséum National d'Histoire Naturelle, Paris, France
| | - S Sonsthagen
- Department of Vertebrate Zoology, Division of Birds, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - C Dove
- Department of Vertebrate Zoology, Division of Birds, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - P-A Crochet
- CNRS-UMR5175 CEFE, Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier Cedex 5, France
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811
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Jennings RM, Etter RJ, Ficarra L. Population differentiation and species formation in the deep sea: the potential role of environmental gradients and depth. PLoS One 2013; 8:e77594. [PMID: 24098590 PMCID: PMC3788136 DOI: 10.1371/journal.pone.0077594] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/12/2013] [Indexed: 11/19/2022] Open
Abstract
Ecological speciation probably plays a more prominent role in diversification than previously thought, particularly in marine ecosystems where dispersal potential is great and where few obvious barriers to gene flow exist. This may be especially true in the deep sea where allopatric speciation seems insufficient to account for the rich and largely endemic fauna. Ecologically driven population differentiation and speciation are likely to be most prevalent along environmental gradients, such as those attending changes in depth. We quantified patterns of genetic variation along a depth gradient (1600-3800m) in the western North Atlantic for a protobranch bivalve (Nuculaatacellana) to test for population divergence. Multilocus analyses indicated a sharp discontinuity across a narrow depth range, with extremely low gene flow inferred between shallow and deep populations for thousands of generations. Phylogeographical discordance occurred between nuclear and mitochondrial loci as might be expected during the early stages of species formation. Because the geographic distance between divergent populations is small and no obvious dispersal barriers exist in this region, we suggest the divergence might reflect ecologically driven selection mediated by environmental correlates of the depth gradient. As inferred for numerous shallow-water species, environmental gradients that parallel changes in depth may play a key role in the genesis and adaptive radiation of the deep-water fauna.
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Affiliation(s)
- Robert M. Jennings
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Ron J. Etter
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Lynn Ficarra
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
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812
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Yang JQ, Tang WQ, Sun Y, Tsai KC, Zhou ZC, Liu ZZ, Liu D, Lin HD. Microsatellite diversity and population genetic structure of Squalidus argentatus (Cyprinidae) on the Island of Hainan and mainland China. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.03.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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813
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Wares JP. Mitochondrial evolution across lineages of the vampire barnacle Notochthamalus scabrosus. ACTA ACUST UNITED AC 2013; 26:7-10. [DOI: 10.3109/19401736.2013.825791] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- John P. Wares
- Department of Genetics, University of Georgia, Athens, GA, USA
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814
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Toews DPL, Mandic M, Richards JG, Irwin DE. MIGRATION, MITOCHONDRIA, AND THE YELLOW-RUMPED WARBLER. Evolution 2013; 68:241-55. [DOI: 10.1111/evo.12260] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 08/15/2013] [Indexed: 01/05/2023]
Affiliation(s)
- David P. L. Toews
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
| | - Milica Mandic
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
| | - Jeffrey G. Richards
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
| | - Darren E. Irwin
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
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815
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Baselga A, Gómez-Rodríguez C, Novoa F, Vogler AP. Rare failures of DNA barcodes [corrected] to separate morphologically distinct species in a biodiversity survey of Iberian leaf beetles. PLoS One 2013; 8:e74854. [PMID: 24040352 PMCID: PMC3764165 DOI: 10.1371/journal.pone.0074854] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 08/06/2013] [Indexed: 11/19/2022] Open
Abstract
During a survey of genetic and species diversity patterns of leaf beetle (Coleoptera: Chrysomelidae) assemblages across the Iberian Peninsula we found a broad congruence between morphologically delimited species and variation in the cytochrome oxidase (cox1) gene. However, one species pair each in the genera Longitarsus Berthold and Pachybrachis Chevrolat was inseparable using molecular methods, whereas diagnostic morphological characters (including male or female genitalia) unequivocally separated the named species. Parsimony haplotype networks and maximum likelihood trees built from cox1 showed high genetic structure within each species pair, but no correlation with the morphological types and neither with geographic distributions. This contrasted with all analysed congeneric species, which were recovered as monophyletic. A limited number of specimens were sequenced for the nuclear 18S rRNA gene, which showed no or very limited variation within the species pair and no separation of morphological types. These results suggest that processes of lineage sorting for either group are lagging behind the clear morphological and presumably reproductive separation. In the Iberian chrysomelids, incongruence between DNA-based and morphological delimitations is a rare exception, but the discovery of these species pairs may be useful as an evolutionary model for studying the process of speciation in this ecological and geographical setting. In addition, the study of biodiversity patterns based on DNA requires an evolutionary understanding of these incongruences and their potential causes.
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Affiliation(s)
- Andrés Baselga
- Departamento de Zoología, Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
- * E-mail:
| | - Carola Gómez-Rodríguez
- Departamento de Zoología, Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Francisco Novoa
- Departamento de Zoología, Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alfried P. Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom
- Division of Biology, Imperial College London, Ascot, United Kingdom
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816
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Rodríguez V, Brown RP, Terrasa B, Pérez-Mellado V, Castro JA, Picornell A, Ramon MM. Multilocus genetic diversity and historical biogeography of the endemic wall lizard from Ibiza and Formentera,Podarcis pityusensis(Squamata: Lacertidae). Mol Ecol 2013; 22:4829-41. [DOI: 10.1111/mec.12443] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 07/04/2013] [Accepted: 07/04/2013] [Indexed: 11/29/2022]
Affiliation(s)
- V. Rodríguez
- Laboratori de Genètica; Universitat de les Illes Balears; 07122 Palma de Mallorca Spain
| | - R. P. Brown
- School of Natural Sciences & Psychology; Liverpool John Moores University; L3 3AF Liverpool UK
| | - B. Terrasa
- Laboratori de Genètica; Universitat de les Illes Balears; 07122 Palma de Mallorca Spain
| | - V. Pérez-Mellado
- Department of Animal Biology; Universidad de Salamanca; 37071 Salamanca Spain
| | - J. A. Castro
- Laboratori de Genètica; Universitat de les Illes Balears; 07122 Palma de Mallorca Spain
| | - A. Picornell
- Laboratori de Genètica; Universitat de les Illes Balears; 07122 Palma de Mallorca Spain
| | - M. M. Ramon
- Laboratori de Genètica; Universitat de les Illes Balears; 07122 Palma de Mallorca Spain
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817
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Paczesniak D, Jokela J, Larkin K, Neiman M. Discordance between nuclear and mitochondrial genomes in sexual and asexual lineages of the freshwater snail Potamopyrgus antipodarum. Mol Ecol 2013; 22:4695-710. [PMID: 23957656 DOI: 10.1111/mec.12422] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 05/29/2013] [Accepted: 06/05/2013] [Indexed: 11/30/2022]
Abstract
The presence and extent of mitonuclear discordance in coexisting sexual and asexual lineages provides insight into 1) how and when asexual lineages emerged, and 2) the spatial and temporal scales at which the ecological and evolutionary processes influencing the evolution of sexual and asexual reproduction occur. Here, we used nuclear single-nucleotide polymorphism (SNP) markers and a mitochondrial gene to characterize phylogeographic structure and the extent of mitonuclear discordance in Potamopyrgus antipodarum. This New Zealand freshwater snail is often used to study the evolution and maintenance of sex because obligately sexual and obligately asexual individuals often coexist. While our data indicate that sexual and asexual P. antipodarum sampled from the same lake population are often genetically similar, suggesting recent origin of these asexuals from sympatric sexual P. antipodarum, we also found significantly more population structure in sexuals vs. asexuals. This latter result suggests that some asexual lineages originated in other lakes and/or in the relatively distant past. When comparing mitochondrial and nuclear population genetic structure, we discovered that one mitochondrial haplotype ('1A') was rare in sexuals, but common and widespread in asexuals. Haplotype 1A frequency and nuclear genetic diversity were not associated, suggesting that the commonness of this haplotype cannot be attributed entirely to genetic drift and pointing instead to a role for selection.
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Affiliation(s)
- Dorota Paczesniak
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland; Department of Environmental Systems Science, ETH-Zürich, Universitätstrasse 16, 8092, Zürich, Switzerland
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818
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Balakirev ES, Romanov NS, Mikheev PB, Ayala FJ. Mitochondrial DNA variation and introgression in Siberian taimen Hucho taimen. PLoS One 2013; 8:e71147. [PMID: 23951096 PMCID: PMC3741329 DOI: 10.1371/journal.pone.0071147] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/22/2013] [Indexed: 11/18/2022] Open
Abstract
Siberian taimen Hucho taimen is the largest representative of the family Salmonidae inhabiting rivers of northern Eurasia. The species is under intensive aquaculture activity. To monitor natural taimen populations we have sequenced a portion (8,141 bp) of the mitochondrial (mt) genome in 28 specimens of H. taimen from six localities in the Amur River basin. Nucleotide variability is low (π = 0.0010), but structured in two divergent haplotype groups. A comparison of the data with the GenBank H. taimen mt genome (HQ897271) reveals significant differences between them in spite of the fact that the fish specimens come from neighboring geographical areas. The distribution of divergence is non-uniform with two highly pronounced divergent regions centered on two genes, ND3 and ND6. To clarify the pattern of divergence we sequenced the corresponding portion of the mt genome of lenok Brachymystax tumensis and analyzed the GenBank complete mt genomes of related species. We have found that the first and second divergent regions are identical between the GenBank H. taimen and two lenok subspecies, B. lenok and B. lenok tsinlingensis, respectively. Consequently, both divergent regions represent introgressed mtDNA resulting from intergeneric hybridization between the two lenok subspecies and H. taimen. Introgression is, however, not detected in our specimens. This plus the precise identity of the introgressed fragments between the donor and the recipient GenBank sequence suggests that the introgression is local and very recent, probably due to artificial manipulations involving taimen – lenok intergeneric hybridization. Human-mediated hybridization may become a major threat to aquatic biodiversity. Consequently we suggest that due attention needs to be given to this threat by means of responsible breeding program management, so as to prevent a potential spread of hybrid fishes that could jeopardize the resilience of locally adapted gene pools of the native H. taimen populations.
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Affiliation(s)
- Evgeniy S Balakirev
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA.
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819
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Říčanová Š, Koshev Y, Říčan O, Ćosić N, Ćirović D, Sedláček F, Bryja J. Multilocus phylogeography of the European ground squirrel: cryptic interglacial refugia of continental climate in Europe. Mol Ecol 2013; 22:4256-4269. [PMID: 23879230 DOI: 10.1111/mec.12382] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 05/07/2013] [Accepted: 05/09/2013] [Indexed: 11/30/2022]
Abstract
The theory of classical and cryptic Pleistocene refugia is based mainly on historical changes in temperature, and the refugia are usually defined within a latitudinal gradient. However, the gradient of oceanic-continental climate (i.e. longitudinal) was also significantly variable during glacial cycles with important biotic consequences. Range-wide phylogeography of the European ground squirrel (EGS) was used to interpret the evolutionary and palaeogeographical history of the species in Europe and to shed light on its glacial-interglacial dynamic. The EGS is a steppe-inhabiting species and the westernmost member of the genus in the Palaearctic region. We have analysed 915 specimens throughout the present natural range by employing mitochondrial DNA sequences (cytochrome b gene) and 12 nuclear microsatellite markers. The reconstructed phylogeography divides the species into two main geographical groups, with deep substructuring within both groups. Bulgaria is the centre of the ancestral area, and it also has the highest genetic diversity within the species. The northernmost group of the EGS survived in the southern part of Pannonia throughout several glacial-interglacial cycles. Animals from this population probably repeatedly colonized areas further to the north and west during the glacial periods, while in the interglacial periods, the EGS distribution contracted back to this Pannonian refugium. The EGS thus represents a species with a glacial expansion/interglacial contraction palaeogeographical dynamics, and the Pannonian and southeastern Balkanian steppes are supported as cryptic refugia of continental climate during Pleistocene interglacials.
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Affiliation(s)
- Štěpánka Říčanová
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65, Brno, Czech Republic
| | - Yordan Koshev
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Science, 1 Tzar Osvoboditel blvb, 1000, Sofia, Bulgaria
| | - Oldřich Říčan
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Nada Ćosić
- Institute for Biological Research Siniša Stanković, University of Belgrade, Bulevar despota Stefana 142, 11000, Belgrade, Serbia
| | - Duško Ćirović
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia
| | - František Sedláček
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65, Brno, Czech Republic.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
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820
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Marková S, Dufresne F, Manca M, Kotlík P. Mitochondrial capture misleads about ecological speciation in the Daphnia pulex complex. PLoS One 2013; 8:e69497. [PMID: 23869244 PMCID: PMC3711805 DOI: 10.1371/journal.pone.0069497] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 06/11/2013] [Indexed: 11/18/2022] Open
Abstract
The North American ecological species Daphniapulicaria and Daphniapulex are thought to have diverged from a common ancestor by adaptation to sympatric but ecologically distinct lake and pond habitats respectively. Based on mtDNA relationships, European D. pulicaria is considered a different species only distantly related to its North American counterpart, but both species share a lactate dehydrogenase (Ldh) allele F supposedly involved in lake adaptation in North America, and the same allele is also carried by the related Holarctic Daphniatenebrosa. The correct inference of the species' ancestral relationships is therefore critical for understanding the origin of their adaptive divergence. Our species tree inferred from unlinked nuclear loci for D. pulicaria and D. pulex resolved the European and North American D. pulicaria as sister clades, and we argue that the discordant mtDNA gene tree is best explained by capture of D. pulex mtDNA by D. pulicaria in North America. The Ldh gene tree shows that F-class alleles in D. pulicaria and D. tenebrosa are due to common descent (as opposed to introgression), with D. tenebrosa alleles paraphyletic with respect to D. pulicaria alleles. That D. tenebrosa still segregates the ancestral and derived amino acids at the two sites distinguishing the pond and lake alleles suggests that D. pulicaria inherited the derived states from the D. tenebrosa ancestry. Our results suggest that some adaptations restricting the gene flow between D. pulicaria and D. pulex might have evolved in response to selection in ancestral environments rather than in the species' current sympatric habitats. The Arctic (D. tenebrosa) populations are likely to provide important clues about these issues.
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Affiliation(s)
- Silvia Marková
- Institute of Animal Physiology and Genetics, Laboratory of Molecular Ecology, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic
| | - France Dufresne
- Département de Biologie, Centre d’Études Nordiques, Université du Québec à Rimouski, Québec, Canada
| | - Marina Manca
- CNR Istituto per lo Studio degli Ecosistemi, Verbania, Italy
| | - Petr Kotlík
- Institute of Animal Physiology and Genetics, Laboratory of Molecular Ecology, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic
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821
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Causes and evolutionary consequences of population subdivision of an Iberian mountain lizard, Iberolacerta monticola. PLoS One 2013; 8:e66034. [PMID: 23762459 PMCID: PMC3676366 DOI: 10.1371/journal.pone.0066034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 05/06/2013] [Indexed: 11/30/2022] Open
Abstract
Aim The study of the factors that influence population connectivity and spatial distribution of genetic variation is crucial for understanding speciation and for predicting the effects of landscape modification and habitat fragmentation, which are considered severe threats to global biodiversity. This dual perspective is obtained from analyses of subalpine mountain species, whose present distribution may have been shaped both by cyclical climate changes over ice ages and anthropogenic perturbations of their habitats. Here, we examine the phylogeography, population structure and genetic diversity of the lacertid lizard Iberolacerta monticola, an endemism considered to be facing a high risk of extinction in several populations. Location Northwestern quadrant of the Iberian Peninsula. Methods We analyzed the mtDNA variation at the control region (454 bp) and the cytochrome b (598 bp) loci, as well as at 10 nuclear microsatellite loci from 17 populations throughout the distribution range of the species. Results According to nuclear markers, most sampling sites are defined as distinct, genetically differentiated populations, and many of them show traces of recent bottlenecks. Mitochondrial data identify a relatively old, geographically restricted lineage, and four to six younger geographically vicariant sister clades, whose origin may be traced back to the mid-Pleistocene revolution, with several subclades possibly associated to the mid-Bruhnes transition. Geographic range fragmentation of one of these clades, which includes lowland sites, is very recent, and most likely due to the accelerated loss of Atlantic forests by human intervention. Main Conclusions Altogether, the data fit a “refugia within refugia” model, some lack of pattern uniformity notwithstanding, and suggest that these mountains might be the cradles of new species of Iberolacerta. However, the changes operated during the Holocene severely compromise the long-term survival of those genetic lineages more exposed to the anthropogenic perturbations of their habitats.
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822
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A genome-wide survey of genetic variation in gorillas using reduced representation sequencing. PLoS One 2013; 8:e65066. [PMID: 23750230 PMCID: PMC3672199 DOI: 10.1371/journal.pone.0065066] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 04/22/2013] [Indexed: 11/19/2022] Open
Abstract
All non-human great apes are endangered in the wild, and it is therefore important to gain an understanding of their demography and genetic diversity. Whole genome assembly projects have provided an invaluable foundation for understanding genetics in all four genera, but to date genetic studies of multiple individuals within great ape species have largely been confined to mitochondrial DNA and a small number of other loci. Here, we present a genome-wide survey of genetic variation in gorillas using a reduced representation sequencing approach, focusing on the two lowland subspecies. We identify 3,006,670 polymorphic sites in 14 individuals: 12 western lowland gorillas (Gorilla gorilla gorilla) and 2 eastern lowland gorillas (Gorilla beringei graueri). We find that the two species are genetically distinct, based on levels of heterozygosity and patterns of allele sharing. Focusing on the western lowland population, we observe evidence for population substructure, and a deficit of rare genetic variants suggesting a recent episode of population contraction. In western lowland gorillas, there is an elevation of variation towards telomeres and centromeres on the chromosomal scale. On a finer scale, we find substantial variation in genetic diversity, including a marked reduction close to the major histocompatibility locus, perhaps indicative of recent strong selection there. These findings suggest that despite their maintaining an overall level of genetic diversity equal to or greater than that of humans, population decline, perhaps associated with disease, has been a significant factor in recent and long-term pressures on wild gorilla populations.
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823
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Arthofer W, Rauch H, Thaler-Knoflach B, Moder K, Muster C, Schlick-Steiner BC, Steiner FM. How diverse isMitopus morio? Integrative taxonomy detects cryptic species in a small-scale sample of a widespread harvestman. Mol Ecol 2013; 22:3850-63. [DOI: 10.1111/mec.12340] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 04/04/2013] [Accepted: 04/08/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Wolfgang Arthofer
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
| | - Hannes Rauch
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
| | - Barbara Thaler-Knoflach
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
| | - Karl Moder
- Institute of Mathematics and Applied Statistics; Department of Spatial, Landscape, and Infrastructure Sciences; University of Natural Resources and Life Sciences; Peter Jordan-Strasse 82, 1180 Vienna Austria
| | - Christoph Muster
- General Zoology and Zoological Systematics; Zoological Institute and Museum; University of Greifswald; Johann Sebastian Bach-Str 11/12, 17487 Greifswald Germany
| | - Birgit C. Schlick-Steiner
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
| | - Florian M. Steiner
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
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824
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Bolfíková B, Konečný A, Pfäffle M, Skuballa J, Hulva P. Population biology of establishment in New Zealand hedgehogs inferred from genetic and historical data: conflict or compromise? Mol Ecol 2013; 22:3709-20. [PMID: 23711046 DOI: 10.1111/mec.12331] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 03/24/2013] [Accepted: 03/28/2013] [Indexed: 11/26/2022]
Abstract
The crucial steps in biological invasions, related to the shaping of genetic architecture and the current evolution of adaptations to a novel environment, usually occur in small populations during the phases of introduction and establishment. However, these processes are difficult to track in nature due to invasion lag, large geographic and temporal scales compared with human observation capabilities, the frequent depletion of genetic variance, admixture and other phenomena. In this study, we compared genetic and historical evidence related to the invasion of the West European hedgehog to New Zealand to infer details about the introduction and establishment. Historical information indicates that the species was initially established on the South Island. A molecular assay of populations from Great Britain and New Zealand using mitochondrial sequences and nuclear microsatellite loci was performed based on a set of analyses including approximate Bayesian computation, a powerful approach for disentangling complex population demographies. According to these analyses, the population of the North Island was most similar to that of the native area and showed greatest reduction in genetic variation caused by founder demography and/or drift. This evidence indicated the location of the establishment phase. The hypothesis was corroborated by data on climate and urbanization. We discuss the contrasting results obtained by the molecular and historical approaches in the light of their different explanatory power and the possible biases influencing the description of particular aspects of invasions, and we advocate the integration of the two types of approaches in invasion biology.
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Affiliation(s)
- Barbora Bolfíková
- Department of Zoology, Faculty of Science Charles University in Prague, Viničná 7, 12843, Prague, Czech Republic.
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825
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Juste J, Benda P, Garcia-Mudarra JL, Ibáñez C. Phylogeny and systematics of Old World serotine bats (genusEptesicus, Vespertilionidae, Chiroptera): an integrative approach. ZOOL SCR 2013. [DOI: 10.1111/zsc.12020] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Javier Juste
- Estación Biológica de Doñana (CSIC); P.O. Box 1056; 41080; Sevilla; Spain
| | | | | | - Carlos Ibáñez
- Estación Biológica de Doñana (CSIC); P.O. Box 1056; 41080; Sevilla; Spain
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826
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López H, Hernández-Teixidor D, Macías-Hernández N, Juan C, Oromí P. A taxonomic revision and species delimitation of the genus Purpuraria
Enderlein, 1929 (Orthoptera: Pamphagidae) using an integrative approach. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Heriberto López
- Island Ecology and Evolution Research Group (IPNA-CSIC); Tenerife Canary Islands Spain
- Department of Biología Animal; Universidad La Laguna; Tenerife Canary Islands Spain
| | | | | | - Carlos Juan
- Department of Biologia; Universitat Illes Balears; Palma de Mallorca Spain
| | - Pedro Oromí
- Department of Biología Animal; Universidad La Laguna; Tenerife Canary Islands Spain
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827
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Lamb T, Bauer AM. To be or not to beAngolosaurus: a multilocus perspective on the phylogenetic position of Africa's desert plated lizard (Gerrhosauridae). ZOOL SCR 2013. [DOI: 10.1111/zsc.12016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Trip Lamb
- Department of Biology; East Carolina University; Greenville; NC; 27858; USA
| | - Aaron M. Bauer
- Department of Biology; Villanova University; Villanova; PA; 19085; USA
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828
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Husemann M, Llucià-Pomares D, Hochkirch A. A review of the Iberian Sphingonotini with description of two novel species (Orthoptera: Acrididae: Oedipodinae). Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Axel Hochkirch
- Department of Biogeography; Trier University; D-54286 Trier Germany
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829
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Nascimento FF, Lazar A, Menezes AN, Durans ADM, Moreira JC, Salazar-Bravo J, D′Andrea PS, Bonvicino CR. The role of historical barriers in the diversification processes in open vegetation formations during the Miocene/Pliocene using an ancient rodent lineage as a model. PLoS One 2013; 8:e61924. [PMID: 24349576 PMCID: PMC3630152 DOI: 10.1371/journal.pone.0061924] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 03/18/2013] [Indexed: 11/24/2022] Open
Abstract
The Neotropics harbors a high diversity of species and several hypotheses have been proposed to account for this pattern. However, while species of forested domains are frequently studied, less is known of species from open vegetation formations occupying, altogether, a larger area than the Amazon Forest. Here we evaluate the role of historical barriers and the riverine hypothesis in the speciation patterns of small mammals by analyzing an ancient rodent lineage (Thrichomys, Hystricomorpha). Phylogenetic and biogeographic analyses were carried out with mitochondrial and nuclear DNA markers to analyze the evolutionary relationships between Thrichomys lineages occurring in dry domains along both banks of the Rio São Francisco. This river is one of the longest of South America whose course and water flow have been modified by inland tectonic activities and climate changes. Molecular data showed a higher number of lineages than previously described. The T. inermis species complex with 2n = 26, FN = 48 was observed in both banks of the river showing a paraphyletic arrangement, suggesting that river crossing had occurred, from east to west. A similar pattern was also observed for the T. apereoides complex. Thrichomys speciation occurred in Late Miocene when the river followed a different course. The current geographic distribution of Thrichomys species and their phylogenetic relationships suggested the existence of frequent past connections between both banks in the middle section of the Rio São Francisco. The extensive palaeodune region found in this area has been identified as a centre of endemism of several vertebrate species and is likely to be a center of Thrichomys diversification.
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Affiliation(s)
- Fabrícia F. Nascimento
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Ana Lazar
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Albert N. Menezes
- Genetics Division, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Andressa da Matta Durans
- Programa de Pós Graduação em Biociências, Pavilhão Américo Piquet Carneiro, UERJ, Vila Isabel, Rio de Janeiro, RJ, Brazil
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Jânio C. Moreira
- Setor de Mastozoologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista s/n, São Cristovão, Rio de Janeiro, RJ, Brazil
- Programa de Pós-Graduação em Biodiversidade e Biologia Evolutiva, UFRJ, Ilha do Fundão, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Jorge Salazar-Bravo
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Paulo S. D′Andrea
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Cibele R. Bonvicino
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
- Genetics Division, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
- * E-mail:
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830
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Pavlova A, Amos JN, Joseph L, Loynes K, Austin JJ, Keogh JS, Stone GN, Nicholls JA, Sunnucks P. PERCHED AT THE MITO-NUCLEAR CROSSROADS: DIVERGENT MITOCHONDRIAL LINEAGES CORRELATE WITH ENVIRONMENT IN THE FACE OF ONGOING NUCLEAR GENE FLOW IN AN AUSTRALIAN BIRD. Evolution 2013; 67:3412-28. [DOI: 10.1111/evo.12107] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 03/04/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Alexandra Pavlova
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
| | - J. Nevil Amos
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
| | - Leo Joseph
- Australian National Wildlife Collection; CSIRO Ecosystem Sciences; GPO Box 1700 Canberra Australian Capital Territory 2601 Australia
| | - Kate Loynes
- Division of Evolution; Ecology and Genetics, Building 116, Daley Road, Research School of Biology, The Australian National University; Canberra Australian Capital Territory 0200 Australia
| | - Jeremy J. Austin
- Australian Centre for Ancient DNA (ACAD); School of Earth & Environmental Sciences, The University of Adelaide; Darling Building North Terrace Campus South Australia 5005 Australia
- Sciences Department; Museum Victoria; Carlton Gardens Melbourne Victoria 3001 Australia
| | - J. Scott Keogh
- Division of Evolution; Ecology and Genetics, Building 116, Daley Road, Research School of Biology, The Australian National University; Canberra Australian Capital Territory 0200 Australia
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road Edinburgh EH9 3JT Scotland
| | - James A. Nicholls
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road Edinburgh EH9 3JT Scotland
| | - Paul Sunnucks
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
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831
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Andrews KR, Perrin WF, Oremus M, Karczmarski L, Bowen BW, Puritz JB, Toonen RJ. The evolving male: spinner dolphin (Stenella longirostris) ecotypes are divergent at Y chromosome but not mtDNA or autosomal markers. Mol Ecol 2013; 22:2408-23. [DOI: 10.1111/mec.12193] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 11/30/2012] [Accepted: 12/04/2012] [Indexed: 11/26/2022]
Affiliation(s)
| | - William F. Perrin
- Southwest Fisheries Science Center, National Marine Fisheries Service; NOAA; 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Marc Oremus
- Opération Cétacés; 16 rue Henri Niautou 98800 Nouméa New Caledonia
| | - Leszek Karczmarski
- The Swire Institute of Marine Science; School of Biological Sciences; The University of Hong Kong; Cape d'Aguilar Shek O Hong Kong
| | - Brian W. Bowen
- Hawai'i Institute of Marine Biology; PO Box 1346 Kāne'ohe HI 96744 USA
| | | | - Robert J. Toonen
- Hawai'i Institute of Marine Biology; PO Box 1346 Kāne'ohe HI 96744 USA
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832
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Litvinchuk SN, Crottini A, Federici S, De Pous P, Donaire D, Andreone F, Kalezić ML, Džukić G, Lada GA, Borkin LJ, Rosanov JM. Phylogeographic patterns of genetic diversity in the common spadefoot toad, Pelobates fuscus (Anura: Pelobatidae), reveals evolutionary history, postglacial range expansion and secondary contact. ORG DIVERS EVOL 2013. [DOI: 10.1007/s13127-013-0127-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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833
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Unmack PJ, Hammer MP, Adams M, Johnson JB, Dowling TE. The role of continental shelf width in determining freshwater phylogeographic patterns in south-eastern Australian pygmy perches (Teleostei: Percichthyidae). Mol Ecol 2013; 22:1683-99. [DOI: 10.1111/mec.12204] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 12/03/2012] [Accepted: 12/04/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Peter J. Unmack
- School of Life Sciences; Arizona State University; PO Box 874501 Tempe AZ 85287-4501 USA
- WIDB 401; Department of Biology; Brigham Young University; Provo UT 84602 USA
- National Evolutionary Synthesis Center; 2024 W Main Street Suite A200 Durham NC 27705-4667 USA
| | - Michael P. Hammer
- Evolutionary Biology Unit; South Australian Museum; North Terrace SA 5000 Australia
- Curator of Fishes; Museum and Art Gallery of the Northern Territory; PO Box 4646 Darwin NT 0801 Australia
| | - Mark Adams
- Evolutionary Biology Unit; South Australian Museum; North Terrace SA 5000 Australia
- Australian Centre for Evolutionary Biology and Biodiversity; School of Earth and Environmental Science; The University of Adelaide; Adelaide SA 5005 Australia
| | - Jerald B. Johnson
- WIDB 401; Department of Biology; Brigham Young University; Provo UT 84602 USA
| | - Thomas E. Dowling
- School of Life Sciences; Arizona State University; PO Box 874501 Tempe AZ 85287-4501 USA
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834
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Zieliński P, Nadachowska-Brzyska K, Wielstra B, Szkotak R, Covaciu-Marcov SD, Cogălniceanu D, Babik W. No evidence for nuclear introgression despite complete mtDNA replacement in the Carpathian newt (Lissotriton montandoni). Mol Ecol 2013; 22:1884-903. [DOI: 10.1111/mec.12225] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 11/26/2022]
Affiliation(s)
- P. Zieliński
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - K. Nadachowska-Brzyska
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-75236 Uppsala Sweden
| | - B. Wielstra
- Netherlands Biodiversity Center; P. O. Box 9517 2300 RA Leiden The Netherlands
| | - R. Szkotak
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - S. D. Covaciu-Marcov
- University of Oradea; Faculty of Sciences; Department of Biology; Universităţii str. 1 410087 Oradea Romania
| | - D. Cogălniceanu
- Faculty of Natural Sciences and Agricultural Sciences; University Ovidius Constanţa; Aleea Universităţii nr. 1, corp B 900470 Constanţa Romania
| | - W. Babik
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
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835
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Liu M, Lin L, Gao T, Yanagimoto T, Sakurai Y, Grant WS. What maintains the central North Pacific genetic discontinuity in Pacific herring? PLoS One 2012; 7:e50340. [PMID: 23300525 PMCID: PMC3532504 DOI: 10.1371/journal.pone.0050340] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 10/17/2012] [Indexed: 11/18/2022] Open
Abstract
Pacific herring show an abrupt genetic discontinuity in the central North Pacific that represents secondary contact between refuge populations previously isolated during Pleistocene glaciations. Paradoxically, high levels of gene flow produce genetic homogeneity among ocean-type populations within each group. Here, we surveyed variability in mtDNA control-region sequences (463 bp) and nine microsatellite loci in Pacific herring from sites across the North Pacific to further explore the nature of the genetic discontinuity around the Alaska Peninsula. Consistent with previous studies, little divergence (Φ(ST) = 0.011) was detected between ocean-type populations of Pacific herring in the North West Pacific, except for a population in the Yellow Sea (Φ(ST) = 0.065). A moderate reduction in genetic diversity for both mtDNA and microsatellites in the Yellow Sea likely reflects founder effects during the last colonization of this sea. Reciprocal monophyly between divergent mtDNA lineages (Φ(ST) = 0.391) across the Alaska Peninsula defines the discontinuity across the North Pacific. However, microsatellites did not show a strong break, as eastern Bering Sea (EBS) herring were more closely related to NE Pacific than to NW Pacific herring. This discordance between mtDNA and microsatellites may be due to microsatellite allelic convergence or to sex-biased dispersal across the secondary contact zone. The sharp discontinuity between Pacific herring populations may be maintained by high-density blocking, competitive exclusion or hybrid inferiority.
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Affiliation(s)
- Ming Liu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong, China
| | - Longshan Lin
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong, China
| | - Tianxiang Gao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong, China
| | - Takashi Yanagimoto
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - Yasunori Sakurai
- Graduate School of Fisheries Science, Hokkaido University, Hakodate, Hokkaido, Japan
| | - W. Stewart Grant
- Alaska Department of Fish and Game, Anchorage, Alaska, United States of America
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836
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Turchetto-Zolet AC, Pinheiro F, Salgueiro F, Palma-Silva C. Phylogeographical patterns shed light on evolutionary process in South America. Mol Ecol 2012; 22:1193-213. [PMID: 23279129 DOI: 10.1111/mec.12164] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 10/31/2012] [Accepted: 11/06/2012] [Indexed: 11/28/2022]
Abstract
The South American continent is composed of several biogeographical regions harbouring the highest biodiversity on the globe, encompassing five of the world's biodiversity 'hot spots'. Nonetheless, the patterns and processes responsible for shaping its astonishing species diversity are largely unknown. Here, we present a review of current South American phylogeographical knowledge based on published articles on this topic. An appraisal of the literature reveals emerging phylogeographical patterns in the biota of South America. The striking phylogeographical divergence observed among organism lineages in South American studies is suggestive of high levels of undocumented species diversity. The interplay between Pleistocene climatic oscillations and Pliocene/Miocene orogenic events has contributed to shaping the current diversity and distribution of modern lineages in both the tropical and temperate regions of South America. Although older divergence times were observed for a range of species, most herpetofauna underwent an intraspecific lineage split much earlier than other organisms. The geographical ranges of species associated with forest habitats were reduced mainly during glacial cycles, whereas species associated with open vegetation domains have shown variable responses to climatic oscillations. The results suggest a highly complex mosaic of phylogeographical patterns in South America. We suggest future research directions to promote a better understanding of the origin and maintenance of the South American biota.
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Affiliation(s)
- A C Turchetto-Zolet
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, IB/UFRGS, Porto Alegre, RS, Brazil
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837
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Kvie KS, Hogner S, Aarvik L, Lifjeld JT, Johnsen A. Deep sympatric mtDNA divergence in the autumnal moth (Epirrita autumnata). Ecol Evol 2012; 3:126-44. [PMID: 23404314 PMCID: PMC3568849 DOI: 10.1002/ece3.434] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 10/29/2012] [Accepted: 11/01/2012] [Indexed: 02/01/2023] Open
Abstract
Deep sympatric intraspecific divergence in mtDNA may reflect cryptic species or formerly distinct lineages in the process of remerging. Preliminary results from DNA barcoding of Scandinavian butterflies and moths showed high intraspecific sequence variation in the autumnal moth, Epirrita autumnata. In this study, specimens from different localities in Norway and some samples from Finland and Scotland, with two congeneric species as outgroups, were sequenced with mitochondrial and nuclear markers to resolve the discrepancy found between mtDNA divergence and present species-level taxonomy. We found five COI sub-clades within the E. autumnata complex, most of which were sympatric and with little geographic structure. Nuclear markers (ITS2 and Wingless) showed little variation and gave no indications that E. autumnata comprises more than one species. The samples were screened with primers for Wolbachia outer surface gene (wsp) and 12% of the samples tested positive. Two Wolbachia strains were associated with different mtDNA sub-clades within E. autumnata, which may indicate indirect selection/selective sweeps on haplotypes. Our results demonstrate that deep mtDNA divergences are not synonymous with cryptic speciation and this has important implications for the use of mtDNA in species delimitation, like in DNA barcoding.
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Affiliation(s)
- Kjersti S Kvie
- Natural History Museum, University of Oslo P.O. Box 1172, Blindern, N-0318, Oslo, Norway ; Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science P.O. Box 8146 Dep, N-0033, Oslo, Norway
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838
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Springer MS, Meredith RW, Gatesy J, Emerling CA, Park J, Rabosky DL, Stadler T, Steiner C, Ryder OA, Janečka JE, Fisher CA, Murphy WJ. Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS One 2012; 7:e49521. [PMID: 23166696 PMCID: PMC3500307 DOI: 10.1371/journal.pone.0049521] [Citation(s) in RCA: 270] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 10/09/2012] [Indexed: 01/24/2023] Open
Abstract
Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71-63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event ("Grande Coupure") at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.
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Affiliation(s)
- Mark S. Springer
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Robert W. Meredith
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Department of Biology and Molecular Biology, Montclair State University, Montclair, New Jersey, United States of America
| | - John Gatesy
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Christopher A. Emerling
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Jong Park
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Daniel L. Rabosky
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tanja Stadler
- Institut für Integrative Biologie, Eidgenössiche Technische Hochschule Zurich, Zurich, Switzerland
| | - Cynthia Steiner
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, San Diego, California, United States of America
| | - Oliver A. Ryder
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, San Diego, California, United States of America
| | - Jan E. Janečka
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Colleen A. Fisher
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
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839
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Hogner S, Laskemoen T, Lifjeld JT, Porkert J, Kleven O, Albayrak T, Kabasakal B, Johnsen A. Deep sympatric mitochondrial divergence without reproductive isolation in the common redstart Phoenicurus phoenicurus. Ecol Evol 2012; 2:2974-88. [PMID: 23301165 PMCID: PMC3538993 DOI: 10.1002/ece3.398] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 09/17/2012] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial DNA usually shows low sequence variation within and high sequence divergence among species, which makes it a useful marker for phylogenetic inference and DNA barcoding. A previous study on the common redstart (Phoenicurus phoenicurus) revealed two very different mtDNA haplogroups (5% K2P distance). This divergence is comparable to that among many sister species; however, both haplogroups coexist and interbreed in Europe today. Herein, we describe the phylogeographic pattern of these lineages and test hypotheses for how such high diversity in mtDNA has evolved. We found no evidence for mitochondrial pseudogenes confirming that both haplotypes are of mitochondrial origin. When testing for possible reproductive barriers, we found no evidence for lineage-specific assortative mating and no difference in sperm morphology, indicating that they are not examples of cryptic species, nor likely to reflect the early stages of speciation. A gene tree based on a short fragment of cytochrome c oxidase subunit 1 from the common redstart and 10 other Phoenicurus species, showed no introgression from any of the extant congenerics. However, introgression from an extinct congeneric cannot be excluded. Sequences from two nuclear introns did not show a similar differentiation into two distinct groups. Mismatch distributions indicated that the lineages have undergone similar demographic changes. Taken together, these results confirm that deeply divergent mitochondrial lineages can coexist in biological species. Sympatric mtDNA divergences are relatively rare in birds, but the fact that they occur argues against the use of threshold mtDNA divergences in species delineation.
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Affiliation(s)
- Silje Hogner
- National Centre for Biosystematics, Natural History Museum, University of Oslo P.O. Box 1172, Blindern, NO-0318, Oslo, Norway
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840
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Reilly SB, Marks SB, Jennings WB. Defining evolutionary boundaries across parapatric ecomorphs of Black Salamanders (Aneides flavipunctatus) with conservation implications. Mol Ecol 2012; 21:5745-61. [DOI: 10.1111/mec.12068] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 08/30/2012] [Accepted: 09/11/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Sean B. Reilly
- Department of Biological Sciences; Humboldt State University; 1 Harpst Street; Arcata; CA; 95521; USA
| | - Sharyn B. Marks
- Department of Biological Sciences; Humboldt State University; 1 Harpst Street; Arcata; CA; 95521; USA
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841
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Pritchard VL, Edmands S. THE GENOMIC TRAJECTORY OF HYBRID SWARMS: OUTCOMES OF REPEATED CROSSES BETWEEN POPULATIONS OFTIGRIOPUS CALIFORNICUS. Evolution 2012; 67:774-91. [DOI: 10.1111/j.1558-5646.2012.01814.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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842
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Scally A, Durbin R. Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet 2012; 13:745-53. [PMID: 22965354 DOI: 10.1038/nrg3295] [Citation(s) in RCA: 413] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is now possible to make direct measurements of the mutation rate in modern humans using next-generation sequencing. These measurements reveal a value that is approximately half of that previously derived from fossil calibration, and this has implications for our understanding of demographic events in human evolution and other aspects of population genetics. Here, we discuss the implications of a lower-than-expected mutation rate in relation to the timescale of human evolution.
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843
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Wielstra B, Arntzen JW. Postglacial species displacement in Triturus newts deduced from asymmetrically introgressed mitochondrial DNA and ecological niche models. BMC Evol Biol 2012; 12:161. [PMID: 22935041 PMCID: PMC3520116 DOI: 10.1186/1471-2148-12-161] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/25/2012] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND If the geographical displacement of one species by another is accompanied by hybridization, mitochondrial DNA can introgress asymmetrically, from the outcompeted species into the invading species, over a large area. We explore this phenomenon using the two parapatric crested newt species, Triturus macedonicus and T. karelinii, distributed on the Balkan Peninsula in south-eastern Europe, as a model. RESULTS We first delimit a ca. 54,000 km(2) area in which T. macedonicus contains T. karelinii mitochondrial DNA. This introgression zone bisects the range of T. karelinii, cutting off a T. karelinii enclave. The high similarity of introgressed mitochondrial DNA haplotypes with those found in T. karelinii suggests a recent transfer across the species boundary. We then use ecological niche modeling to explore habitat suitability of the location of the present day introgression zone under current, mid-Holocene and Last Glacial Maximum conditions. This area was inhospitable during the Last Glacial Maximum for both species, but would have been habitable at the mid-Holocene. Since the mid-Holocene, habitat suitability generally increased for T. macedonicus, whereas it decreased for T. karelinii. CONCLUSION The presence of a T. karelinii enclave suggests that T. karelinii was the first to colonize the area where the present day introgression zone is positioned after the Last Glacial Maximum. Subsequently, we propose T. karelinii was outcompeted by T. macedonicus, which captured T. karelinii mitochondrial DNA via introgressive hybridization in the process. Ecological niche modeling suggests that this replacement was likely facilitated by a shift in climate since the mid-Holocene. We suggest that the northwestern part of the current introgression zone was probably never inhabited by T. karelinii itself, and that T. karelinii mitochondrial DNA spread there through T. macedonicus exclusively. Considering the spatial distribution of the introgressed mitochondrial DNA and the signal derived from ecological niche modeling, we do not favor the hypothesis that foreign mitochondrial DNA was pulled into the T. macedonicus range by natural selection.
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Affiliation(s)
- Ben Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
- Faculty of Geo-Information Science and Earth Observation – ITC, University of Twente, P.O. Box 6, 7500 AA, Enschede, The Netherlands
| | - Jan W Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
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