751
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Habel JC, Zachos FE, Dapporto L, Rödder D, Radespiel U, Tellier A, Schmitt T. Population genetics revisited - towards a multidisciplinary research field. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12481] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jan Christian Habel
- Terrestrial Ecology Research Group; Department of Ecology and Ecosystem Management; School of Life Sciences Weihenstephan; Technische Universität München; D-85354 Freising-Weihenstephan Germany
| | | | - Leonardo Dapporto
- Department of Biological and Medical Sciences; Oxford Brookes University; Headington Oxford OX3 0BP UK
| | - Dennis Rödder
- Zoologisches Forschungsmuseum Alexander Koenig; D-53113 Bonn Germany
| | - Ute Radespiel
- Institute of Zoology; University of Veterinary Medicine Hannover; D-30559 Hannover Germany
| | - Aurélien Tellier
- Section of Population Genetics; Technische Universität München; D-85354 Freising Germany
| | - Thomas Schmitt
- Senckenberg German Entomological Institute; D-15374 Müncheberg Germany
- Department of Zoology; Institute of Biology; Faculty of Natural Sciences I; Martin-Luther-University Halle-Wittenberg; D-06099 Halle (Saale) Germany
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752
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Seal JN, Brown L, Ontiveros C, Thiebaud J, Mueller UG. Gone to Texas: phylogeography of twoTrachymyrmex(Hymenoptera: Formicidae) species along the southeastern coastal plain of North America. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12426] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jon N. Seal
- Integrative Biology; University of Texas at Austin; 1 University Station #C0930 Austin TX 78712 USA
- Department of Biology; University of Texas at Tyler; 3900 University Blvd Tyler TX 75799 USA
| | - Larrimy Brown
- Department of Biology; University of Texas at Tyler; 3900 University Blvd Tyler TX 75799 USA
| | - Cynthia Ontiveros
- Department of Biology; University of Texas at Tyler; 3900 University Blvd Tyler TX 75799 USA
| | - Jeffrey Thiebaud
- Integrative Biology; University of Texas at Austin; 1 University Station #C0930 Austin TX 78712 USA
| | - Ulrich G. Mueller
- Integrative Biology; University of Texas at Austin; 1 University Station #C0930 Austin TX 78712 USA
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753
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Wachter GA, Muster C, Arthofer W, Raspotnig G, Föttinger P, Komposch C, Steiner FM, Schlick-Steiner BC. Taking the discovery approach in integrative taxonomy: decrypting a complex of narrow-endemic Alpine harvestmen (Opiliones: Phalangiidae: Megabunus). Mol Ecol 2015; 24:863-89. [PMID: 25583278 DOI: 10.1111/mec.13077] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/29/2014] [Accepted: 01/07/2015] [Indexed: 02/05/2023]
Abstract
Species delimitation is fundamental for biological studies, yet precise delimitation is not an easy task, and every involved approach has an inherent failure rate. Integrative taxonomy, a method that merges multiple lines of evidence, can profoundly contribute to reliable alpha-taxonomy and shed light on the processes behind speciation. In this study, we explored and validated species limits in a group of closely related Megabunus harvestmen (Eupnoi, Phalangiidae) endemic to the European Alps. Without a priori species hypotheses, we used multiple sources of inference, including mitochondrial and multilocus nuclear DNA, morphometrics and chemistry. The results of these discovery approaches revealed morphological crypsis and multiple new species within two of the five hitherto known species. Based on our analyses, we discussed the most plausible evolutionary scenarios, invoked the most reasonable species hypotheses and validated the new species limits. Building upon the achieved rigour, three new species, Megabunus cryptobergomas Muster and Wachter sp. nov., Megabunus coelodonta Muster and Steiner sp. nov., and Megabunus lentipes Muster and Komposch sp. nov., are formally described. In addition, we provide a dichotomous morphological key to the Megabunus species of the Alps. Our work demonstrates the suitability of integrative, discovery-based approaches in combination with validation approaches to precisely characterize species and enabled us to implement nomenclatural consequences for this genus.
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Affiliation(s)
- Gregor A Wachter
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
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754
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Melo-Ferreira J, Lemos de Matos A, Areal H, Lissovsky AA, Carneiro M, Esteves PJ. The phylogeny of pikas (Ochotona) inferred from a multilocus coalescent approach. Mol Phylogenet Evol 2015; 84:240-4. [PMID: 25637497 DOI: 10.1016/j.ympev.2015.01.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 12/18/2014] [Accepted: 01/19/2015] [Indexed: 11/18/2022]
Abstract
The clarification of the systematics of pikas (genus Ochotona) has been hindered by largely overlapping morphological characters among species and the lack of a comprehensive molecular phylogeny. Here we estimate the first multilocus phylogeny of the genus to date, by analysing 12 nuclear DNA markers (total of 7.5Kb) in 11 species of pikas from the four classified subgenera (Pika, Ochotona, Lagotona and Conothoa) using a multispecies coalescent-based framework. The species-tree confirmed the subgeneric classification by retrieving as monophyletic the subgenera represented here by more than one species. Contrary to previous phylogenies based on mtDNA alone, Lagotona was found to be sister to Pika. Also, support for the monophyly of the alpina group was not strong, thus caution should be used in future analyses of this group. A relaxed molecular clock calibrated using the Ochotonidae-Leporidae divergence resulted in more recent estimates of divergence times relative to previous studies. Strong concordance with inferences based on fossil records was found, suggesting that the initial diversification of the genus took place by the end of late Miocene. Finally, this work sets up methodologies and gathers molecular markers that can be used to extend the understanding of the evolutionary history of the genus.
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Affiliation(s)
- José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Ana Lemos de Matos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
| | - Helena Areal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
| | - Andrey A Lissovsky
- Zoological Museum of Moscow State University, B. Nikitskaya, 6, Moscow 125009, Russia
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Pedro J Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal
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755
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Evidence for high dispersal ability and mito-nuclear discordance in the small brown planthopper, Laodelphax striatellus. Sci Rep 2015; 5:8045. [PMID: 25622966 PMCID: PMC4309506 DOI: 10.1038/srep08045] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 12/30/2014] [Indexed: 01/22/2023] Open
Abstract
Understanding dispersal ability in pest species is critical for both theoretical aspects of
evolutionary and population biology and from a practical standpoint, such as implementing effective
forecasting systems. The small brown planthopper (SBPH), Laodelphax striatellus
(Fallén), is an economically important pest, but few data exist on its dispersal ability.
Here, we used mitochondrial and nuclear markers to elucidate the population genetic structure of
SBPH and of the parasitic bacterium Wolbachia throughout temperate and subtropical China. Our
results showed that the SBPH populations in China lack significant differences in genetic structure,
suggesting extensive gene flow. Multilocus sequence typing revealed that Wolbachia infection
was systematic and due to the same strain (wStri) within and across populations. However, the
mtDNA haplogroups had a nonrandom distribution across the sampling localities, which correlated to
latitudinal and climatic gradients. We explain this mito-nuclear discordance as a result of
historical population recolonization or mitochondria adaptation to climate.
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756
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Montelongo T, Gómez-Zurita J. Nonrandom Patterns of Genetic Admixture Expose the Complex Historical Hybrid Origin of Unisexual Leaf Beetle Species in the GenusCalligrapha. Am Nat 2015; 185:113-34. [DOI: 10.1086/678408] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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757
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Differential introgression and effective size of marker type influence phylogenetic inference of a recently divergent avian group (Phasianidae: Tympanuchus). Mol Phylogenet Evol 2014; 84:1-13. [PMID: 25554526 DOI: 10.1016/j.ympev.2014.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/12/2014] [Accepted: 12/18/2014] [Indexed: 11/20/2022]
Abstract
Life history strategies can influence the effective population size (Ne) of loci differently based on their mode of inheritance. Recognizing how this may affect the rate of lineage sorting among marker types is important for studies focused on resolving phylogenetic relationships among recently divergent taxa. In this study, we use gene tree, coalescent-based species tree, and isolation-with-migration analyses to explore the differences between marker types (autosomal, Z-linked, and mitochondrial) in resolving phylogenetic relationships among North American prairie grouse (Tympanuchus). We found that Z-linked loci were more likely to identify monophyletic relationships among prairie grouse species compared to autosomal and mtDNA loci in both species and gene tree analyses, with species tree analyses outperforming gene trees. These results were further supported with isolation-with-migration analyses, where Z-linked loci largely followed a strict isolation model while autosomal loci were more likely to fit a model with gene flow between species following population divergence. While accounting for differences in inheritance pattern (or Ne) for marker type, results suggest that additional factors, such as strong sexual selection and sex-biased introgression (i.e., male-biased postzygotic hybrid behavioral isolation or "unsexy son"), may further explain the decreased diversity levels and increased rate of lineage sorting observed with the Z-linked loci relative to autosomal and mtDNA loci. In fact, to our knowledge no hybrid male prairie grouse have been observed breeding in the wild, yet hybrid females along with backcross females are known to produce viable offspring. Overall, this study highlights that more work is needed to determine how complex models of gene flow (i.e., sex biased introgression) and differences in the effective size among marker types based on differing life history strategies influence divergence date estimation and species delimitation.
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758
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Dong F, Zou FS, Lei FM, Liang W, Li SH, Yang XJ. Testing hypotheses of mitochondrial gene-tree paraphyly: unravelling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (Pomatorhinus musicus). Mol Ecol 2014; 23:5855-67. [DOI: 10.1111/mec.12981] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/02/2014] [Accepted: 10/14/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Feng Dong
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
| | - Fa-Sheng Zou
- South China Institute of Endangered Animals; Guangzhou 510260 China
| | - Fu-Min Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Wei Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology; College of Life Sciences; Hainan Normal University; Haikou 571158 China
| | - Shou-Hsien Li
- Department of Life Science; National Taiwan Normal University; Taipei 116 Taiwan
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
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759
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Miller MJ, Lipshutz SE, Smith NG, Bermingham E. Genetic and phenotypic characterization of a hybrid zone between polyandrous Northern and Wattled Jacanas in Western Panama. BMC Evol Biol 2014; 14:227. [PMID: 25394718 PMCID: PMC4237789 DOI: 10.1186/s12862-014-0227-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 10/17/2014] [Indexed: 01/15/2023] Open
Abstract
Background Hybridization provides a unique perspective into the ecological, genetic and behavioral context of speciation. Hybridization is common in birds, but has not yet been reported among bird species with a simultaneously polyandrous mating system; a mating system where a single female defends a harem of males who provide nearly all parental care. Unlike simple polyandry, polyandrous mating is extremely rare in birds, with only 1% of bird species employing this mating system. Although it is classically held that females are “choosy” in avian hybrid systems, nearly-exclusive male parental care raises the possibility that female selection against heterospecific matings might be reduced compared to birds with other mating systems. Results We describe a narrow hybrid zone in southwestern Panama between two polyandrous freshwater waders: Northern Jacana, Jacana spinosa and Wattled Jacana, J. jacana. We document coincident cline centers for three phenotypic traits, mtDNA, and one of two autosomal introns. Cline widths for these six markers varied from seven to 142 km, with mtDNA being the narrowest, and five of the six markers having widths less than 100 km. Cline tails were asymmetrical, with greater introgression of J. jacana traits extending westward into the range of J. spinosa. Likewise, within the hybrid zone, the average hybrid index of phenotypic hybrids was significantly biased towards J. spinosa. Species distribution models indicate that the hybrid zone is located at the edge of a roughly 100 km wide overlap where habitat is predicted to be suitable for both species, with more westerly areas suitable only for spinosa and eastward habitats suitable only for J. jacana. Conclusion The two species of New World jacanas maintain a narrow, and persistent hybrid zone in western Panama. The hybrid zone may be maintained by the behavioral dominance of J. spinosa counterbalanced by unsuitable habitat for J. spinosa east of the contact zone. Although the two parental species are relatively young, mitochondrial cline width was extremely narrow. This result suggests strong selection against maternally-inherited markers, which may indicate either mitonuclear incompatibilities and/or female choice against heterospecific matings typical of avian hybrid systems, despite jacana sex role reversal. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0227-7) contains supplementary material, which is available to authorized users.
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760
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Huang DI, Hefer CA, Kolosova N, Douglas CJ, Cronk QCB. Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae). THE NEW PHYTOLOGIST 2014; 204:693-703. [PMID: 25078531 DOI: 10.1111/nph.12956] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/16/2014] [Indexed: 05/03/2023]
Abstract
As molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance - the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees - are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6-7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a 'ghost lineage' of a now-extinct North American poplar.
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Affiliation(s)
- Daisie I Huang
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
- Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Charles A Hefer
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
- Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Natalia Kolosova
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Carl J Douglas
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
- Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada
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761
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Qi Y, Lu B, Gao H, Hu P, Fu J. Hybridization and mitochondrial genome introgression between Rana chensinensis and R. kukunoris. Mol Ecol 2014; 23:5575-88. [PMID: 25308955 DOI: 10.1111/mec.12960] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 10/01/2014] [Accepted: 10/03/2014] [Indexed: 02/01/2023]
Abstract
Mitochondrial genome (mito-genome) introgression among metazoans is commonplace, and several biological processes may promote such introgression. We examined two proposed processes for the mito-genome introgression between Rana chensinensis and R. kukunoris: natural hybridization and sex-biased dispersal. We sampled 477 individuals from 28 sites in the potential hybrid zone in the western Tsinling Mountains. Mitochondrial gene (cyt-b) trees were used to examine the introgression events. Microsatellite DNA loci, cyt-b and morphological data were used to identify hybrids and to examine the extent of natural hybridization. We detected rampant bidirectional introgressions, both ancient and recent, between the two species. Furthermore, we found a wide hybrid zone, and frequent and asymmetric hybridization. The hybrid zone cline analysis revealed a clear mitochondrial-nuclear discordance; while most nuclear markers displayed similar and steep clines, cyt-b had a displaced cline centre and a more gradual and wider cline. We also detected strong and asymmetric historical maternal gene flow across the hybrid zone. This widespread hybridization and detected low mito-nuclear conflicts may, at least partially, explain the high frequency of introgression. Lastly, microsatellite data and population genetic methods were used to assess sex-biased dispersal. A weak pattern of female-biased dispersal was detected in both species, suggesting it may not play an important role in the observed introgression. Our data are consistent with the hybridization hypothesis, but support for the sex-biased dispersal hypothesis is weak. We further suggest that selective advantages of the R. kukunoris-type mito-genome in thermal adaptation may also contribute to the introgression between the two species.
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Affiliation(s)
- Yin Qi
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
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762
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Bock F, Fennessy J, Bidon T, Tutchings A, Marais A, Deacon F, Janke A. Mitochondrial sequences reveal a clear separation between Angolan and South African giraffe along a cryptic rift valley. BMC Evol Biol 2014; 14:219. [PMID: 25927851 PMCID: PMC4207324 DOI: 10.1186/s12862-014-0219-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 10/03/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The current taxonomy of the African giraffe (Giraffa camelopardalis) is primarily based on pelage pattern and geographic distribution, and nine subspecies are currently recognized. Although genetic studies have been conducted, their resolution is low, mainly due to limited sampling. Detailed knowledge about the genetic variation and phylogeography of the South African giraffe (G. c. giraffa) and the Angolan giraffe (G. c. angolensis) is lacking. We investigate genetic variation among giraffe matrilines by increased sampling, with a focus on giraffe key areas in southern Africa. RESULTS The 1,562 nucleotides long mitochondrial DNA dataset (cytochrome b and partial control region) comprises 138 parsimony informative sites among 161 giraffe individuals from eight populations. We additionally included two okapis as an outgroup. The analyses of the maternally inherited sequences reveal a deep divergence between northern and southern giraffe populations in Africa, and a general pattern of distinct matrilineal clades corresponding to their geographic distribution. Divergence time estimates among giraffe populations place the deepest splits at several hundred thousand years ago. CONCLUSIONS Our increased sampling in southern Africa suggests that the distribution ranges of the Angolan and South African giraffe need to be redefined. Knowledge about the phylogeography and genetic variation of these two maternal lineages is crucial for the development of appropriate management strategies.
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Affiliation(s)
- Friederike Bock
- Biodiversity and Climate Research Centre (BiK-F) - Ecological Genomics & Senckenberg Gesellschaft für Naturforschung (SGN), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
| | - Julian Fennessy
- Giraffe Conservation Foundation, 26 Grasmere Road, Purley, Surrey, CR8 1DU, England. .,School of Biological Earth and Environmental Studies (BEES), University of New South Wales (UNSW), Sydney, New South Wales, 2052, Australia.
| | - Tobias Bidon
- Biodiversity and Climate Research Centre (BiK-F) - Ecological Genomics & Senckenberg Gesellschaft für Naturforschung (SGN), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
| | - Andy Tutchings
- Giraffe Conservation Foundation, 26 Grasmere Road, Purley, Surrey, CR8 1DU, England.
| | - Andri Marais
- Giraffe Conservation Foundation, 26 Grasmere Road, Purley, Surrey, CR8 1DU, England.
| | - Francois Deacon
- Giraffe Conservation Foundation, 26 Grasmere Road, Purley, Surrey, CR8 1DU, England. .,Department Animal, Wildlife & Grassland Science, University of Free State, Faculty of Natural and Agricultural Sciences, Bloemfontein, South Africa.
| | - Axel Janke
- Biodiversity and Climate Research Centre (BiK-F) - Ecological Genomics & Senckenberg Gesellschaft für Naturforschung (SGN), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,Goethe University Frankfurt, Institute for Ecology, Evolution & Diversity, Biologicum, Max-von-Laue-Straße 13, 60439, Frankfurt am Main, Germany.
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763
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Phuong MA, Lim MCW, Wait DR, Rowe KC, Moritz C. Delimiting species in the genusOtospermophilus(Rodentia: Sciuridae), using genetics, ecology, and morphology. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12391] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Mark A. Phuong
- Department of Integrative Biology; Museum of Vertebrate Zoology; University of California; Berkeley, 3101 Valley Life Science Building Berkeley CA 94720 USA
| | - Marisa C. W. Lim
- Department of Integrative Biology; Museum of Vertebrate Zoology; University of California; Berkeley, 3101 Valley Life Science Building Berkeley CA 94720 USA
| | - Daniel R. Wait
- Department of Integrative Biology; Museum of Vertebrate Zoology; University of California; Berkeley, 3101 Valley Life Science Building Berkeley CA 94720 USA
| | - Kevin C. Rowe
- Department of Integrative Biology; Museum of Vertebrate Zoology; University of California; Berkeley, 3101 Valley Life Science Building Berkeley CA 94720 USA
- Sciences Department; Museum Victoria; Melbourne VIC 3001 Australia
| | - Craig Moritz
- Department of Integrative Biology; Museum of Vertebrate Zoology; University of California; Berkeley, 3101 Valley Life Science Building Berkeley CA 94720 USA
- Research School of Biology; The Australian National University; Acton ACT 0200 Australia
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764
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Bock DG, Andrew RL, Rieseberg LH. On the adaptive value of cytoplasmic genomes in plants. Mol Ecol 2014; 23:4899-911. [PMID: 25223488 DOI: 10.1111/mec.12920] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 01/30/2023]
Abstract
Is DNA variation maintained in organelle genomes selectively neutral? The answer to this question has important implications for many aspects of ecology and evolution. While traditionally the answer has been 'yes', recent studies in animals have shown that, on the contrary, mitochondrial DNA polymorphism is frequently adaptive. In plants, however, the neutrality assumption has not been strongly challenged. Here, we begin with a critical evaluation of arguments in favour of this long-held view. We then discuss the latest empirical evidence for the opposing prediction that sequence variation in plant cytoplasmic genomes is frequently adaptive. While outstanding research progress is being made towards understanding this fundamental topic, we highlight the need for studies that combine information ranging from field experiments to physiology to molecular evolutionary biology. Such an interdisciplinary approach provides a means for determining the frequency, drivers and evolutionary significance of adaptive organelle DNA variation.
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Affiliation(s)
- Dan G Bock
- Department of Botany, Biodiversity Research Centre, University of British Columbia, 3529-6270 University Blvd., Vancouver, British Columbia, Canada, V6T 1Z4
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765
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Galarza JA, Nokelainen O, Ashrafi R, Hegna RH, Mappes J. Temporal relationship between genetic and warning signal variation in the aposematic wood tiger moth (Parasemia plantaginis). Mol Ecol 2014; 23:4939-57. [PMID: 25211063 DOI: 10.1111/mec.12913] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 09/05/2014] [Accepted: 09/08/2014] [Indexed: 11/29/2022]
Abstract
Many plants and animals advertise unpalatability through warning signals in the form of colour and shape. Variation in warning signals within local populations is not expected because they are subject to directional selection. However, mounting evidence of warning signal variation within local populations suggests that other selective forces may be acting. Moreover, different selective pressures may act on the individual components of a warning signal. At present, we have a limited understanding about how multiple selection processes operate simultaneously on warning signal components, and even less about their temporal and spatial dynamics. Here, we examined temporal variation of several wing warning signal components (colour, UV-reflectance, signal size and pattern) of two co-occurring colour morphs of the aposematic wood tiger moth (Parasemia plantaginis). Sampling was carried out in four geographical regions over three consecutive years. We also evaluated each morph's temporal genetic structure by analysing mitochondrial sequence data and nuclear microsatellite markers. Our results revealed temporal differences between the morphs for most signal components measured. Moreover, variation occurred differently in the fore- and hindwings. We found no differences in the genetic structure between the morphs within years and regions, suggesting single local populations. However, local genetic structure fluctuated temporally. Negative correlations were found between variation produced by neutrally evolving genetic markers and those of the different signal components, indicating a non-neutral evolution for most warning signal components. Taken together, our results suggest that differential selection on warning signal components and fluctuating population structure can be one explanation for the maintenance of warning signal variation in this aposematic species.
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Affiliation(s)
- Juan A Galarza
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, Jyväskylä, 40500, Finland
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766
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Extensive unidirectional introgression between two salamander lineages of ancient divergence and its evolutionary implications. Sci Rep 2014; 4:6516. [PMID: 25269625 PMCID: PMC5377473 DOI: 10.1038/srep06516] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/12/2014] [Indexed: 11/17/2022] Open
Abstract
Hybridization and introgression, contrary to previous beliefs, are now considered to be widespread processes even among animal species. Nonetheless, the range of their possible outcomes and roles in moulding biodiversity patterns are still far from being fully appraised. Here we investigated the pattern of hybridization and introgression between Salamandrina perspicillata and S. terdigitata, two salamanders endemic to the Italian peninsula. Using a set of diagnostic or differentiated genetic markers (9 nuclear and 1 mitochondrial), we documented extensive unidirectional introgression of S. terdigitata alleles into the S. perspicillata gene pool in central Italy, indicating that barriers against hybridization were permeable when they came into secondary contact, and despite their ancient divergence. Nonetheless, purebred S. terdigitata, as well as F1, F2, and backcrosses were not found within the hybrid zone. Moreover, Bayesian analyses of population structure identified admixed populations belonging to a differentiated gene pool with respect to both parental populations. Overall, the observed genetic structure, together with their geographic pattern of distribution, suggests that Salamandrina populations in central Italy could have entered a distinct evolutionary pathway. How far they have gone along this pathway will deserve future investigation.
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767
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Olano-Marin J, Plis K, Sönnichsen L, Borowik T, Niedziałkowska M, Jędrzejewska B. Weak population structure in European roe deer (Capreolus capreolus) and evidence of introgressive hybridization with Siberian roe deer (C. pygargus) in northeastern Poland. PLoS One 2014; 9:e109147. [PMID: 25271423 PMCID: PMC4182808 DOI: 10.1371/journal.pone.0109147] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 08/22/2014] [Indexed: 12/02/2022] Open
Abstract
We investigated contemporary and historical influences on the pattern of genetic diversity of European roe deer (Capreolus capreolus). The study was conducted in northeastern Poland, a zone where vast areas of primeval forests are conserved and where the European roe deer was never driven to extinction. A total of 319 unique samples collected in three sampling areas were genotyped at 16 microsatellites and one fragment (610 bp) of mitochondrial DNA (mtDNA) control region. Genetic diversity was high, and a low degree of genetic differentiation among sampling areas was observed with both microsatellites and mtDNA. No evidence of genetic differentiation between roe deer inhabiting open fields and forested areas was found, indicating that the ability of the species to exploit these contrasting environments might be the result of its phenotypic plasticity. Half of the studied individuals carried an mtDNA haplotype that did not belong to C. capreolus, but to a related species that does not occur naturally in the area, the Siberian roe deer (C. pygargus). No differentiation between individuals with Siberian and European mtDNA haplotypes was detected at microsatellite loci. Introgression of mtDNA of Siberian roe deer into the genome of European roe deer has recently been detected in eastern Europe. Such introgression might be caused by human-mediated translocations of Siberian roe deer within the range of European roe deer or by natural hybridization between these species in the past.
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Affiliation(s)
- Juanita Olano-Marin
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
- * E-mail:
| | - Kamila Plis
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Leif Sönnichsen
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Tomasz Borowik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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768
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Sotelo G, Andree KB, López MA, Alexandrino P, Gisbert E, Faria R. The puzzling demographic history and genetic differentiation of the twaite shad (Alosa fallax) in the Ebro River. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0597-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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769
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Darling JA, Tsai YHE, Blakeslee AMH, Roman J. Are genes faster than crabs? Mitochondrial introgression exceeds larval dispersal during population expansion of the invasive crab Carcinus maenas. ROYAL SOCIETY OPEN SCIENCE 2014; 1:140202. [PMID: 26064543 PMCID: PMC4448889 DOI: 10.1098/rsos.140202] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/13/2014] [Indexed: 06/04/2023]
Abstract
Biological invasions offer unique opportunities to investigate evolutionary dynamics at the peripheries of expanding populations. Here, we examine genetic patterns associated with admixture between two distinct invasive lineages of the European green crab, Carcinus maenas L., independently introduced to the northwest Atlantic. Previous investigations based on mitochondrial DNA sequences demonstrated that larval dispersal driven by advective currents could explain observed southward displacement of an admixture zone between the two invasions. Comparison of published mitochondrial results with new nuclear data from nine microsatellite loci, however, reveals striking discordance in their introgression patterns. Specifically, introgression of mitochondrial genomes relative to nuclear background suggests that demographic processes such as sex-biased reproductive dynamics and population size imbalances-and not solely larval dispersal-play an important role in driving the evolution of the genetic cline. In particular, the unpredicted introgression of mitochondrial alleles against the direction of mean larval dispersal in the region is consistent with recent models invoking similar demographic processes to explain movements of genes into invading populations. These observations have important implications for understanding historical shifts in C. maenas range limits, and more generally for inferences of larval dispersal based on genetic data.
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Affiliation(s)
- John A. Darling
- National Exposure Research Laboratory, United States Environmental Protection Agency, 109 TW Alexander Drive, Durham, NC 27711, USA
| | - Yi-Hsin Erica Tsai
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - April M. H. Blakeslee
- Department of Biology, Long Island University, 720 Northern Boulevard, Brookville, NY 11548, USA
| | - Joe Roman
- Gund Institute for Ecological Economics, University of Vermont, Burlington, VT 05405, USA
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770
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Pavan SE, Jansa SA, Voss RS. Molecular phylogeny of short-tailed opossums (Didelphidae: Monodelphis ): Taxonomic implications and tests of evolutionary hypotheses. Mol Phylogenet Evol 2014; 79:199-214. [DOI: 10.1016/j.ympev.2014.05.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/23/2014] [Accepted: 05/26/2014] [Indexed: 02/01/2023]
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771
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Dong J, Mao X, Sun H, Irwin DM, Zhang S, Hua P. Introgression of mitochondrial DNA promoted by natural selection in the Japanese pipistrelle bat (Pipistrellus abramus). Genetica 2014; 142:483-94. [DOI: 10.1007/s10709-014-9794-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/23/2014] [Indexed: 10/24/2022]
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772
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Matosiuk M, Sheremetyeva IN, Sheremetyev IS, Saveljev AP, Borkowska A. Evolutionary neutrality of mtDNA introgression: evidence from complete mitogenome analysis in roe deer. J Evol Biol 2014; 27:2483-94. [PMID: 25262616 DOI: 10.1111/jeb.12491] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 08/17/2014] [Accepted: 09/01/2014] [Indexed: 01/29/2023]
Abstract
Introgressive hybridization offers a unique platform for studying the molecular basis of natural selection acting on mitogenomes. Most of the mtDNA protein-coding genes are extremely conserved; however, some of the observed variations have potentially adaptive significance. Here, we evaluated whether the evolution of mtDNA in closely related roe deer species affected by widespread mtDNA introgression is neutral or adaptive. We characterized and compared 16 complete mitogenomes of European (Capreolus capreolus) and Siberian (C. pygargus) roe deer, including four of Siberian origin introgressed into European species. The average sequence divergence of species-specific lineages was estimated at 2.8% and varied across gene classes. Only 21 of 315 fixed differences identified in protein-coding genes represented nonsynonymous changes. Only three of them were determined to have arisen in the C. pygargus lineage since the time to the most recent common ancestor (TMRCA) of both Capreolus species, reflecting a decelerated evolutionary ratio. The almost four-fold higher dN /dS ratio described for the European roe deer lineage is constrained by overall purifying selection, especially pronounced in the ND4 and ND5 genes. We suggest that the highly divergent C. capreolus lineage could have maintained a capability for genomic incorporation of the well-preserved and almost ancestral type of mtDNA present in C. pygargus. Our analyses did not indicate any signs of positive selection for Siberian roe deer mtDNA, suggesting that the present widespread introgression is evolutionarily neutral.
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Affiliation(s)
- M Matosiuk
- Institute of Biology, University of Bialystok, Bialystok, Poland
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773
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Statham MJ, Murdoch J, Janecka J, Aubry KB, Edwards CJ, Soulsbury CD, Berry O, Wang Z, Harrison D, Pearch M, Tomsett L, Chupasko J, Sacks BN. Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories. Mol Ecol 2014; 23:4813-30. [DOI: 10.1111/mec.12898] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Mark J. Statham
- Mammalian Ecology and Conservation Unit; Veterinary Genetics Laboratory; University of California; One Shields Avenue/Old Davis Road Davis CA 95616-8744 USA
| | - James Murdoch
- Rubenstein School of Environment and Natural Resources; 303A Aiken Center; University of Vermont; 81 Carrigan Drive Burlington VT 05405 USA
| | - Jan Janecka
- Department of Biological Sciences; Duquesne University; 600 Forbes Avenue Pittsburgh PA 15282 USA
| | - Keith B. Aubry
- U.S. Forest Service; Pacific Northwest Research Station; Olympia WA 98512 USA
| | - Ceiridwen J. Edwards
- Research Laboratory for Archaeology; University of Oxford; Dyson Perrins Building; South Parks Road Oxford OX1 3QY UK
| | - Carl D. Soulsbury
- School of Life Sciences; University of Lincoln; Brayford Pool Lincoln LN6 7TS UK
| | - Oliver Berry
- CSIRO Marine and Atmospheric Research; Centre for Environment and Life Sciences; Floreat WA 6014 Australia
- Invasive Animals Cooperative Research Centre; School of Animal Biology (M092); The University of Western Australia; Crawley WA 6009 Australia
| | - Zhenghuan Wang
- School of Life Sciences; East China Normal University; No. 3663 North Zhongshan Road 200062 Shanghai China
| | - David Harrison
- Harrison Institute; Bowerwood House; 15 St. Botolph's Road Sevenoaks Kent TN13 3AQ UK
| | - Malcolm Pearch
- Harrison Institute; Bowerwood House; 15 St. Botolph's Road Sevenoaks Kent TN13 3AQ UK
| | - Louise Tomsett
- Mammal Section; Department of Life Sciences; The Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Judith Chupasko
- Mammalogy Department; Harvard Museum of Comparative Zoology; 52 Oxford Street Cambridge MA 02138 USA
| | - Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit; Veterinary Genetics Laboratory; University of California; One Shields Avenue/Old Davis Road Davis CA 95616-8744 USA
- Department of Population Health and Reproduction; University of California; One Shields Avenue/Old Davis Road Davis CA 95616-8744 USA
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774
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Jockusch EL, Martínez-Solano I, Timpe EK. The Effects of Inference Method, Population Sampling, and Gene Sampling on Species Tree Inferences: An Empirical Study in Slender Salamanders (Plethodontidae: Batrachoseps). Syst Biol 2014; 64:66-83. [DOI: 10.1093/sysbio/syu078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Elizabeth L. Jockusch
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Iñigo Martínez-Solano
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Elizabeth K. Timpe
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
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775
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Brunes TO, Alexandrino J, Baêta D, Zina J, Haddad CF, Sequeira F. Species limits, phylogeographic and hybridization patterns in Neotropical leaf frogs (Phyllomedusinae). ZOOL SCR 2014. [DOI: 10.1111/zsc.12079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tuliana O. Brunes
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; 4169-007 Porto Portugal
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - João Alexandrino
- Departamento de Ciências Biológicas; Universidade Federal de São Paulo; 09972-270 Diadema Brasil
| | - Délio Baêta
- Departamento de Zoologia; Instituto de Biociências; Universidade Estadual Paulista; 13506-900 Rio Claro São Paulo Brasil
- Museu Nacional; Departamento de Vertebrados; Setor de Herpetologia; Universidade Federal do Rio de Janeiro; 20940-040 Rio de Janeiro Brasil
| | - Juliana Zina
- Departamento de Ciências Biológicas; Universidade Estadual do Sudoeste da Bahia; 45206-190 Jequié Bahia Brasil
| | - Célio F.B. Haddad
- Departamento de Zoologia; Instituto de Biociências; Universidade Estadual Paulista; 13506-900 Rio Claro São Paulo Brasil
| | - Fernando Sequeira
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
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776
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Furman A, Çoraman E, Çelik YE, Postawa T, Bachanek J, Ruedi M. Cytonuclear discordance and the species status ofMyotis myotisandMyotis blythii(Chiroptera). ZOOL SCR 2014. [DOI: 10.1111/zsc.12076] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrzej Furman
- Institute of Environmental Sciences; Boğazici University; Turkey 34342 Istanbul
| | - Emrah Çoraman
- Institute of Environmental Sciences; Boğazici University; Turkey 34342 Istanbul
| | - Yalin E. Çelik
- Institute of Environmental Sciences; Boğazici University; Turkey 34342 Istanbul
| | - Tomasz Postawa
- Institute of Systematics and Evolution of Animals; Polish Academy of Sciences; Sławkowska 17 31-016 Krakow Poland
| | - Justyna Bachanek
- Institute of Systematics and Evolution of Animals; Polish Academy of Sciences; Sławkowska 17 31-016 Krakow Poland
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology; Natural History Museum of Geneva; Route de Malagnou 1 BP 6434 1211 Geneva 6 Switzerland
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777
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Maura M, Salvi D, Bologna MA, Nascetti G, Canestrelli D. Northern richness and cryptic refugia: phylogeography of the Italian smooth newtLissotriton vulgaris meridionalis. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12360] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michela Maura
- Dipartimento di Scienze; Università degli studi Roma Tre; Viale G. Marconi 446 00146 Rome Italy
| | - Daniele Salvi
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - Marco A. Bologna
- Dipartimento di Scienze; Università degli studi Roma Tre; Viale G. Marconi 446 00146 Rome Italy
| | - Giuseppe Nascetti
- Dipartimento di Scienze Ecologiche e Biologiche; Università della Tuscia; Viale dell'Università s.n.c. I-01100 Viterbo Italy
| | - Daniele Canestrelli
- Dipartimento di Scienze Ecologiche e Biologiche; Università della Tuscia; Viale dell'Università s.n.c. I-01100 Viterbo Italy
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778
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Lee-Yaw JA, Jacobs CGC, Irwin DE. Individual performance in relation to cytonuclear discordance in a northern contact zone between long-toed salamander (Ambystoma macrodactylum) lineages. Mol Ecol 2014; 23:4590-602. [DOI: 10.1111/mec.12878] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 07/01/2014] [Accepted: 07/10/2014] [Indexed: 01/29/2023]
Affiliation(s)
- Julie A. Lee-Yaw
- Department of Zoology; University of British Columbia; 6270 University Blvd. Vancouver British Columbia Canada V6T 1Z4
| | - Chris G. C. Jacobs
- Institute of Biology Leiden; Leiden University; Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Darren E. Irwin
- Department of Zoology; University of British Columbia; 6270 University Blvd. Vancouver British Columbia Canada V6T 1Z4
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779
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Song JH, Ahn KJ. Species delimitation in theAleochara fucicolaspecies complex (Coleoptera: Staphylinidae: Aleocharinae) and its phylogenetic relationships. ZOOL SCR 2014. [DOI: 10.1111/zsc.12077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Jeong-Hun Song
- Department of Biology; Chungnam National University; Daejeon 305-764 South Korea
| | - Kee-Jeong Ahn
- Department of Biology; Chungnam National University; Daejeon 305-764 South Korea
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780
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Malyarchuk B, Derenko M, Denisova G. A mitogenomic phylogeny and genetic history of sable (Martes zibellina). Gene 2014; 550:56-67. [PMID: 25110108 DOI: 10.1016/j.gene.2014.08.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 07/29/2014] [Accepted: 08/06/2014] [Indexed: 12/21/2022]
Abstract
We assessed phylogeny of sable (Martes zibellina, Linnaeus, 1758) by sequence analysis of nearly complete, new mitochondrial genomes in 36 specimens from different localities in northern Eurasia (Primorye, Khabarovsk and Krasnoyarsk regions, the Kamchatka Peninsula, the Kuril Islands and the Urals). Phylogenetic analysis of mtDNA sequences demonstrates that two clades, A and BC, radiated about 200-300 thousandyears ago (kya) according to results of Bayesian molecular clock and RelTime analyses of different mitogenome alignments (nearly complete mtDNA sequences, protein-coding region, and synonymous sites), while the age estimates of clades A, B and C fall within the Late Pleistocene (~50-140 kya). Bayesian skyline plots (BSPs) of sable population size change based on analysis of nearly complete mtDNAs show an expansion around 40 kya in the warm Karganian time, without a decline of population size around the Last Glacial Maximum (21 kya). The BSPs based on synonymous clock rate indicate that M. zibellina experienced demographic expansions later, approximately 22 kya. The A2a clade that colonized Kamchatka ~23-50 kya (depending on the mutation rate used) survived the last glaciation there as demonstrated by the BSP analysis. In addition, we have found evidence of positive selection acting at ND4 and cytochrome b genes, thereby suggesting adaptive evolution of the A2a clade in Kamchatka.
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Affiliation(s)
- Boris Malyarchuk
- Institute of Biological Problems of the North, Magadan, 685000 Russia.
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Magadan, 685000 Russia
| | - Galina Denisova
- Institute of Biological Problems of the North, Magadan, 685000 Russia
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781
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Bryson RW, Smith BT, Nieto-Montes de Oca A, García-Vázquez UO, Riddle BR. The role of mitochondrial introgression in illuminating the evolutionary history of Nearctic treefrogs. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12169] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert W. Bryson
- School of Life Sciences; University of Nevada Las Vegas; Las Vegas NV 89154-4004 USA
- Department of Biology and Burke Museum of Natural History and Culture; University of Washington; Seattle WA 98195-1800 USA
| | - Brian Tilston Smith
- Museum of Natural Science; Louisiana State University; Baton Rouge LA 70803 USA
| | - Adrian Nieto-Montes de Oca
- Museo de Zoología Alfonso L. Herrera; Facultad de Ciencias; Universidad Nacional Autónoma de México; Circuito exterior s/n, Cd. Universitaria México 04510 Distrito Federal Mexico
| | - Uri Omar García-Vázquez
- Museo de Zoología Alfonso L. Herrera; Facultad de Ciencias; Universidad Nacional Autónoma de México; Circuito exterior s/n, Cd. Universitaria México 04510 Distrito Federal Mexico
| | - Brett R. Riddle
- School of Life Sciences; University of Nevada Las Vegas; Las Vegas NV 89154-4004 USA
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782
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Hung CM, Hung HY, Yeh CF, Fu YQ, Chen D, Lei F, Yao CT, Yao CJ, Yang XJ, Lai YT, Li SH. Species delimitation in the Chinese bamboo partridgeBambusicola thoracica(Phasianidae; Aves). ZOOL SCR 2014. [DOI: 10.1111/zsc.12071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chih-Ming Hung
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Hsin-Yi Hung
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Chia-Fen Yeh
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Yi-Qiang Fu
- College of Life Science; Leshan Normal University; Leshan 614000 China
| | - De Chen
- Department of Life Science; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Cheng-Te Yao
- Division of Zoology; Endemic Species Research Institute; Chi-chi Nantou 55244 Taiwan
| | - Chiou-Ju Yao
- Department of Biology; National Museum of Natural Science; Taichung 40453 Taiwan
| | - Xiao-Jun Yang
- Kunming Institute Zoology; Chinese Academy of Sciences; Kunming Yunnan China
| | - Yu-Ting Lai
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Shou-Hsien Li
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
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783
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Dapporto L, Vodă R, Dincă V, Vila R. Comparing population patterns for genetic and morphological markers with uneven sample sizes. An example for the butterflyManiola jurtina. Methods Ecol Evol 2014. [DOI: 10.1111/2041-210x.12220] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Leonardo Dapporto
- Department of Biological and Medical Sciences; Oxford Brookes University; Headington Oxford OX3 0BP UK
| | - Raluca Vodă
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra); Passeig Marítim de la Barceloneta 37 Barcelona 08003 Spain
- Departament de Genètica i Microbiologia; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - Vlad Dincă
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra); Passeig Marítim de la Barceloneta 37 Barcelona 08003 Spain
- Department of Zoology; Stockholm University; Stockholm S-106 91 Sweden
- Biodiversity Institute of Ontario; University of Guelph; Guelph N1G 2W1 ON Canada
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra); Passeig Marítim de la Barceloneta 37 Barcelona 08003 Spain
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784
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Choleva L, Musilova Z, Kohoutova-Sediva A, Paces J, Rab P, Janko K. Distinguishing between incomplete lineage sorting and genomic introgressions: complete fixation of allospecific mitochondrial DNA in a sexually reproducing fish (Cobitis; Teleostei), despite clonal reproduction of hybrids. PLoS One 2014; 9:e80641. [PMID: 24971792 PMCID: PMC4074047 DOI: 10.1371/journal.pone.0080641] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 10/15/2013] [Indexed: 11/19/2022] Open
Abstract
Distinguishing between hybrid introgression and incomplete lineage sorting causing incongruence among gene trees in that they exhibit topological differences requires application of statistical approaches that are based on biologically relevant models. Such study is especially challenging in hybrid systems, where usual vectors mediating interspecific gene transfers--hybrids with Mendelian heredity--are absent or unknown. Here we study a complex of hybridizing species, which are known to produce clonal hybrids, to discover how one of the species, Cobitis tanaitica, has achieved a pattern of mito-nuclear mosaic genome over the whole geographic range. We appplied three distinct methods, including the method using solely the information on gene tree topologies, and found that the contrasting mito-nuclear signal might not have resulted from the retention of ancestral polymorphism. Instead, we found two signs of hybridization events related to C. tanaitica; one concerning nuclear gene flow and the other suggested mitochondrial capture. Interestingly, clonal inheritance (gynogenesis) of contemporary hybrids prevents genomic introgressions and non-clonal hybrids are either absent or too rare to be detected among European Cobitis. Our analyses therefore suggest that introgressive hybridizations are rather old episodes, mediated by previously existing hybrids whose inheritance was not entirely clonal. Cobitis complex thus supports the view that the type of resulting hybrids depends on a level of genomic divergence between sexual species.
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Affiliation(s)
- Lukas Choleva
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Zuzana Musilova
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
- Zoological Institute, Evolutionary Biology, University of Basel, Basel, Switzerland
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Alena Kohoutova-Sediva
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
- Institute of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jan Paces
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the ASCR, v.v.i., Prague, Czech Republic
| | - Petr Rab
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
- Life Science Research Centre, Department of Biology and Ecology, Faculty of Natural Sciences, University of Ostrava, Ostrava, Czech Republic
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785
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Gowen FC, Maley JM, Cicero C, Peterson AT, Faircloth BC, Warr TC, McCormack JE. Speciation in Western Scrub-Jays, Haldane's rule, and genetic clines in secondary contact. BMC Evol Biol 2014; 14:135. [PMID: 24938753 PMCID: PMC4078322 DOI: 10.1186/1471-2148-14-135] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/04/2014] [Indexed: 12/26/2022] Open
Abstract
Background Haldane’s Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between species where females are heterogametic. Therefore, it is important when studying speciation and species limits in female-heterogametic species like birds to assess the signature of gene flow in the nuclear genome as well. We studied introgression of microsatellites and mtDNA across a secondary contact zone between coastal and interior lineages of Western Scrub-Jays (Aphelocoma californica) to test for a signature of Haldane’s Rule: a narrower cline of introgression in mtDNA compared to nuclear markers. Results Our initial phylogeographic analysis revealed that there is only one major area of contact between coastal and interior lineages and identified five genetic clusters with strong spatial structuring: Pacific Slope, Interior US, Edwards Plateau (Texas), Northern Mexico, and Southern Mexico. Consistent with predictions from Haldane’s Rule, mtDNA showed a narrower cline than nuclear markers across a transect through the hybrid zone. This result is not being driven by female-biased dispersal because neutral diffusion analysis, which included estimates of sex-specific dispersal rates, also showed less diffusion of mtDNA. Lineage-specific plumage traits were associated with nuclear genetic profiles for individuals in the hybrid zone, indicating that these differences are under genetic control. Conclusions This study adds to a growing list of studies that support predictions of Haldane’s Rule using cline analysis of multiple loci of differing inheritance modes, although alternate hypotheses like selection on different mtDNA types cannot be ruled out. That Haldane’s Rule appears to be operating in this system suggests a measure of reproductive isolation between the Pacific Slope and interior lineages. Based on a variety of evidence from the phenotype, ecology, and genetics, we recommend elevating three lineages to species level: A. californica (Pacific Slope); A. woodhouseii (Interior US plus Edwards Plateau plus Northern Mexico); A. sumichrasti (Southern Mexico). The distinctive Edwards Plateau population in Texas, which was monophyletic in mtDNA except for one individual, should be studied in greater detail given habitat threat.
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Affiliation(s)
| | | | | | | | | | | | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, USA.
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786
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Peters JL, Winker K, Millam KC, Lavretsky P, Kulikova I, Wilson RE, Zhuravlev YN, McCracken KG. Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas). Mol Ecol 2014; 23:2961-74. [PMID: 24854419 DOI: 10.1111/mec.12799] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/15/2014] [Accepted: 05/16/2014] [Indexed: 11/29/2022]
Abstract
Many species have Holarctic distributions that extend across Europe, Asia and North America. Most genetics research on these species has examined only mitochondrial (mt) DNA, which has revealed wide variance in divergence between Old World (OW) and New World (NW) populations, ranging from shallow, unstructured genealogies to deeply divergent lineages. In this study, we sequenced 20 nuclear introns to test for concordant patterns of OW-NW differentiation between mtDNA and nuclear (nu) DNA for six lineages of Holarctic ducks (genus Anas). Genetic differentiation for both marker types varied widely among these lineages (idiosyncratic population histories), but mtDNA and nuDNA divergence within lineages was not significantly correlated. Moreover, compared with the association between mtDNA and nuDNA divergence observed among different species, OW-NW nuDNA differentiation was generally lower than mtDNA divergence, at least for lineages with deeply divergent mtDNA. Furthermore, coalescent estimates indicated significantly higher rates of gene flow for nuDNA than mtDNA for four of the six lineages. Thus, Holarctic ducks show prominent mito-nuclear discord between OW and NW populations, and we reject differences in sorting rates as the sole cause of the within-species discord. Male-mediated intercontinental gene flow is likely a leading contributor to this discord, although selection could also cause increased mtDNA divergence relative to weak nuDNA differentiation. The population genetics of these ducks contribute to growing evidence that mtDNA can be an unreliable indicator of stage of speciation and that more holistic approaches are needed for species delimitation.
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Affiliation(s)
- Jeffrey L Peters
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA
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787
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Okada A, Suzuki H, Inaba M, Horikoshi K, Shindo J. Genetic Structure and Cryptic Genealogy of the Bonin Flying FoxPteropus pselaphonRevealed by Mitochondrial DNA and Microsatellite Markers. ACTA CHIROPTEROLOGICA 2014. [DOI: 10.3161/150811014x683237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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788
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Barrow LN, Ralicki HF, Emme SA, Lemmon EM. Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing. Mol Phylogenet Evol 2014; 75:78-90. [DOI: 10.1016/j.ympev.2014.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 12/24/2013] [Accepted: 02/13/2014] [Indexed: 11/28/2022]
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789
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Gottscho AD, Marks SB, Jennings WB. Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern. Ecol Evol 2014; 4:2546-62. [PMID: 25360285 PMCID: PMC4203297 DOI: 10.1002/ece3.1111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/20/2014] [Accepted: 04/23/2014] [Indexed: 11/16/2022] Open
Abstract
The North American deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA sequences for 14 nuclear loci, and found that U. scoparia has low genetic diversity relative to the U. notata species complex, comparable to that of chimpanzees and southern elephant seals. Analyses of genotypes using Bayesian clustering algorithms did not identify discrete populations within U. scoparia. Using isolation-with-migration (IM) models and a novel coalescent-based hypothesis testing approach, we estimated that U. scoparia diverged from U. notata in the Pleistocene epoch. The likelihood ratio test and the Akaike Information Criterion consistently rejected nested speciation models that included parameters for migration and population growth of U. scoparia. We reject the Neogene vicariance hypothesis for the speciation of U. scoparia and define this species as a single evolutionarily significant unit for conservation purposes.
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Affiliation(s)
- Andrew D Gottscho
- Department of Biological Sciences, Humboldt State University 1 Harpst Street, Arcata, California, 95521 ; Department of Biology, University of California Riverside, California, 92521
| | - Sharyn B Marks
- Department of Biological Sciences, Humboldt State University 1 Harpst Street, Arcata, California, 95521
| | - W Bryan Jennings
- Department of Biological Sciences, Humboldt State University 1 Harpst Street, Arcata, California, 95521
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790
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Canestrelli D, Bisconti R, Sacco F, Nascetti G. What triggers the rising of an intraspecific biodiversity hotspot? Hints from the agile frog. Sci Rep 2014; 4:5042. [PMID: 24853644 PMCID: PMC4031470 DOI: 10.1038/srep05042] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 04/30/2014] [Indexed: 11/09/2022] Open
Abstract
Hotspots of genetic diversity are regions of utmost importance for species survival and conservation, and their intimate link with the geographic location of glacial refugia has been well established. Nonetheless, the microevolutionary processes underlying the generation of hotspots in such regions have only recently become a fervent field of research. We investigated the phylogeographic and population genetic structure of the agile frog, Rana dalmatina, within its putative refugium in peninsular Italy. We found this region to harbour far more diversity, phylogeographic structure, and lineages of ancient origin than that by the rest of the species' range in Europe. This pattern appeared to be well explained by climate-driven microevolutionary processes that occurred during both glacial and interglacial epochs. Therefore, the inferred evolutionary history of R. dalmatina in Italy supports a view of glacial refugia as 'factories' rather than as repositories of genetic diversity, with significant implications for conservation strategies for hotspots.
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Affiliation(s)
- Daniele Canestrelli
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia. Viale dell'Università s.n.c., I-01100 Viterbo, Italy
| | - Roberta Bisconti
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia. Viale dell'Università s.n.c., I-01100 Viterbo, Italy
| | - Florinda Sacco
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia. Viale dell'Università s.n.c., I-01100 Viterbo, Italy
| | - Giuseppe Nascetti
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia. Viale dell'Università s.n.c., I-01100 Viterbo, Italy
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791
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Denton RD, Kenyon LJ, Greenwald KR, Gibbs HL. Evolutionary basis of mitonuclear discordance between sister species of mole salamanders (Ambystoma sp.). Mol Ecol 2014; 23:2811-24. [PMID: 24787951 DOI: 10.1111/mec.12775] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/07/2014] [Accepted: 04/16/2014] [Indexed: 11/29/2022]
Abstract
Distinct genetic markers should show similar patterns of differentiation between species reflecting their common evolutionary histories, yet there are increasing examples of differences in the biogeographic distribution of species-specific nuclear (nuDNA) and mitochondrial DNA (mtDNA) variants within and between species. Identifying the evolutionary processes that underlie these anomalous patterns of genetic differentiation is an important goal. Here, we analyse the putative mitonuclear discordance observed between sister species of mole salamanders (Ambystoma barbouri and A. texanum) in which A. barbouri-specific mtDNA is found in animals located within the range of A. texanum. We test three hypotheses for this discordance (undetected range expansion, mtDNA introgression, and hybridization) using nuDNA and mtDNA data analysed with methods that varied in the parameters estimated and the timescales measured. Results from a Bayesian clustering technique (structure), bidirectional estimates of gene flow (migrate-n and IMa2) and phylogeny-based methods (*beast, bucky) all support the conclusion that the discordance is due to geographically restricted mtDNA introgression from A. barbouri into A. texanum. Limited data on species-specific tooth morphology match this conclusion. Significant differences in environmental conditions exist between sites where A. texanum with and without A. barbouri-like mtDNA occur, suggesting a possible role for selection in the process of introgression. Overall, our study provides a general example of the value of using complimentary analyses to make inferences of the directionality, timescale, and source of mtDNA introgression in animals.
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Affiliation(s)
- Robert D Denton
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, 43210, USA
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792
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van Els P, Spellman GM, Smith BT, Klicka J. Extensive gene flow characterizes the phylogeography of a North American migrant bird: Black-headed Grosbeak (Pheucticus melanocephalus). Mol Phylogenet Evol 2014; 78:148-59. [PMID: 24841539 DOI: 10.1016/j.ympev.2014.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/17/2014] [Accepted: 04/23/2014] [Indexed: 11/26/2022]
Abstract
We describe range-wide phylogeographic variation in the Black-headed Grosbeak (Pheucticus melanocephalus), a songbird that is widely distributed across North American scrublands and forests. Phylogenetic analysis of mitochondrial DNA (mtDNA, n=424) revealed three geographically structured clades. One widespread clade occurs throughout the Rocky Mountains, Great Basin, and Mexican Plateau, a second clade is found on the Pacific coast and in coastal ranges; and, a third in the Sierra Madre del Sur of Oaxaca and Guerrero. Some geographical structuring occurs in Mexican Plateau and Sierra Madre Oriental mtDNA clade, presumably because these populations have been more stable over time than northern populations. Multiple mitochondrial groups are found sympatrically in the Okanogan River Valley in Washington, the eastern Sierra Nevada, and the Transvolcanic Belt across central Mexico, indicating that there is a potential for introgression. Analyses of 12 nuclear loci did not recover the same geographically structured clades. Population analyses show high levels of gene flow in nucDNA from the Interior into the Sierra Madre del Sur and Pacific population groups, possibly indicating expansion of the Interior population at the expense of peripheral populations.
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Affiliation(s)
- Paul van Els
- University of Nevada Las Vegas, Marjorie Barrick Museum of Natural History, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA.
| | - Garth M Spellman
- Center for the Conservation of Biological Resources, School of Natural Sciences, Black Hills State University, Spearfish, SD 57799, USA
| | - Brian Tilston Smith
- University of Nevada Las Vegas, Marjorie Barrick Museum of Natural History, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
| | - John Klicka
- University of Nevada Las Vegas, Marjorie Barrick Museum of Natural History, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
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793
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Wang W, Dai C, Alström P, Zhang C, Qu Y, Li SH, Yang X, Zhao N, Song G, Lei F. Past hybridization between two East Asian long-tailed tits (Aegithalos bonvaloti and A. fuliginosus). Front Zool 2014; 11:40. [PMID: 24883074 PMCID: PMC4040119 DOI: 10.1186/1742-9994-11-40] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/28/2014] [Indexed: 11/13/2022] Open
Abstract
Introduction Incomplete lineage sorting and hybridization are two major nonexclusive causes of haplotype sharing between species. Distinguishing between these two processes is notoriously difficult as they can generate similar genetic signatures. Previous studies revealed that the mitochondrial DNA (mtDNA) differentiation between two East Asian long-tailed tits (Aegithalos bonvaloti and A. fuliginosus) was extremely low, even lower than intraspecific differentiation in some other long-tailed tits. Using a combination of multilocus and coalescent analyses, we explored the causes of the anomalous lack of mtDNA differentiation between the two species. Results The mtDNA divergence between the two species was shallow, while the nuclear DNA (nuDNA) divergence was considerably deeper. The IMa analyses based on the mtDNA dataset suggested relatively high gene flow from A. fuliginosus to A. bonvaloti, while negligible gene flow in the opposite direction. In contrast to mtDNA, the migration rates at autosomal and Z-linked nuDNA loci were negligible or much lower. The NEWHYBRIDS analysis assigned all individuals except one to pure parental species with high posterior probability. The Bayesian skyline plot showed that both species underwent population expansions during the Last Glacial Maximum (LGM), and the ecological niche modelling suggested that their ranges overlapped more during the LGM than at present. Conclusions We suggest that historical hybridization, in combination with selective sweep and/or genetic drift might be the main causes of the extremely low mtDNA differentiation between the two species. The hybridization probably occurred mainly between A. fuliginosus females and A. bonvaloti males. The LGM distribution expansion might have facilitated hybridization, while the post-LGM distribution contraction could have facilitated some mtDNA sorting. Ongoing hybridization between the two species might be very limited, but further studies with more samples from the contact zone are needed to test this conclusion.
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Affiliation(s)
- Wenjuan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, 100101 Beijing, China ; Center for Watershed Ecology, Institute of Life Science, Nanchang University, 330031 Nanchang, China
| | - Chuanyin Dai
- School of Chemistry and Life Sciences, Guizhou Normal College, 550001 Guiyang, China
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, 100101 Beijing, China ; Swedish Species Information Centre, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Chunlan Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, 100101 Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, 100101 Beijing, China
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Xiaojun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
| | - Na Zhao
- Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, 430079 Wuhan, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, 100101 Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, 100101 Beijing, China
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794
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Dunning LT, Dennis AB, Sinclair BJ, Newcomb RD, Buckley TR. Divergent transcriptional responses to low temperature among populations of alpine and lowland species of New Zealand stick insects (Micrarchus). Mol Ecol 2014; 23:2712-26. [DOI: 10.1111/mec.12767] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 04/10/2014] [Accepted: 04/16/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Luke T. Dunning
- Landcare Research; Private Bag 92170 Auckland New Zealand
- School of Biological Sciences; The University of Auckland; Private Bag 92019 Auckland New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution; Palmerston North New Zealand
| | - Alice B. Dennis
- Landcare Research; Private Bag 92170 Auckland New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution; Palmerston North New Zealand
| | - Brent J. Sinclair
- Department of Biology; The University of Western Ontario; London ON Canada N6G 1L3
| | - Richard D. Newcomb
- School of Biological Sciences; The University of Auckland; Private Bag 92019 Auckland New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution; Palmerston North New Zealand
- The New Zealand Institute of Plant & Food Research Limited; Private Bag 92169 Auckland New Zealand
| | - Thomas R. Buckley
- Landcare Research; Private Bag 92170 Auckland New Zealand
- School of Biological Sciences; The University of Auckland; Private Bag 92019 Auckland New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution; Palmerston North New Zealand
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795
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Ashfaq M, Hebert PDN, Mirza JH, Khan AM, Zafar Y, Mirza MS. Analyzing mosquito (Diptera: culicidae) diversity in Pakistan by DNA barcoding. PLoS One 2014; 9:e97268. [PMID: 24827460 PMCID: PMC4036727 DOI: 10.1371/journal.pone.0097268] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 04/16/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Although they are important disease vectors mosquito biodiversity in Pakistan is poorly known. Recent epidemics of dengue fever have revealed the need for more detailed understanding of the diversity and distributions of mosquito species in this region. DNA barcoding improves the accuracy of mosquito inventories because morphological differences between many species are subtle, leading to misidentifications. METHODOLOGY/PRINCIPAL FINDINGS Sequence variation in the barcode region of the mitochondrial COI gene was used to identify mosquito species, reveal genetic diversity, and map the distribution of the dengue-vector species in Pakistan. Analysis of 1684 mosquitoes from 491 sites in Punjab and Khyber Pakhtunkhwa during 2010-2013 revealed 32 species with the assemblage dominated by Culex quinquefasciatus (61% of the collection). The genus Aedes (Stegomyia) comprised 15% of the specimens, and was represented by six taxa with the two dengue vector species, Ae. albopictus and Ae. aegypti, dominant and broadly distributed. Anopheles made up another 6% of the catch with An. subpictus dominating. Barcode sequence divergence in conspecific specimens ranged from 0-2.4%, while congeneric species showed from 2.3-17.8% divergence. A global haplotype analysis of disease-vectors showed the presence of multiple haplotypes, although a single haplotype of each dengue-vector species was dominant in most countries. Geographic distribution of Ae. aegypti and Ae. albopictus showed the later species was dominant and found in both rural and urban environments. CONCLUSIONS As the first DNA-based analysis of mosquitoes in Pakistan, this study has begun the construction of a barcode reference library for the mosquitoes of this region. Levels of genetic diversity varied among species. Because of its capacity to differentiate species, even those with subtle morphological differences, DNA barcoding aids accurate tracking of vector populations.
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Affiliation(s)
- Muhammad Ashfaq
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
- * E-mail:
| | - Paul D. N. Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | - Jawwad H. Mirza
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
| | - Arif M. Khan
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
| | - Yusuf Zafar
- Pakistan Atomic Energy Commission, Islamabad, Pakistan
| | - M. Sajjad Mirza
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
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796
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Sullivan J, Demboski JR, Bell KC, Hird S, Sarver B, Reid N, Good JM. Divergence with gene flow within the recent chipmunk radiation (Tamias). Heredity (Edinb) 2014; 113:185-94. [PMID: 24781803 DOI: 10.1038/hdy.2014.27] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/08/2014] [Accepted: 01/17/2014] [Indexed: 12/25/2022] Open
Abstract
Increasing data have supported the importance of divergence with gene flow (DGF) in the generation of biological diversity. In such cases, lineage divergence occurs on a shorter timescale than does the completion of reproductive isolation. Although it is critical to explore the mechanisms driving divergence and preventing homogenization by hybridization, it is equally important to document cases of DGF in nature. Here we synthesize data that have accumulated over the last dozen or so years on DGF in the chipmunk (Tamias) radiation with new data that quantify very high rates of mitochondrial DNA (mtDNA) introgression among para- and sympatric species in the T. quadrivittatus group in the central and southern Rocky Mountains. These new data (188 cytochrome b sequences) bring the total number of sequences up to 1871; roughly 16% (298) of the chipmunks we have sequenced exhibit introgressed mtDNA. This includes ongoing introgression between subspecies and between both closely related and distantly related taxa. In addition, we have identified several taxa that are apparently fixed for ancient introgressions and in which there is no evidence of ongoing introgression. A recurrent observation is that these introgressions occur between ecologically and morphologically diverged, sometimes non-sister taxa that engage in well-documented niche partitioning. Thus, the chipmunk radiation in western North America represents an excellent mammalian example of speciation in the face of recurrent gene flow among lineages and where biogeography, habitat differentiation and mating systems suggest important roles for both ecological and sexual selection.
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Affiliation(s)
- J Sullivan
- 1] Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA [2] BEACON Center for the Study of Evolution in Action
| | - J R Demboski
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO, USA
| | - K C Bell
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - S Hird
- Department of Biological Sciences and Museum of Natural Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - B Sarver
- 1] Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA [2] BEACON Center for the Study of Evolution in Action
| | - N Reid
- Department of Biological Sciences and Museum of Natural Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - J M Good
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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797
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Matosiuk M, Borkowska A, Świsłocka M, Mirski P, Borowski Z, Krysiuk K, Danilkin AA, Zvychaynaya EY, Saveljev AP, Ratkiewicz M. Unexpected population genetic structure of European roe deer in Poland: an invasion of the mtDNA genome from Siberian roe deer. Mol Ecol 2014; 23:2559-72. [PMID: 24697866 DOI: 10.1111/mec.12745] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 03/31/2014] [Accepted: 03/31/2014] [Indexed: 11/30/2022]
Abstract
Introgressive hybridization is a widespread evolutionary phenomenon which may lead to increased allelic variation at selective neutral loci and to transfer of fitness-related traits to introgressed lineages. We inferred the population genetic structure of the European roe deer (Capreolus capreolus) in Poland from mitochondrial (CR and cyt b) and sex-linked markers (ZFX, SRY, DBY4 and DBY8). Analyses of CR mtDNA sequences from 452 individuals indicated widespread introgression of Siberian roe deer (C. pygargus) mtDNA in the European roe deer genome, 2000 km from the current distribution range of C. pygargus. Introgressed individuals constituted 16.6% of the deer studied. Nearly 75% of them possessed haplotypes belonging to the group which arose 23 kyr ago and have not been detected within the natural range of Siberian roe deer, indicating that majority of present introgression has ancient origin. Unlike the mtDNA results, sex-specific markers did not show signs of introgression. Species distribution modelling analyses suggested that C. pygargus could have extended its range as far west as Central Europe after last glacial maximum. The main hybridization event was probably associated with range expansion of the most abundant European roe deer lineage from western refugia and took place in Central Europe after the Younger Dryas (10.8-10.0 ka BP). Initially, introgressed mtDNA variants could have spread out on the wave of expansion through the mechanism of gene surfing, reaching high frequencies in European roe deer populations and leading to observed asymmetrical gene flow. Human-mediated introductions of C. pygargus had minimal effect on the extent of mtDNA introgression.
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Affiliation(s)
- Maciej Matosiuk
- Institute of Biology, University of Bialystok, Świerkowa 20B, 15-950, Białystok, Poland
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798
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Wielstra B, Arntzen JW. Exploring the effect of asymmetric mitochondrial DNA introgression on estimating niche divergence in morphologically cryptic species. PLoS One 2014; 9:e95504. [PMID: 24743746 PMCID: PMC3990694 DOI: 10.1371/journal.pone.0095504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/27/2014] [Indexed: 11/18/2022] Open
Abstract
If potential morphologically cryptic species, identified based on differentiated mitochondrial DNA, express ecological divergence, this increases support for their treatment as distinct species. However, mitochondrial DNA introgression hampers the correct estimation of ecological divergence. We test the hypothesis that estimated niche divergence differs when considering nuclear DNA composition or mitochondrial DNA type as representing the true species range. We use empirical data of two crested newt species (Amphibia: Triturus) which possess introgressed mitochondrial DNA from a third species in part of their ranges. We analyze the data in environmental space by determining Fisher distances in a principal component analysis and in geographical space by determining geographical overlap of species distribution models. We find that under mtDNA guidance in one of the two study cases niche divergence is overestimated, whereas in the other it is underestimated. In the light of our results we discuss the role of estimated niche divergence in species delineation.
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Affiliation(s)
- Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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799
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Geraghty PT, Williamson JE, Macbeth WG, Blower DC, Morgan JAT, Johnson G, Ovenden JR, Gillings MR. Genetic structure and diversity of two highly vulnerable carcharhinids in Australian waters. ENDANGER SPECIES RES 2014. [DOI: 10.3354/esr00580] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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800
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Boratyński Z, Melo-Ferreira J, Alves PC, Berto S, Koskela E, Pentikäinen OT, Tarroso P, Ylilauri M, Mappes T. Molecular and ecological signs of mitochondrial adaptation: consequences for introgression? Heredity (Edinb) 2014; 113:277-86. [PMID: 24690754 DOI: 10.1038/hdy.2014.28] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 02/18/2014] [Accepted: 02/20/2014] [Indexed: 02/01/2023] Open
Abstract
The evolution of the mitochondrial genome and its potential adaptive impact still generates vital debates. Even if mitochondria have a crucial functional role, as they are the main cellular energy suppliers, mitochondrial DNA (mtDNA) introgression is common in nature, introducing variation in populations upon which selection may act. Here we evaluated whether the evolution of mtDNA in a rodent species affected by mtDNA introgression is explained by neutral expectations alone. Variation in one mitochondrial and six nuclear markers in Myodes glareolus voles was examined, including populations that show mtDNA introgression from its close relative, Myodes rutilus. In addition, we modelled protein structures of the mtDNA marker (cytochrome b) and estimated the environmental envelopes of mitotypes. We found that massive mtDNA introgression occurred without any trace of introgression in the analysed nuclear genes. The results show that the native glareolus mtDNA evolved under past positive selection, suggesting that mtDNA in this system has selective relevance. The environmental models indicate that the rutilus mitotype inhabits colder and drier habitats than the glareolus one that can result from local adaptation or from the geographic context of introgression. Finally, homology models of the cytochrome b protein revealed a substitution in rutilus mtDNA in the vicinity of the catalytic fraction, suggesting that differences between mitotypes may result in functional changes. These results suggest that the evolution of mtDNA in Myodes may have functional, ecological and adaptive significance. This work opens perspective onto future experimental tests of the role of natural selection in mtDNA introgression in this system.
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Affiliation(s)
- Z Boratyński
- 1] Centre of Excellence in Evolutionary Research, Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland [2] CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Associate Laboratory, Universidade do Porto, Vairão, Portugal
| | - J Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Associate Laboratory, Universidade do Porto, Vairão, Portugal
| | - P C Alves
- 1] CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Associate Laboratory, Universidade do Porto, Vairão, Portugal [2] Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal [3] Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - S Berto
- 1] Centre of Excellence in Evolutionary Research, Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland [2] 'TFome and Trancriptome Evolution', Universität Leipzig, Leipzig, Germany
| | - E Koskela
- Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - O T Pentikäinen
- Computational Bioscience Laboratory, Division of Cell and Molecular Biology, Department of Biological and Environmental Science & Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - P Tarroso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Associate Laboratory, Universidade do Porto, Vairão, Portugal
| | - M Ylilauri
- Computational Bioscience Laboratory, Division of Cell and Molecular Biology, Department of Biological and Environmental Science & Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - T Mappes
- Centre of Excellence in Evolutionary Research, Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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