51
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Kuo HC, Chen SF, Fang YP, Cotton JA, Parker JD, Csorba G, Lim BK, Eger JL, Chen CH, Chou CH, Rossiter SJ. Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data. Mol Ecol 2015; 24:5910-26. [PMID: 26475683 DOI: 10.1111/mec.13425] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/13/2015] [Indexed: 11/27/2022]
Abstract
Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and Murina recondita are both endemic to Taiwan and are putative sister species. To test for nonallopatric divergence and gene flow in these taxa, we generated sequences using Sanger and next-generation sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita; however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species Murina eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *beast and isolation-with-migration and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.
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Affiliation(s)
- Hao-Chih Kuo
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Shiang-Fan Chen
- Center for General Education, National Taipei University, New Taipei City, 23741, Taiwan
| | - Yin-Ping Fang
- Department of Biological Resources, National Chiayi University, Chiayi City, 60004, Taiwan
| | - James A Cotton
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Joe D Parker
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Gábor Csorba
- Department of Zoology, Hungarian Natural History Museum, 1088, Budapest, Hungary
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada
| | - Judith L Eger
- Department of Natural History, Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada
| | - Chia-Hong Chen
- Shei-Pa National Park Headquarters, Miaoli County, 36443, Taiwan
| | - Cheng-Han Chou
- Division of Zoology, Endemic Species Research Institute, Nantou County, 552, Taiwan
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
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52
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van de Crommenacker J, Bourgeois YXC, Warren BH, Jackson H, Fleischer-Dogley F, Groombridge J, Bunbury N. Using molecular tools to guide management of invasive alien species: assessing the genetic impact of a recently introduced island bird population. DIVERS DISTRIB 2015. [DOI: 10.1111/ddi.12364] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- J. van de Crommenacker
- Seychelles Islands Foundation; La Ciotat Building, Mont Fleuri, Mahé Victoria Seychelles
- Durrell Institute of Conservation and Ecology (DICE); School of Anthropology and Conservation; University of Kent; Marlowe Building Canterbury Kent UK
| | - Y. X. C. Bourgeois
- Zoologisches Institut, Evolutionsbiologie; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - B. H. Warren
- Institute of Systematic Botany; University of Zurich; Zollikerstrasse 107 8008 Zurich Switzerland
| | - H. Jackson
- Durrell Institute of Conservation and Ecology (DICE); School of Anthropology and Conservation; University of Kent; Marlowe Building Canterbury Kent UK
| | - F. Fleischer-Dogley
- Seychelles Islands Foundation; La Ciotat Building, Mont Fleuri, Mahé Victoria Seychelles
| | - J. Groombridge
- Durrell Institute of Conservation and Ecology (DICE); School of Anthropology and Conservation; University of Kent; Marlowe Building Canterbury Kent UK
| | - N. Bunbury
- Seychelles Islands Foundation; La Ciotat Building, Mont Fleuri, Mahé Victoria Seychelles
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53
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Hague MTJ, Routman EJ. Does population size affect genetic diversity? A test with sympatric lizard species. Heredity (Edinb) 2015; 116:92-8. [PMID: 26306730 DOI: 10.1038/hdy.2015.76] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 06/25/2015] [Accepted: 07/16/2015] [Indexed: 01/09/2023] Open
Abstract
Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations.
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Affiliation(s)
- M T J Hague
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - E J Routman
- Department of Biology, San Francisco State University, San Francisco, CA, USA
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54
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Mosaic genetic differentiation along environmental and geographic gradients indicate divergent selection in a white pine species complex. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9785-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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55
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Liu J, Wang C, Fu D, Hu X, Xie X, Liu P, Zhang Q, Li MH. Phylogeography of Nanorana parkeri (Anura: Ranidae) and multiple refugia on the Tibetan Plateau revealed by mitochondrial and nuclear DNA. Sci Rep 2015; 5:9857. [PMID: 25985205 PMCID: PMC4434895 DOI: 10.1038/srep09857] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/23/2015] [Indexed: 01/31/2023] Open
Abstract
Quaternary climatic changes have been recognized to influence the distribution patterns and evolutionary histories of extant organisms, but their effects on alpine species are not well understood. To investigate the Pleistocene climatic oscillations on the genetic structure of amphibians, we sequenced one mitochondrial and three nuclear DNA fragments in Nanorana parkeri, a frog endemic to the Tibetan Plateau, across its distribution range in the southern plateau. Mitochondrial cytochrome b (Cytb) and three nuclear genes (c-Myc2, Rhod, and Tyr) revealed two distinct lineages (i.e. the lineages East and West), which were strongly geographically structured. The split of the two divergent lineages was dated back earlier than the Middle Pleistocene, probably being associated with climatic and ecological factors. Species distribution modeling, together with the phylogeographic structuring, supported the hypothesis of multiple refugia for N. parkeri on the Tibetan Plateau during the Pleistocene glaciations, and suggested the Yarlung Zangbo valley and the Kyichu catchment to be the potential refugia. Our findings indicate that Pleistocene climatic changes have had a great impact on the evolution and demographic history of N. parkeri. Our study has important implications for conservation of this and other frog species in the Tibetan Plateau.
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Affiliation(s)
- Jun Liu
- 1] CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China [2] Deep-Sea Research Department, Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences (CAS), Sanya 572000, China
| | - Cuimin Wang
- 1] CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China [2] College of Life Sciences, University of the Academy of Sciences, Beijing 100049, China
| | - Dongli Fu
- Gansu Provincial Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaoju Hu
- 1] CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China [2] College of Life Sciences, University of the Academy of Sciences, Beijing 100049, China
| | - Xiangmo Xie
- 1] CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China [2] College of Life Sciences, Yangtze University, Jingzhou 434025, Hubei, China
| | - Pengfei Liu
- 1] CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China [2] College of Life Sciences, University of the Academy of Sciences, Beijing 100049, China
| | - Qiong Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
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56
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Stanley WT, Hutterer R, Giarla TC, Esselstyn JA. Phylogeny, phylogeography and geographical variation in theCrocidura monax(Soricidae) species complex from the montane islands of Tanzania, with descriptions of three new species. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12230] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- William T. Stanley
- Science and Education; Field Museum of Natural History; 1400 South Lake Shore Drive Chicago IL 60605 USA
| | - Rainer Hutterer
- Zoologisches Forschungsmuseum Alexander Koenig; Adenauerallee 160 53113 Bonn Germany
| | - Thomas C. Giarla
- Museum of Natural Science and Department of Biological Sciences; Louisiana State University; 119 Foster Hall Baton Rouge LA 70803 USA
| | - Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences; Louisiana State University; 119 Foster Hall Baton Rouge LA 70803 USA
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57
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Peres EA, Sobral-Souza T, Perez MF, Bonatelli IAS, Silva DP, Silva MJ, Solferini VN. Pleistocene niche stability and lineage diversification in the subtropical spider Araneus omnicolor (Araneidae). PLoS One 2015; 10:e0121543. [PMID: 25856149 PMCID: PMC4391720 DOI: 10.1371/journal.pone.0121543] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/02/2015] [Indexed: 11/19/2022] Open
Abstract
The influence of Quaternary climate oscillations on the diversification of the South American fauna is being increasingly explored. However, most of these studies have focused on taxa that are endemic to tropical environments, and relatively few have treated organisms restricted to subtropical biomes. Here we used an integrative phylogeographical framework to investigate the effects of these climate events on the ecological niche and genetic patterns of the subtropical orb-weaver spider Araneus omnicolor (Araneidae). We analyzed the mitochondrial (Cytochrome Oxidase I, COI) and nuclear (Internal Transcribed Subunit II, ITS2) DNA of 130 individuals throughout the species' range, and generated distribution models in three different climate scenarios [present, Last Glacial Maximum (LGM), and Last Interglacial Maximum (LIG)]. Additionally, we used an Approximate Bayesian Computation (ABC) approach to compare possible demographic scenarios and select the hypothesis that better explains the genetic patterns of A. omnicolor. We obtained high haplotype diversity but low nucleotide variation among sequences. The population structure and demographic analyses showed discrepancies between markers, suggesting male-biased dispersal in the species. The time-calibrated COI phylogenetic inference showed a recent diversification of lineages (Middle/Late Pleistocene), while the paleoclimate modeling indicated niche stability since ~120 Kya. The ABC results agreed with the niche models, supporting a panmictic population as the most likely historical scenario for the species. These results indicate that A. omnicolor experienced no niche or population reductions during the Late Pleistocene, despite the intense landscape modifications that occurred in the subtropical region, and that other factors beside LGM and LIG climate oscillations might have contributed to the demographic history of this species. This pattern may be related to the high dispersal ability and wide environmental tolerance of A. omnicolor, highlighting the need for more phylogeographical studies with invertebrates and other generalist taxa, in order to understand the effects of Quaternary climate changes on Neotropical biodiversity.
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Affiliation(s)
- Elen A. Peres
- Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Thadeu Sobral-Souza
- Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Manolo F. Perez
- Department of Biology, Federal University of São Carlos, Sorocaba, São Paulo, Brazil
| | | | - Daniel P. Silva
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Márcio J. Silva
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Vera N. Solferini
- Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
- * E-mail:
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58
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Laakkonen HM, Strelkov P, Väinölä R. Molecular lineage diversity and inter-oceanic biogeographical history inHiatella(Mollusca, Bivalvia). ZOOL SCR 2015. [DOI: 10.1111/zsc.12105] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Hanna M. Laakkonen
- Finnish Museum of Natural History; POB 17 FI-00014 University of Helsinki Finland
| | - Petr Strelkov
- Department of Ichthyology and Hydrobiology; St. Petersburg State University; 16 Line, 29 Vasilevsky Island Saint Petersburg 199178 Russia
| | - Risto Väinölä
- Finnish Museum of Natural History; POB 17 FI-00014 University of Helsinki Finland
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59
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Garrick RC, Kajdacsi B, Russello MA, Benavides E, Hyseni C, Gibbs JP, Tapia W, Caccone A. Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises. Ecol Evol 2015; 5:676-94. [PMID: 25691990 PMCID: PMC4328771 DOI: 10.1002/ece3.1388] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 02/05/2023] Open
Abstract
Long-term population history can influence the genetic effects of recent bottlenecks. Therefore, for threatened or endangered species, an understanding of the past is relevant when formulating conservation strategies. Levels of variation at neutral markers have been useful for estimating local effective population sizes (N e ) and inferring whether population sizes increased or decreased over time. Furthermore, analyses of genotypic, allelic frequency, and phylogenetic information can potentially be used to separate historical from recent demographic changes. For 15 populations of Galápagos giant tortoises (Chelonoidis sp.), we used 12 microsatellite loci and DNA sequences from the mitochondrial control region and a nuclear intron, to reconstruct demographic history on shallow (past ∽100 generations, ∽2500 years) and deep (pre-Holocene, >10 thousand years ago) timescales. At the deep timescale, three populations showed strong signals of growth, but with different magnitudes and timing, indicating different underlying causes. Furthermore, estimated historical N e of populations across the archipelago showed no correlation with island age or size, underscoring the complexity of predicting demographic history a priori. At the shallow timescale, all populations carried some signature of a genetic bottleneck, and for 12 populations, point estimates of contemporary N e were very small (i.e., < 50). On the basis of the comparison of these genetic estimates with published census size data, N e generally represented ∽0.16 of the census size. However, the variance in this ratio across populations was considerable. Overall, our data suggest that idiosyncratic and geographically localized forces shaped the demographic history of tortoise populations. Furthermore, from a conservation perspective, the separation of demographic events occurring on shallow versus deep timescales permits the identification of naturally rare versus newly rare populations; this distinction should facilitate prioritization of management action.
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Affiliation(s)
- Ryan C Garrick
- Department of Biology, University of MississippiOxford, Mississippi, 38677
| | - Brittney Kajdacsi
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
| | - Michael A Russello
- Department of Biology, University of British ColumbiaOkanagan Campus, Kelowna, British Columbia, V1V 1V7, Canada
| | - Edgar Benavides
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
| | - Chaz Hyseni
- Department of Biology, University of MississippiOxford, Mississippi, 38677
| | - James P Gibbs
- College of Environmental Science and Forestry, State University of New YorkSyracuse, New York, 13210
| | - Washington Tapia
- Department of Applied Research, Galápagos National Park ServicePuerto Ayora, Galápagos, Ecuador
- Biodiver S.A. ConsultoresKm 5 Vía a Baltra, Isla Santa Cruz, Galápagos, Ecuador
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
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60
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Cytonuclear discordance and historical demography of two brown frogs, Rana tagoi and R. sakuraii (Amphibia: Ranidae). Mol Phylogenet Evol 2014; 79:231-9. [DOI: 10.1016/j.ympev.2014.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 11/19/2022]
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61
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Melo-Ferreira J, Seixas FA, Cheng E, Mills LS, Alves PC. The hidden history of the snowshoe hare,Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation. Mol Ecol 2014; 23:4617-30. [DOI: 10.1111/mec.12886] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 01/09/2023]
Affiliation(s)
- José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO - Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - Fernando A. Seixas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO - Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Departamento Biologia; Faculdade de Ciências da Universidade do Porto; 4099-002 Porto Portugal
| | - Ellen Cheng
- Wildlife Biology; University of Montana; 32 Campus Drive Missoula MT 59812 USA
- Ugyen Wangchuck Institute for Conservation and Environment; Lamai Goempa Bumthang Bhutan
| | - L. Scott Mills
- Wildlife Biology; University of Montana; 32 Campus Drive Missoula MT 59812 USA
- Fisheries, Wildlife and Conservation Biology Program; North Carolina State University; Raleigh NC 27695-7617 USA
| | - Paulo C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO - Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Departamento Biologia; Faculdade de Ciências da Universidade do Porto; 4099-002 Porto Portugal
- Wildlife Biology; University of Montana; 32 Campus Drive Missoula MT 59812 USA
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62
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Quinzin MC, Mardulyn P. Multi-locus DNA sequence variation in a complex of four leaf beetle species with parapatric distributions: Mitochondrial and nuclear introgressions reveal recent hybridization. Mol Phylogenet Evol 2014; 78:14-24. [DOI: 10.1016/j.ympev.2014.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 04/05/2014] [Accepted: 05/02/2014] [Indexed: 11/30/2022]
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63
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Ornelas JF, González C. Interglacial genetic diversification of Moussonia deppeana (Gesneriaceae), a hummingbird-pollinated, cloud forest shrub in northern Mesoamerica. Mol Ecol 2014; 23:4119-36. [PMID: 24954419 DOI: 10.1111/mec.12841] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 11/27/2022]
Abstract
Recent empirical work on cloud forest-adapted species supports the role of both old divergences across major geographical areas and more recent divergences attributed to Pleistocene climate changes. The shrub Moussonia deppeana is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling throughout the species range and employing plastid and nuclear markers, we (i) test whether the fragmented distribution is correlated with main evolutionary lineages, (ii) reconstruct its phylogeographical history to infer the history of cloud forest in northern Mesoamerica and (iii) evaluate a set of refugia/vicariance scenarios for the region and demographic patterns of the populations whose ranges expanded and tracked cloud forest conditions during the Last Glacial Maximum. We found a deep evolutionary split in M. deppeana about 6-3 Ma, which could be consistent with a Pliocene divergence. Comparison of variation in plastid and nuclear markers revealed several lineages mostly congruent with their isolated geographical distribution and restricted gene flow among groups. Results of species distribution modelling and coalescent simulations fit a model of multiple refugia diverging during interglacial cycles. The demographic history of M. deppeana is not consistent with an expanding-contracting cloud forest archipelago model during the Last Glacial Maximum. Instead, our data suggest that populations persisted across the geographical range throughout the glacial cycles, and experienced isolation and divergence during interglacial periods.
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Affiliation(s)
- Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec No. 351, El Haya, Xalapa, Veracruz, 91070, México
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64
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Moreno-Letelier A, Mastretta-Yanes A, Barraclough TG. Late Miocene lineage divergence and ecological differentiation of rare endemic Juniperus blancoi: clues for the diversification of North American conifers. THE NEW PHYTOLOGIST 2014; 203:335-347. [PMID: 24611638 DOI: 10.1111/nph.12761] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 02/08/2014] [Indexed: 06/03/2023]
Abstract
Western North America and Mexico contain a large number of conifer species. This diversity could be the product of orographic and climate changes of the late Tertiary and Quaternary. In this study, we focus on the evolutionary history of Juniperus blancoi, in order to determine the impact of climate change and environmental heterogeneity on population differentiation. We estimated the population structure, phylogenetic relationships and historical demography of J. blancoi populations using nuclear genes. We correlated genetic structure with ecological differentiation, divergence times and changes in population size. Populations of J. blancoi are differentiated into three lineages that correspond to low-, mid- and high-altitude populations. The three groups diversified in the late Miocene, early Pliocene, with only a few events of gene flow since then. Two lineages in the north exhibited a pattern of population growth during the Pleistocene that could be linked to climate changes. Populations of J. blancoi experienced significant ecological differentiation and early divergence events, which correspond to periods of global cooling and mountain uplift during the Miocene. This suggests that mountain ranges in tropical and subtropical latitudes play an important role in the speciation and persistence of conifer taxa in diversity hotspots, by providing diverse environmental conditions.
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65
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Kutschera VE, Bidon T, Hailer F, Rodi JL, Fain SR, Janke A. Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow. Mol Biol Evol 2014; 31:2004-17. [PMID: 24903145 PMCID: PMC4104321 DOI: 10.1093/molbev/msu186] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes such as incomplete lineage sorting and introgression can cause gene tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and gene flow estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than 2 My. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional gene flow from Asian black into sloth bears. Moreover, gene flow detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among gene trees hence needs to be recognized as a biologically meaningful signal.
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Affiliation(s)
- Verena E Kutschera
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Tobias Bidon
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Frank Hailer
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Julia L Rodi
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Steven R Fain
- National Fish and Wildlife Forensic Laboratory, Ashland, OR
| | - Axel Janke
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, GermanyInstitute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
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66
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Walter KS, Brown JE, Powell JR. Microhabitat partitioning of Aedes simpsoni (Diptera: Culicidae). JOURNAL OF MEDICAL ENTOMOLOGY 2014; 51:596-604. [PMID: 24897852 PMCID: PMC4119429 DOI: 10.1603/me13097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Yellow fever virus is a reemerging infection responsible for widespread, sporadic outbreaks across Africa. Although Aedes aegypti (L.) is the most important vector globally, in East Africa, epidemics may be vectored by Aedes bromeliae (Theobald), a member of the Aedes simpsoni (Theobald) species complex. The Ae. simpsoni complex contains 10 subspecies, of which Ae. bromeliae alone has been incriminated as a vector of yellow fever virus. However, morphological markers cannot distinguish Ae. bromeliae from conspecifics, including the sympatric and non-anthropophilic Aedes lilii (Theobald). Here, we used three sequenced nuclear markers to examine the population structure of Ae. simpsoni complex mosquitoes collected from diverse habitats in Rabai, Kenya. Gene trees consistently show strong support for the existence of two clades in Rabai, with segregation by habitat. Domestic mosquitoes segregate separately from forest-collected mosquitoes, providing evidence of habitat partitioning on a small spatial scale (< 5 km). Although speculative, these likely represent what have been described as Ae. bromeliae and Ae. lilii, respectively. The observation of high levels of diversity within Rabai indicates that this species complex may exhibit significant genetic differentiation across East Africa. The genetic structure, ecology, and range of this important disease vector are surprisingly understudied and need to be further characterized.
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67
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Ribeiro ÂM, Lloyd P, Dean WRJ, Brown M, Bowie RCK. The ecological and geographic context of morphological and genetic divergence in an understorey-dwelling bird. PLoS One 2014; 9:e85903. [PMID: 24516521 PMCID: PMC3917827 DOI: 10.1371/journal.pone.0085903] [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: 07/08/2013] [Accepted: 12/08/2013] [Indexed: 11/19/2022] Open
Abstract
Advances in understanding the process of species formation require an integrated perspective that includes the evaluation of spatial, ecological and genetic components. One approach is to focus on multiple stages of divergence within the same species. Species that comprise phenotypically different populations segregated in apparently distinct habitats, in which range is presently continuous but was putatively geographically isolated provide an interesting system to study the mechanisms of population divergence. Here, we attempt to elucidate the role of ecology and geography in explaining observed morphological and genetic variation in an understorey-dwelling bird endemic to southeastern Africa, where two subspecies are recognized according to phenotype and habitat affinity. We carried out a range-wide analysis of climatic requirements, morphological and genetic variation across southeast Africa to test the hypothesis that the extent of gene flow among populations of the brown scrub-robin are influenced by their distinct climatic niches. We recovered two distinct trends depending on whether our analyses were hierarchically structured at the subspecies or at the within subspecies level. Between subspecies we found pronounced morphological differentiation associated with strong reproductive isolation (no gene flow) between populations occupying divergent climatic niches characterized by changes in the temperature of the warmest and wettest month. In contrast, within subspecies, we recovered continuous morphological variation with extensive gene flow among populations inhabiting the temperate and sub-tropical forests of southern Africa, despite divergence along the climate axis that is mainly determined by minimum temperature and precipitation of the coldest months. Our results highlight the role of niche divergence as a diversifying force that can promote reproductive isolation in vertebrates.
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Affiliation(s)
- Ângela M. Ribeiro
- Percy FitzPatrick Institute, DST/NRF Centre of Excellence, University of Cape Town, Cape Town, South Africa
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
| | - Penn Lloyd
- Percy FitzPatrick Institute, DST/NRF Centre of Excellence, University of Cape Town, Cape Town, South Africa
| | - W. Richard J. Dean
- Percy FitzPatrick Institute, DST/NRF Centre of Excellence, University of Cape Town, Cape Town, South Africa
| | - Mark Brown
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Rauri C. K. Bowie
- Percy FitzPatrick Institute, DST/NRF Centre of Excellence, University of Cape Town, Cape Town, South Africa
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, United States of America
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68
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Hidden diversity in the Andes: Comparison of species delimitation methods in montane marsupials. Mol Phylogenet Evol 2014; 70:137-51. [DOI: 10.1016/j.ympev.2013.09.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 09/17/2013] [Accepted: 09/20/2013] [Indexed: 11/20/2022]
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69
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Tollis M, Boissinot S. Genetic variation in the green anole lizard (Anolis carolinensis) reveals island refugia and a fragmented Florida during the quaternary. Genetica 2013; 142:59-72. [PMID: 24379168 DOI: 10.1007/s10709-013-9754-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/23/2013] [Indexed: 11/27/2022]
Abstract
The green anole lizard (Anolis carolinensis) is a model organism for behavior and genomics that is native to the southeastern United States. It is currently thought that the ancestors of modern green anoles dispersed to peninsular Florida from Cuba. However, the climatic changes and geological features responsible for the early diversification of A. carolinensis in North America have remained largely unexplored. This is because previous studies (1) differ in their estimates of the divergence times of populations, (2) are based on a single genetic locus or (3) did not test specific hypotheses regarding the geologic and topographic history of Florida. Here we provide a multi-locus study of green anole genetic diversity and find that the Florida peninsula contains a larger number of genetically distinct populations that are more diverse than those on the continental mainland. As a test of the island refugia hypothesis in Pleistocene Florida, we use a coalescent approach to estimate the divergence times of modern green anole lineages. We find that all demographic events occurred during or after the Upper Pliocene and suggest that green anole diversification was driven by population divergence on interglacial island refugia in Florida during the Lower Pleistocene, while the region was often separated from continental North America. When Florida reconnected to the mainland, two separate dispersal events led to the expansion of green anole populations across the Atlantic Seaboard and Gulf Coastal Plain.
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Affiliation(s)
- Marc Tollis
- Biology Department, Queens College, City University of New York (CUNY), 65-30 Kissena Boulevard, Flushing, New York, NY, USA,
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70
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Lischer HE, Excoffier L, Heckel G. Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles. Mol Biol Evol 2013; 31:817-31. [DOI: 10.1093/molbev/mst271] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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71
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Novaes RML, Ribeiro RA, Lemos-Filho JP, Lovato MB. Concordance between phylogeographical and biogeographical patterns in the Brazilian Cerrado: diversification of the endemic tree Dalbergia miscolobium (Fabaceae). PLoS One 2013; 8:e82198. [PMID: 24312640 PMCID: PMC3846898 DOI: 10.1371/journal.pone.0082198] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 10/22/2013] [Indexed: 01/09/2023] Open
Abstract
Few studies have addressed the phylogeography of species of the Cerrado, the largest savanna biome of South America. Here we aimed to investigate the phylogeographical structure of Dalbergia miscolobium, a widespread tree from the Cerrado, and to verify its concordance with plant phylogeographical and biogeographical patterns so far described. A total of 287 individuals from 32 populations were analyzed by sequencing the trnL intron of the chloroplast DNA and the internal transcribed spacer of the nuclear ribosomal DNA. Analysis of population structure and tests of population expansion were performed and the time of divergence of haplotypes was estimated. Twelve and 27 haplotypes were identified in the cpDNA and nrDNA data, respectively. The star-like network configuration and the mismatch distributions indicated a recent spatial and demographic expansion of the species. Consistent with previous tree phylogeographical studies of Cerrado trees, the cpDNA also suggested a recent expansion towards the southern Cerrado. The diversity of D. miscolobium was widespread but high levels of genetic diversity were found in the Central Eastern and in the southern portion of Central Western Cerrado. The combined analysis of cpDNA and nrDNA supported a phylogeographic structure into seven groups. The phylogeographical pattern showed many concordances with biogeographical and phylogeographical studies in the Cerrado, mainly with the Cerrado phytogeographic provinces superimposed to our sampling area. The data reinforced the uniqueness of Northeastern and Southeastern Cerrados and the differentiation between Eastern and Western Central Cerrados. The recent diversification of the species (estimated between the Pliocene and the Pleistocene) and the ‘genealogical concordances’ suggest that a shared and persistent pattern of species diversification might have been present in the Cerrado over time. This is the first time that an extensive ‘genealogical concordance’ between phylogeographic and phytogeographic patterns is shown for the Cerrado biome.
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Affiliation(s)
| | - Renata Acácio Ribeiro
- Departamento de Ciências Biológicas, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brasil
| | - José Pires Lemos-Filho
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
| | - Maria Bernadete Lovato
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
- * E-mail:
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72
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Multi-locus species tree for the Amazonian peacock basses (Cichlidae: Cichla): Emergent phylogenetic signal despite limited nuclear variation. Mol Phylogenet Evol 2013; 69:479-90. [DOI: 10.1016/j.ympev.2013.07.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 07/31/2013] [Accepted: 07/31/2013] [Indexed: 11/18/2022]
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73
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Camargo A, Werneck FP, Morando M, Sites JW, Avila LJ. Quaternary range and demographic expansion of Liolaemus darwinii (Squamata: Liolaemidae) in the Monte Desert of Central Argentina using Bayesian phylogeography and ecological niche modelling. Mol Ecol 2013; 22:4038-54. [PMID: 23786355 DOI: 10.1111/mec.12369] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 04/25/2013] [Accepted: 04/25/2013] [Indexed: 12/29/2022]
Abstract
Until recently, most phylogeographic approaches have been unable to distinguish between demographic and range expansion processes, making it difficult to test for the possibility of range expansion without population growth and vice versa. In this study, we applied a Bayesian phylogeographic approach to reconstruct both demographic and range expansion in the lizard Liolaemus darwinii of the Monte Desert in Central Argentina, during the Late Quaternary. Based on analysis of 14 anonymous nuclear loci and the cytochrome b mitochondrial DNA gene, we detected signals of demographic expansion starting at ~55 ka based on Bayesian Skyline and Skyride Plots. In contrast, Bayesian relaxed models of spatial diffusion suggested that range expansion occurred only between ~95 and 55 ka, and more recently, diffusion rates were very low during demographic expansion. The possibility of population growth without substantial range expansion could account for the shared patterns of demographic expansion during the Last Glacial Maxima (OIS 2 and 4) in fish, small mammals and other lizards of the Monte Desert. We found substantial variation in diffusion rates over time, and very high rates during the range expansion phase, consistent with a rapidly advancing expansion front towards the southeast shown by palaeo-distribution models. Furthermore, the estimated diffusion rates are congruent with observed dispersal rates of lizards in field conditions and therefore provide additional confidence to the temporal scale of inferred phylogeographic patterns. Our study highlights how the integration of phylogeography with palaeo-distribution models can shed light on both demographic and range expansion processes and their potential causes.
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Affiliation(s)
- Arley Camargo
- Unidad de Diversidad, Sistemática y Evolución, Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Boulevard Almirante Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina.
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74
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Bánlaki Z, Szabó JA, Szilágyi Á, Patócs A, Prohászka Z, Füst G, Doleschall M. Intraspecific evolution of human RCCX copy number variation traced by haplotypes of the CYP21A2 gene. Genome Biol Evol 2013; 5:98-112. [PMID: 23241443 PMCID: PMC3595039 DOI: 10.1093/gbe/evs121] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The RCCX region is a complex, multiallelic, tandem copy number variation (CNV). Two complete genes, complement component 4 (C4) and steroid 21-hydroxylase (CYP21A2, formerly CYP21B), reside in its variable region. RCCX is prone to nonallelic homologous recombination (NAHR) such as unequal crossover, generating duplications and deletions of RCCX modules, and gene conversion. A series of allele-specific long-range polymerase chain reaction coupled to the whole-gene sequencing of CYP21A2 was developed for molecular haplotyping. By means of the developed techniques, 35 different kinds of CYP21A2 haplotype variant were experimentally determined from 112 unrelated European subjects. The number of the resolved CYP21A2 haplotype variants was increased to 61 by bioinformatic haplotype reconstruction. The CYP21A2 haplotype variants could be assigned to the haplotypic RCCX CNV structures (the copy number of RCCX modules) in most cases. The genealogy network constructed from the CYP21A2 haplotype variants delineated the origin of RCCX structures. The different RCCX structures were located in tight groups. The minority of groups with identical RCCX structure occurred once in the network, implying monophyletic origin, but the majority of groups occurred several times and in different locations, indicating polyphyletic origin. The monophyletic groups were often created by single unequal crossover, whereas recurrent unequal crossover events generated some of the polyphyletic groups. As a result of recurrent NAHR events, more CYP21A2 haplotype variants with different allele patterns belonged to the same RCCX structure. The intraspecific evolution of RCCX CNV described here has provided a reasonable expectation for that of complex, multiallelic, tandem CNVs in humans.
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Affiliation(s)
- Zsófia Bánlaki
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
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75
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Pavlova A, Amos JN, Joseph L, Loynes K, Austin JJ, Keogh JS, Stone GN, Nicholls JA, Sunnucks P. PERCHED AT THE MITO-NUCLEAR CROSSROADS: DIVERGENT MITOCHONDRIAL LINEAGES CORRELATE WITH ENVIRONMENT IN THE FACE OF ONGOING NUCLEAR GENE FLOW IN AN AUSTRALIAN BIRD. Evolution 2013; 67:3412-28. [DOI: 10.1111/evo.12107] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 03/04/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Alexandra Pavlova
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
| | - J. Nevil Amos
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
| | - Leo Joseph
- Australian National Wildlife Collection; CSIRO Ecosystem Sciences; GPO Box 1700 Canberra Australian Capital Territory 2601 Australia
| | - Kate Loynes
- Division of Evolution; Ecology and Genetics, Building 116, Daley Road, Research School of Biology, The Australian National University; Canberra Australian Capital Territory 0200 Australia
| | - Jeremy J. Austin
- Australian Centre for Ancient DNA (ACAD); School of Earth & Environmental Sciences, The University of Adelaide; Darling Building North Terrace Campus South Australia 5005 Australia
- Sciences Department; Museum Victoria; Carlton Gardens Melbourne Victoria 3001 Australia
| | - J. Scott Keogh
- Division of Evolution; Ecology and Genetics, Building 116, Daley Road, Research School of Biology, The Australian National University; Canberra Australian Capital Territory 0200 Australia
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road Edinburgh EH9 3JT Scotland
| | - James A. Nicholls
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road Edinburgh EH9 3JT Scotland
| | - Paul Sunnucks
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
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76
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Thomas M, Demeulenaere E, Dawson JC, Khan AR, Galic N, Jouanne-Pin S, Remoue C, Bonneuil C, Goldringer I. On-farm dynamic management of genetic diversity: the impact of seed diffusions and seed saving practices on a population-variety of bread wheat. Evol Appl 2013; 5:779-95. [PMID: 23346224 PMCID: PMC3552397 DOI: 10.1111/j.1752-4571.2012.00257.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 02/20/2012] [Indexed: 12/03/2022] Open
Abstract
Since the domestication of crop species, humans have derived specific varieties for particular uses and shaped the genetic diversity of these varieties. Here, using an interdisciplinary approach combining ethnobotany and population genetics, we document the within-variety genetic structure of a population-variety of bread wheat (Triticum aestivum L.) in relation to farmers’ practices to decipher their contribution to crop species evolution. Using 19 microsatellites markers, we conducted two complementary graph theory-based methods to analyze population structure and gene flow among 19 sub-populations of a single population-variety [Rouge de Bordeaux (RDB)]. The ethnobotany approach allowed us to determine the RDB history including diffusion and reproduction events. We found that the complex genetic structure among the RDB sub-populations is highly consistent with the structure of the seed diffusion and reproduction network drawn based on the ethnobotanical study. This structure highlighted the key role of the farmer-led seed diffusion through founder effects, selection and genetic drift because of human practices. An important result is that the genetic diversity conserved on farm is complementary to that found in the genebank indicating that both systems are required for a more efficient crop diversity conservation.
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Affiliation(s)
- Mathieu Thomas
- INRA, UMR 0320 / UMR 8120 Génétique Végétale Gif-sur-Yvette, France
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77
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Lizards on ice: evidence for multiple refugia in Liolaemus pictus (Liolaemidae) during the last glacial maximum in the Southern Andean beech forests. PLoS One 2012; 7:e48358. [PMID: 23209552 PMCID: PMC3507886 DOI: 10.1371/journal.pone.0048358] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/24/2012] [Indexed: 11/23/2022] Open
Abstract
Historical climate changes and orogenesis are two important factors that have shaped intraspecific biodiversity patterns worldwide. Although southern South America has experienced such complex events, there is a paucity of studies examining the effects on intraspecific diversification in this part of the world. Liolaemus pictus is the southernmost distributed lizard in the Chilean temperate forest, whose genetic structure has likely been influenced by Pleistocene glaciations. We conducted a phylogeographic study of L. pictus in Chile and Argentina based on one mitochondrial and two nuclear genes recovering two strongly divergent groups, Northern and Southern clades. The first group is distributed from the northernmost limit of the species to the Araucanía region while the second group is distributed throughout the Andes and the Chiloé archipelago in Southern Chile. Our results suggest that L. pictus originated 751 Kya, with divergence between the two clades occurring in the late Pleistocene. Demographic reconstructions for the Northern and Southern clades indicate a decrease in effective population sizes likely associated with Pleistocene glaciations. Surprisingly, patterns of genetic variation, clades age and historical gene flow in populations distributed within the limits of the Last Glacial Maximum (LGM) are not explained by recent colonization. We propose an “intra-Andean multiple refuge” hypothesis, along with the classical refuge hypothesis previously proposed for the biota of the Chilean Coastal range and Eastern Andean Cordillera. Our hypothesis is supported by niche modelling analysis suggesting the persistence of fragments of suitable habitat for the species within the limits of the LGM ice shield. This type of refuge hypothesis is proposed for the first time for an ectothermic species.
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78
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Paupério J, Herman JS, Melo-Ferreira J, Jaarola M, Alves PC, Searle J. Cryptic speciation in the field vole: a multilocus approach confirms three highly divergent lineages in Eurasia. Mol Ecol 2012; 21:6015-32. [DOI: 10.1111/mec.12024] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 07/14/2012] [Accepted: 07/25/2012] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - J. 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
| | - M. Jaarola
- Department of Clinical and Experimental Medicine; Linköping University; 581 85; Linköping; Sweden
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79
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Zhou W, Yan F, Fu J, Wu S, Murphy RW, Che J, Zhang Y. River islands, refugia and genetic structuring in the endemic brown frog Rana kukunoris (Anura, Ranidae) of the Qinghai-Tibetan Plateau. Mol Ecol 2012; 22:130-42. [PMID: 23116243 DOI: 10.1111/mec.12087] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/30/2012] [Accepted: 09/04/2012] [Indexed: 11/30/2022]
Abstract
Frequently, Pleistocene climatic cycling has been found to be the diver of genetic structuring in populations, even in areas that did not have continental ice sheets, such as on the Qinghai-Tibetan Plateau (QTP). Typically, species distributed on the plateau have been hypothesized to re-treat to south-eastern refugia, especially during the Last Glacial Maximum (LGM). We evaluated sequence variation in the mitochondrial DNA gene Cytb and the nuclear DNA gene RAG-1 in Rana kukunoris, a species endemic to the QTP. Two major lineages, N and S, were identified, and lineage N was further subdivided into N1 and N2. The geographical distribution and genealogical divergences supported the hypothesis of multiple refugia. However, major lineages and sublineages diverged prior to the LGM. Demographical expansion was detected only in lineage S and sublineage N2. Sublineage N1 might have survived several glacial cycles in situ and did not expand after the LGM because of the absence of suitable habitat; it survived in river islands. Genetic analysis and environment modelling suggested that the north-eastern edge of QTP contained a major refugium for R. kukunoris. From here, lineage S dispersed southwards after the LGM. Two microrefugia in northern Qilian Mountains greatly contributed to current level of intraspecific genetic diversity. These results were found to have important implications for the habitat conservation in Northwest China.
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Affiliation(s)
- Weiwei Zhou
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
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80
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Dobson AE, Schmidt DJ, Hughes JM. Sequence Variation in the Melanocortin-1 Receptor (MC1R) Does Not Explain Continent-wide Plumage Color Differences in the Australian Magpie (Cracticus tibicen). J Hered 2012; 103:769-80. [DOI: 10.1093/jhered/ess053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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81
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Ribeiro AM, Lopes RJ, Bowie RCK. Historical demographic dynamics underlying local adaptation in the presence of gene flow. Ecol Evol 2012; 2:2710-21. [PMID: 23170207 PMCID: PMC3501624 DOI: 10.1002/ece3.390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 08/28/2012] [Accepted: 09/03/2012] [Indexed: 11/11/2022] Open
Abstract
The range of a species is the result of the relative contribution of spatial tracking of environmental requirements and adaptation to ecological conditions outside the ancestral niche. The appearance of novel habitats caused by climatic oscillation can promote range expansion and accompanying demographic growth. The demographic dynamics of populations leave a signal in \ patterns. We modeled three competing scenarios pertaining to the circumstance of a range expansion by the Karoo Scrub-Robin into newly available habitat resulting from the increasing aridification of southern Africa. Genetic variation was contrasted with the theoretical expectations of a spatial range expansion, and compared with data of a putative adaptive trait. We infer that this bird likely colonized the arid zone, as a consequence of adaptive evolution in a small peripheral population, followed by an expansion with recurrent exchange of migrants with the ancestral populations.
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Affiliation(s)
- Angela M Ribeiro
- Percy FitzPatrick Institute, DST/NRF Centre of Excellence, University of Cape Town Rondebosch, 7701, South Africa ; Museum of Vertebrate Zoology, Department of Integrative Biology, University of California 3101 Valley Life Science Building, Berkeley, California, 94720, USA
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82
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Jacobsen F, Omland KE. Extensive introgressive hybridization within the northern oriole group (Genus Icterus) revealed by three-species isolation with migration analysis. Ecol Evol 2012; 2:2413-29. [PMID: 23145328 PMCID: PMC3492769 DOI: 10.1002/ece3.365] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 07/30/2012] [Accepted: 07/31/2012] [Indexed: 12/18/2022] Open
Abstract
Until recently, studies of divergence and gene flow among closely-related taxa were generally limited to pairs of sister taxa. However, organisms frequently exchange genes with other non-sister taxa. The “northern oriole” group within genus Icterus exemplifies this problem. This group involves the extensively studied hybrid zone between Baltimore oriole (Icterus galbula) and Bullock's oriole (I. bullockii), an alleged hybrid zone between I. bullockii and black-backed oriole (I. abeillei), and likely mtDNA introgression between I. galbula and I. abeillei. Here, we examine the divergence population genetics of the entire northern oriole group using a multipopulation Isolation-with-Migration (IM) model. In accordance with Haldane's rule, nuclear loci introgress extensively beyond the I. galbula–I. bullockii hybrid zone, while mtDNA does not. We found no evidence of introgression between I. bullockii and I. abeillei or between I. galbula and I. abeillei when all three species were analyzed together in a three-population model. However, traditional pairwise analysis suggested some nuclear introgression from I. abeillei into I. galbula, probably reflecting genetic contributions from I. bullockii unaccounted for in a two-population model. Thus, only by including all members of this group in the analysis was it possible to rigorously estimate the level of gene flow among these three closely related species.
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Affiliation(s)
- Frode Jacobsen
- Department of Biological Sciences, University of Maryland Baltimore County 1000 Hilltop Circle, Baltimore, MD, 21250, USA
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83
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CHENUIL A. How to infer reliable diploid genotypes from NGS or traditional sequence data: from basic probability to experimental optimization. J Evol Biol 2012; 25:949-60. [DOI: 10.1111/j.1420-9101.2012.02488.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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84
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Melo-Ferreira J, Boursot P, Carneiro M, Esteves PJ, Farelo L, Alves PC. Recurrent Introgression of Mitochondrial DNA Among Hares (Lepus spp.) Revealed by Species-Tree Inference and Coalescent Simulations. Syst Biol 2011; 61:367-81. [DOI: 10.1093/sysbio/syr114] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- J. Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485−661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099−002 Porto, Portugal
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l'Evolution, 34095 Montpellier cedex 5, France
| | - P. Boursot
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l'Evolution, 34095 Montpellier cedex 5, France
| | - M. Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485−661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099−002 Porto, Portugal
| | - P. J. Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485−661 Vairão, Portugal
- CITS—Centro de Investigação em Tecnologias da Saúde, IPSN, Gandra, CESPU, Portugal
| | - L. Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485−661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099−002 Porto, Portugal
| | - P. C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485−661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099−002 Porto, Portugal
- University of Montana, Wildlife Biology Program, College of Forestry and Conservation, Missoula, MT 59812, USA
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85
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ROCHA SARA, HARRIS DJAMES, POSADA DAVID. Cryptic diversity within the endemic prehensile-tailed geckoUrocotyledon inexpectataacross the Seychelles Islands: patterns of phylogeographical structure and isolation at the multilocus level. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01710.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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86
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The Invertebrate Life of New Zealand: A Phylogeographic Approach. INSECTS 2011; 2:297-325. [PMID: 26467729 PMCID: PMC4553545 DOI: 10.3390/insects2030297] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/16/2011] [Accepted: 06/17/2011] [Indexed: 11/17/2022]
Abstract
Phylogeography contributes to our knowledge of regional biotas by integrating spatial and genetic information. In New Zealand, comprising two main islands and hundreds of smaller ones, phylogeography has transformed the way we view our biology and allowed comparison with other parts of the world. Here we review studies on New Zealand terrestrial and freshwater invertebrates. We find little evidence of congruence among studies of different taxa; instead there are signatures of partitioning in many different regions and expansion in different directions. A number of studies have revealed unusually high genetic distances within putative species, and in those where other data confirm this taxonomy, the revealed phylogeographic structure contrasts with northern hemisphere continental systems. Some taxa show a signature indicative of Pliocene tectonic events encompassing land extension and mountain building, whereas others are consistent with range expansion following the last glacial maximum (LGM) of the Pleistocene. There is some indication that montane taxa are more partitioned than lowland ones, but this observation is obscured by a broad range of patterns within the sample of lowland/forest taxa. We note that several geophysical processes make similar phylogeographic predictions for the same landscape, rendering confirmation of the drivers of partitioning difficult. Future multi-gene analyses where applied to testable alternative hypotheses may help resolve further the rich evolutionary history of New Zealand's invertebrates.
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87
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Sorenson MD, DaCosta JM. Genotyping HapSTR loci: phase determination from direct sequencing of PCR products. Mol Ecol Resour 2011; 11:1068-75. [PMID: 21692999 DOI: 10.1111/j.1755-0998.2011.03036.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
HapSTRs combine information from a microsatellite (or simple tandem repeat, STR) with one or more single nucleotide polymorphisms in the DNA sequence immediately flanking the STR. These loci may offer increased power for the estimation of demographic parameters, but also present some challenges for data collection and analysis. We describe a process for inferring HapSTR alleles, including the flanking haplotypes, STR alleles and their phase relative to each other, directly from DNA sequence electropherograms of PCR products from heterozygous individuals. Our approach eliminates the need for more costly and time-consuming processes, such as cloning or acrylamide gel electrophoresis to separate alleles prior to sequencing.
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Affiliation(s)
- Michael D Sorenson
- Department of Biology, Boston University, 5 Cummington St., Boston, MA 02215, USA.
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88
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Miraldo A, Hewitt GM, Paulo OS, Emerson BC. Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: multiple refugia, range expansions and secondary contact zones. BMC Evol Biol 2011; 11:170. [PMID: 21682856 PMCID: PMC3141430 DOI: 10.1186/1471-2148-11-170] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 06/17/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Iberian Peninsula is recognized as an important refugial area for species survival and diversification during the climatic cycles of the Quaternary. Recent phylogeographic studies have revealed Iberia as a complex of multiple refugia. However, most of these studies have focused either on species with narrow distributions within the region or species groups that, although widely distributed, generally have a genetic structure that relates to pre-Quaternary cladogenetic events. In this study we undertake a detailed phylogeographic analysis of the lizard species, Lacerta lepida, whose distribution encompasses the entire Iberian Peninsula. We attempt to identify refugial areas, recolonization routes, zones of secondary contact and date demographic events within this species. RESULTS Results support the existence of 6 evolutionary lineages (phylogroups) with a strong association between genetic variation and geography, suggesting a history of allopatric divergence in different refugia. Diversification within phylogroups is concordant with the onset of the Pleistocene climatic oscillations. The southern regions of several phylogroups show a high incidence of ancestral alleles in contrast with high incidence of recently derived alleles in northern regions. All phylogroups show signs of recent demographic and spatial expansions. We have further identified several zones of secondary contact, with divergent mitochondrial haplotypes occurring in narrow zones of sympatry. CONCLUSIONS The concordant patterns of spatial and demographic expansions detected within phylogroups, together with the high incidence of ancestral haplotypes in southern regions of several phylogroups, suggests a pattern of contraction of populations into southern refugia during adverse climatic conditions from which subsequent northern expansions occurred. This study supports the emergent pattern of multiple refugia within Iberia but adds to it by identifying a pattern of refugia coincident with the southern distribution limits of individual evolutionary lineages. These areas are important in terms of long-term species persistence and therefore important areas for conservation.
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Affiliation(s)
- Andreia Miraldo
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7J, UK.
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89
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Domínguez-Domínguez O, Vila M, Pérez-Rodríguez R, Remón N, Doadrio I. Complex evolutionary history of the Mexican stoneroller Campostoma ornatum Girard, 1856 (Actinopterygii: Cyprinidae). BMC Evol Biol 2011; 11:153. [PMID: 21639931 PMCID: PMC3141424 DOI: 10.1186/1471-2148-11-153] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 06/04/2011] [Indexed: 11/12/2022] Open
Abstract
Background Studies of the phylogeography of Mexican species are steadily revealing genetic patterns shared by different species, which will help to unravel the complex biogeographic history of the region. Campostoma ornatum is a freshwater fish endemic to montane and semiarid regions in northwest Mexico and southern Arizona. Its wide range of distribution and the previously observed morphological differentiation between populations in different watersheds make this species a useful model to investigate the biogeographic role of the Sierra Madre Occidental and to disentangle the actions of Pliocene tecto-volcanic processes vs Quaternary climatic change. Our phylogeographic study was based on DNA sequences from one mitochondrial gene (cytb, 1110 bp, n = 285) and two nuclear gene regions (S7 and RAG1, 1822 bp in total, n = 56 and 43, respectively) obtained from 18 to 29 localities, in addition to a morphological survey covering the entire distribution area. Such a dataset allowed us to assess whether any of the populations/lineages sampled deserve to be categorised as an evolutionarily significant unit. Results We found two morphologically and genetically well-differentiated groups within C. ornatum. One is located in the northern river drainages (Yaqui, Mayo, Fuerte, Sonora, Casas Grandes, Santa Clara and Conchos) and another one is found in the southern drainages (Nazas, Aguanaval and Piaxtla). The split between these two lineages took place about 3.9 Mya (CI = 2.1-5.9). Within the northern lineage, there was strong and significant inter-basin genetic differentiation and also several secondary dispersal episodes whit gene homogenization between drainages. Interestingly, three divergent mitochondrial lineages were found in sympatry in two northern localities from the Yaqui river basin. Conclusions Our results indicate that there was isolation between the northern and southern phylogroups since the Pliocene, which was related to the formation of the ancient Nazas River paleosystem, where the southern group originated. Within groups, a complex reticulate biogeographic history for C. ornatum populations emerges, following the taxon pulse theory and mainly related with Pliocene tecto-volcanic processes. In the northern group, several events of vicariance promoted by river or drainage isolation episodes were found, but within both groups, the phylogeographic patterns suggest the occurrence of several events of river capture and fauna interchange. The Yaqui River supports the most diverse populations of C. ornatum, with several events of dispersal and isolation within the basin. Based on our genetic results, we defined three ESUs within C. ornatum as a first attempt to promote the conservation of the evolutionary processes determining the genetic diversity of this species. They will likely be revealed as a valuable tool for freshwater conservation policies in northwest Mexico, where many environmental problems concerning the use of water have rapidly arisen in recent decades.
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Affiliation(s)
- Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico.
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90
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Alcaide M, Rodríguez A, Negro JJ. Sampling strategies for accurate computational inferences of gametic phase across highly polymorphic major histocompatibility complex loci. BMC Res Notes 2011; 4:151. [PMID: 21615903 PMCID: PMC3126723 DOI: 10.1186/1756-0500-4-151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 05/26/2011] [Indexed: 11/22/2022] Open
Abstract
Background Genes of the Major Histocompatibility Complex (MHC) are very popular genetic markers among evolutionary biologists because of their potential role in pathogen confrontation and sexual selection. However, MHC genotyping still remains challenging and time-consuming in spite of substantial methodological advances. Although computational haplotype inference has brought into focus interesting alternatives, high heterozygosity, extensive genetic variation and population admixture are known to cause inaccuracies. We have investigated the role of sample size, genetic polymorphism and genetic structuring on the performance of the popular Bayesian PHASE algorithm. To cover this aim, we took advantage of a large database of known genotypes (using traditional laboratory-based techniques) at single MHC class I (N = 56 individuals and 50 alleles) and MHC class II B (N = 103 individuals and 62 alleles) loci in the lesser kestrel Falco naumanni. Findings Analyses carried out over real MHC genotypes showed that the accuracy of gametic phase reconstruction improved with sample size as a result of the reduction in the allele to individual ratio. We then simulated different data sets introducing variations in this parameter to define an optimal ratio. Conclusions Our results demonstrate a critical influence of the allele to individual ratio on PHASE performance. We found that a minimum allele to individual ratio (1:2) yielded 100% accuracy for both MHC loci. Sampling effort is therefore a crucial step to obtain reliable MHC haplotype reconstructions and must be accomplished accordingly to the degree of MHC polymorphism. We expect our findings provide a foothold into the design of straightforward and cost-effective genotyping strategies of those MHC loci from which locus-specific primers are available.
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Affiliation(s)
- Miguel Alcaide
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
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91
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Deiner K, Lemmon AR, Mack AL, Fleischer RC, Dumbacher JP. A Passerine Bird's evolution corroborates the geologic history of the island of New Guinea. PLoS One 2011; 6:e19479. [PMID: 21573115 PMCID: PMC3089620 DOI: 10.1371/journal.pone.0019479] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2010] [Accepted: 04/07/2011] [Indexed: 11/18/2022] Open
Abstract
New Guinea is a biologically diverse island, with a unique geologic history and topography that has likely played a role in the evolution of species. Few island-wide studies, however, have examined the phylogeographic history of lowland species. The objective of this study was to examine patterns of phylogeographic variation of a common and widespread New Guinean bird species (Colluricincla megarhyncha). Specifically, we test the mechanisms hypothesized to cause geographic and genetic variation (e.g., vicariance, isolation by distance and founder-effect with dispersal). To accomplish this, we surveyed three regions of the mitochondrial genome and a nuclear intron and assessed differences among 23 of the 30 described subspecies from throughout their range. We found support for eight highly divergent lineages within C. megarhyncha. Genetic lineages were found within continuous lowland habitat or on smaller islands, but all individuals within clades were not necessarily structured by predicted biogeographic barriers. There was some evidence of isolation by distance and potential founder-effects. Mitochondrial DNA sequence divergence among lineages was at a level often observed among different species or even genera of birds (5-11%), suggesting lineages within regions have been isolated for long periods of time. When topographical barriers were associated with divergence patterns, the estimated divergence date for the clade coincided with the estimated time of barrier formation. We also found that dispersal distance and range size are positively correlated across lineages. Evidence from this research suggests that different phylogeographic mechanisms concurrently structure lineages of C. megarhyncha and are not mutually exclusive. These lineages are a result of evolutionary forces acting at different temporal and spatial scales concordant with New Guinea's geological history.
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Affiliation(s)
- Kristy Deiner
- Department of Vertebrate Zoology and Anthropology and Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, United States of America
- Genomic Variation Lab, University of California Davis, Davis, California, United States of America
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, Florida, United States of America
| | - Andrew L. Mack
- Powdermill Nature Reserve, Carnegie Museum of Natural History, Pittsburgh, Pennsylvania, United States of America
| | - Robert C. Fleischer
- Center for Conservation and Evolutionary Genetics, National Zoological Park, Smithsonian Institution, Washington, D.C., United States of America
| | - John P. Dumbacher
- Department of Vertebrate Zoology and Anthropology and Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, United States of America
- Center for Conservation and Evolutionary Genetics, National Zoological Park, Smithsonian Institution, Washington, D.C., United States of America
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92
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Powell JR, Dion K, Papaceit M, Aguadé M, Vicario S, Garrick RC. Nonrecombining genes in a recombination environment: the Drosophila "dot" chromosome. Mol Biol Evol 2010; 28:825-33. [PMID: 20940345 DOI: 10.1093/molbev/msq258] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Rate of recombination is a powerful variable affecting several aspects of molecular variation and evolution. A nonrecombining portion of the genome of most Drosophila species, the "dot" chromosome or F element, exhibits very low levels of variation and unusual codon usage. One lineage of Drosophila, the willistoni/saltans groups, has the F element fused to a normally recombining E element. Here, we present polymorphism data for genes on the F element in two Drosophila willistoni and one D. insularis populations, genes previously studied in D. melanogaster. The D. willistoni populations were known to be very low in inversion polymorphism, thus minimizing the recombination suppression effect of inversions. We first confirmed, by in situ hybridization, that D. insularis has the same E + F fusion as D. willistoni, implying this was a monophyletic event. A clear gradient in codon usage exists along the willistoni F element, from the centromere distally to the fusion with E; estimates of recombination rates parallel this gradient and also indicate D. insularis has greater recombination than D. willistoni. In contrast to D. melanogaster, genes on the F element exhibit moderate levels of nucleotide polymorphism not distinguishable from two genes elsewhere in the genome. Although some linkage disequilibrium (LD) was detected between polymorphic sites within genes (generally <500 bp apart), no long-range LD between F element loci exists in the two willistoni group species. In general, the distribution of allele frequencies of F element genes display the typical pattern of expectations of neutral variation at equilibrium. These results are consistent with the hypothesis that recombination allows the accumulation of nucleotide variation as well as allows selection to act on synonymous codon usage. It is estimated that the fusion occurred ∼20 Mya and while the F element in the willistoni lineage has evolved "normal" levels and patterns of nucleotide variation, equilibrium may not have been reached for codon usage.
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Affiliation(s)
- Jeffrey R Powell
- Department of Ecology and Evolutionary Biology, Yale University.
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