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Lichman V, Ozerov M, López ME, Noreikiene K, Kahar S, Pukk L, Burimski O, Gross R, Vasemägi A. Whole-genome analysis reveals phylogenetic and demographic history of Eurasian perch. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38897597 DOI: 10.1111/jfb.15821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 04/19/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
The contemporary diversity and distribution of species are shaped by their evolutionary and ecological history. This can be deciphered with the help of phylogenetic and demographic analysis methods, ideally combining and supplementing information from mitochondrial and nuclear genomes. In this study, we investigated the demographic history of Eurasian perch (Perca fluviatilis), a highly adaptable teleost with a distribution range across Eurasia. We combined whole-genome resequencing data with available genomic resources to analyse the phylogeny, phylogeography, and demographic history of P. fluviatilis populations from Europe and Siberia. We identified five highly diverged evolutionary mtDNA lineages, three of which show a strong signal of admixture in the Baltic Sea region. The estimated mean divergence time between these lineages ranged from 0.24 to 1.42 million years. Based on nuclear genomes, two distinct demographic trajectories were observed in European and Siberian samples reflecting contrasting demographic histories ca. 30,000-100,000 years before the present. A comparison of mtDNA and nuclear DNA evolutionary trees and AMOVA revealed concordances, as well as incongruences, between the two types of data, most likely reflecting recent postglacial colonization and hybridization events. Overall, our findings demonstrate the power and usefulness of genome-wide information for delineating historical processes that have shaped the genome of P. fluviatilis. We also highlight the added value of data-mining existing transcriptomic resources to complement novel sequence data, helping to shed light on putative glacial refugia and postglacial recolonization routes.
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Affiliation(s)
- Vitalii Lichman
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Mikhail Ozerov
- Biodiversity Unit, University of Turku, Turku, Finland
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
- Department of Biology, University of Turku, Turku, Finland
| | - María-Eugenia López
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | - Kristina Noreikiene
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
- Department of Botany and Genetics, Vilnius University, Vilnius, Lithuania
| | - Siim Kahar
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Lilian Pukk
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Oksana Burimski
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Riho Gross
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Anti Vasemägi
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
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2
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Guinand B, Oral M, Tougard C. Brown trout phylogenetics: A persistent mirage towards (too) many species. JOURNAL OF FISH BIOLOGY 2021; 99:298-307. [PMID: 33483952 DOI: 10.1111/jfb.14686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Bruno Guinand
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Münevver Oral
- Faculty of Fisheries and Aquatic Science, Recep Tayyip Erdogan University, Rize, Turkey
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3
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Takács P, Ferincz Á, Imecs I, Kovács B, Nagy AA, Ihász K, Vitál Z, Csoma E. Increased spatial resolution of sampling in the Carpathian basin helps to understand the phylogeny of central European stream-dwelling gudgeons. BMC ZOOL 2021; 6:3. [PMID: 37170347 PMCID: PMC10127091 DOI: 10.1186/s40850-021-00069-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 02/25/2021] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Phylogenetic studies of widespread European fish species often do not completely cover their entire distribution area, and some areas are often excluded from analyses than others. For example, Carpathian stocks are often omitted from these surveys or are under-represented in the samples. However, this area served as an extra-Mediterranean refugia for many species; therefore, it is assumed that fish stocks here may show special phylogenetic features. For this reason, increased spatial resolution of sampling, namely revealing genetic information from unexamined Carpathian areas within the range of doubtful taxa, may help us better understand their phylogenetic features. To test this hypothesis, a phylogenetic investigation using a partial mtCR sequence data was conducted on 56 stream-dwelling freshwater fish (Gobio spp.) individuals collected from 11 rivers of the data-deficient Southeastern Carpathian area. Moreover, we revieved the available phylogenetic data of Middle-Danubian stream-dwelling gudgeon lineages to delineate their distribution in the area.
Results
Seven out of the nine detected haplotypes were newly described, suggesting the studied area hosts distinct and diverse Gobio stocks. Two valid species (G. obtusirostris, G. gobio), and a haplogroup with doubtful phylogenetic position” G. sp. 1" were detected in the area, showing a specific spatial distribution pattern. The distribution of the detected lineages in the Middle-Danubian area correspond with recent and paleo hydrogeographic features, at the same time mainly on their bordering areas show considerable overlap.
Conclusions
Despite the relatively limited geographic range of the study, our results provide important information which contributes to a better understanding of the phylogenetic, taxonomic and distribution features of Central European gudgeons. The genetically confirmed distribution data of the indicated lineages corresponds well with the recent and near-recent hydrogeographic features of the area, and assumes several hybrid zones in the Carpathian Basin. Additionally, the results show that the middle and lower Danubian watershed cannot be excluded from the range of G. gobio. Moreover, the” G. sp. 1", is slightly differentiated but phylogenetically distinct entity, and is the only Gobio taxa thus far detected in the middle and lower Tisza-basin. However, further investigations are necessary to clarify the taxonomic position of this group.
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Zając KS, Proćków M, Zając K, Stec D, Lachowska-Cierlik D. Phylogeography and potential glacial refugia of terrestrial gastropod Faustina faustina (Rossmässler, 1835) (Gastropoda: Eupulmonata: Helicidae) inferred from molecular data and species distribution models. ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00464-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractFaustina faustina is a conchologically highly diverse forest gastropod with several morphological forms. It is a Carpathian species, but it also occurs in northern isolated localities, where it was probably introduced. We performed the first phylogeographic analysis of 22 populations, based on three molecular markers: COI, ITS-2, and 28S rRNA. Genetic data were complemented by paleo-distribution models of spatial occupancy during the Last Glacial Maximum to strengthen inferences of refugial areas. We discovered high genetic variability of COI sequences with p-distances between haplotypes ranged from 0.2 to 18.1% (6.3–16.6% between clades). For nuclear markers, a haplotype distribution pattern was revealed. Species distribution models indicated a few potential refugia in the Carpathians, with the most climatically stable and largest areas in the Southern Carpathians. In some climate scenarios, putative microrefugia were also predicted in the Western and Eastern Carpathians, and in the Apuseni Mts. Our results suggest the glacial in situ survival of F. faustina and its Holocene expansion in the Sudetes. Although our genetic data as well as shell phenotypes showed considerable variation within and between studied populations, the molecular species delimitation approaches still imply only one single species. Our study contributes to the understanding of the impact of processes on shaping contemporary population genetic structure and diversity in low-dispersal, forest species.
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Marta A, Dedukh D, Bartoš O, Majtánová Z, Janko K. Cytogenetic Characterization of Seven Novel satDNA Markers in Two Species of Spined Loaches ( Cobitis) and Their Clonal Hybrids. Genes (Basel) 2020; 11:genes11060617. [PMID: 32512717 PMCID: PMC7348982 DOI: 10.3390/genes11060617] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 01/11/2023] Open
Abstract
Interspecific hybridization is a powerful evolutionary force. However, the investigation of hybrids requires the application of methodologies that provide efficient and indubitable identification of both parental subgenomes in hybrid individuals. Repetitive DNA, and especially the satellite DNA sequences (satDNA), can rapidly diverge even between closely related species, hence providing a useful tool for cytogenetic investigations of hybrids. Recent progress in whole-genome sequencing (WGS) offers unprecedented possibilities for the development of new tools for species determination, including identification of species-specific satDNA markers. In this study, we focused on spined loaches (Cobitis, Teleostei), a group of fishes with frequent interspecific hybridization. Using the WGS of one species, C. elongatoides, we identified seven satDNA markers, which were mapped by fluorescence in situ hybridization on mitotic and lampbrush chromosomes of C. elongatoides, C. taenia and their triploid hybrids (C. elongatoides × 2C. taenia). Two of these markers were chromosome-specific in both species, one had centromeric localization in multiple chromosomes and four had variable patterns between tested species. Our study provided a novel set of cytogenetic markers for Cobitis species and demonstrated that NGS-based development of satDNA cytogenetic markers may provide a very efficient and easy tool for the investigation of hybrid genomes, cell ploidy, and karyotype evolution.
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Affiliation(s)
- Anatolie Marta
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
- Department of Zoology, Faculty of Science, Charles University in Prague, 128 00 Prague, Czech Republic
- Institute of Zoology, Academy of Science of Moldova, MD-2028, Academiei 1, 2001 Chisinau, Moldova
- Correspondence:
| | - Dmitry Dedukh
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
| | - Oldřich Bartoš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
- Department of Zoology, Faculty of Science, Charles University in Prague, 128 00 Prague, Czech Republic
| | - Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
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Karpova EP. Dynamics of the Structure and Diversity of Fish Communities in Mountain Rivers of the Crimea Based on the Example of the Alma River. RUSS J ECOL+ 2020. [DOI: 10.1134/s106741362002006x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bartáková V, Bryja J, Šanda R, Bektas Y, Stefanov T, Choleva L, Smith C, Reichard M. High cryptic diversity of bitterling fish in the southern West Palearctic. Mol Phylogenet Evol 2018; 133:1-11. [PMID: 30586649 DOI: 10.1016/j.ympev.2018.12.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/24/2018] [Accepted: 12/20/2018] [Indexed: 11/17/2022]
Abstract
South-east Europe, along with the adjacent region of south-west Asia, is an important biodiversity hotspot with high local endemism largely contributed by contemporary continental lineages that retreated to southern refugia during colder Quaternary periods. We investigated the genetic diversity of the European bitterling fish (Rhodeus amarus) species complex (Cyprinidae) across its range in the western Palearctic, but with a particular emphasis in the region of Balkan, Pontic and Caspian refugia. We genotyped 12 polymorphic microsatellite loci and a partial sequence of mitochondrial gene cytochrome b (CYTB) for a set of 1,038 individuals from 60 populations. We used mtDNA sequences to infer phylogenetic relationships and historical demography, and microsatellite markers to describe fine-scale genetic variability and structure. Our mtDNA analysis revealed six well-supported lineages, with limited local co-occurrence. Two lineages are distributed throughout central and western Europe (lineages "A" and "B"), with two zones of secondary contact. Another two lineages were restricted to the Ponto-Aegean region of Greece (lineages "C" and "D") and the final two lineages were restricted south of the Caucasus mountains (lineage "E" from the Black Sea watershed and lineage "F" from the Caspian watershed). A signal of recent expansion was revealed in the two widespread lineages and the Ponto-Aegean lineage "C". The geographic distribution of clusters detected by nuclear microsatellites corresponded well with mitochondrial lineages and demonstrated finely sub-structured populations. A profound population structure suggested a significant role of genetic drift in differentiation among lineages. Lineage divergence in the Ponto-Aegean and Caspian regions are substantial, supporting the validity of two described endemic species (Rhodeus meridionalis as lineage "D" and Rhodeus colchicus as lineage "E") and invite taxonomic evaluation of the other two southern lineages (Thracean "C" and Caspian "F").
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Affiliation(s)
- Veronika Bartáková
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Josef Bryja
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Radek Šanda
- National Museum, Department of Zoology, Václavské nám. 68, 115 79 Prague 1, Czech Republic
| | - Yusuf Bektas
- Department of Basic Sciences, Faculty of Fisheries, Recep Tayyip Erdogan University, 53100 Rize, Turkey
| | - Tihomir Stefanov
- National Museum of Natural History, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blv., 1000 Sofia, Bulgaria
| | - Lukáš Choleva
- The Czech Academy of Sciences, Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, Rumburská 89, 277 21 Liběchov, Czech Republic; Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava 710 00, Czech Republic
| | - Carl Smith
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65 Brno, Czech Republic; Department of Ecology & Vertebrate Zoology, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; School of Biology and Bell-Pettigrew Museum of Natural History, University of St Andrews, St Andrews KY16 8LB, UK
| | - Martin Reichard
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65 Brno, Czech Republic.
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8
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Perdices A, Ozeren CS, Erkakan F, Freyhof J. Diversity of spined loaches from Asia Minor in a phylogenetic context (Teleostei: Cobitidae). PLoS One 2018; 13:e0205678. [PMID: 30308027 PMCID: PMC6181420 DOI: 10.1371/journal.pone.0205678] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/29/2018] [Indexed: 11/19/2022] Open
Abstract
Accurate determination of species diversity in areas of high endemicity, particularly those lacking comprehensive systematic knowledge, represents a challenge for both taxonomists and conservationists. This need is particularly evident in areas greatly affected by anthropogenic disturbances such as the Eastern Mediterranean and its freshwater environments. To improve our knowledge of Eastern Mediterranean freshwater fishes, we phylogenetically studied Western Palearctic Cobitis species, focusing on those found in Turkey. Overall, our results provide a robust framework to assess the number of species of Cobitis. Phylogenetic reconstructions based on mitochondrial (cyt b) and nuclear (RAG1) sequences show seven major clades (Clades 1-7) grouping all Western Palearctic Cobitis species, except C. melanoleuca. In general, each major clade comprises Cobitis species that inhabit geographically close areas and have similar secondary sexual characters. Multiple divergent lineages were identified in our analyses, some of which were highly divergent such as the ones inhabiting Turkish freshwaters. Moreover, in some analyses, several of the identified lineages were incongruent with a priori defined species. Furthermore, our analyses identified eight potentially new candidate species, six that had been suggested in previous studies and two that are reported here for the first time. Our results reveal Turkey as the area with the greatest diversity of spined loaches in the Mediterranean.
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Affiliation(s)
- Anabel Perdices
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
- * E-mail:
| | - Cevher S. Ozeren
- Department of Biology, Faculty of Science, University of Ankara, Ankara, Turkey
| | - Füsun Erkakan
- Department of Biology, Faculty of Science, Hacettepe University, Beytepe Campus, Ankara, Turkey
| | - Jörg Freyhof
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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Genetic characterization of Western European noble crayfish populations (Astacus astacus) for advanced conservation management strategies. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0981-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Karpova EP. Alien species of fish in freshwater ichthyofauna of the Crimea. RUSSIAN JOURNAL OF BIOLOGICAL INVASIONS 2016. [DOI: 10.1134/s2075111716040044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Jeffries DL, Copp GH, Lawson Handley L, Olsén KH, Sayer CD, Hänfling B. Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L. Mol Ecol 2016; 25:2997-3018. [PMID: 26971882 DOI: 10.1111/mec.13613] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/19/2016] [Accepted: 02/29/2016] [Indexed: 12/16/2022]
Abstract
The conservation of threatened species must be underpinned by phylogeographic knowledge. This need is epitomized by the freshwater fish Carassius carassius, which is in decline across much of its European range. Restriction site-associated DNA sequencing (RADseq) is increasingly used for such applications; however, RADseq is expensive, and limitations on sample number must be weighed against the benefit of large numbers of markers. This trade-off has previously been examined using simulation studies; however, empirical comparisons between these markers, especially in a phylogeographic context, are lacking. Here, we compare the results from microsatellites and RADseq for the phylogeography of C. carassius to test whether it is more advantageous to genotype fewer markers (microsatellites) in many samples, or many markers (SNPs) in fewer samples. These data sets, along with data from the mitochondrial cytochrome b gene, agree on broad phylogeographic patterns, showing the existence of two previously unidentified C. carassius lineages in Europe: one found throughout northern and central-eastern European drainages and a second almost exclusively confined to the Danubian catchment. These lineages have been isolated for approximately 2.15 m years and should be considered separate conservation units. RADseq recovered finer population structure and stronger patterns of IBD than microsatellites, despite including only 17.6% of samples (38% of populations and 52% of samples per population). RADseq was also used along with approximate Bayesian computation to show that the postglacial colonization routes of C. carassius differ from the general patterns of freshwater fish in Europe, likely as a result of their distinctive ecology.
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Affiliation(s)
- Daniel L Jeffries
- Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hardy Building, Hull, HU6 7RX, UK.,Salmon & Freshwater Team, Cefas, Pakefield Road, Lowestoft, Suffolk, NR33 0HT, UK
| | - Gordon H Copp
- Salmon & Freshwater Team, Cefas, Pakefield Road, Lowestoft, Suffolk, NR33 0HT, UK.,Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, UK
| | - Lori Lawson Handley
- Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hardy Building, Hull, HU6 7RX, UK
| | - K Håkan Olsén
- School of Natural Science, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, Flemingsberg, Huddinge, 141 89, Sweden
| | - Carl D Sayer
- Environmental Change Research Centre, Department of Geography, University College London, Pearson Building, Gower Street, London, WC1E 6BT, UK
| | - Bernd Hänfling
- Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hardy Building, Hull, HU6 7RX, UK
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Yang JQ, Hsu KC, Liu ZZ, Su LW, Kuo PH, Tang WQ, Zhou ZC, Liu D, Bao BL, Lin HD. The population history of Garra orientalis (Teleostei: Cyprinidae) using mitochondrial DNA and microsatellite data with approximate Bayesian computation. BMC Evol Biol 2016; 16:73. [PMID: 27068356 PMCID: PMC4827224 DOI: 10.1186/s12862-016-0645-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 03/27/2016] [Indexed: 02/07/2023] Open
Abstract
Background The South China landmass has been characterized by a complex geological history, including mountain lifting, climate changes, and river capture/reversal events. To determine how this complexity has influenced the landmass’s phylogeography, our study examined the phylogeography of Garra orientalis, a cyprinid widely distributed in South China, using sequences from the mitochondrial DNA control region and cytochrome b gene (1887 bp) and polymorphisms of thirteen microsatellite loci. Results In total, 157 specimens were collected from eight populations. All 88 mtDNA haplotypes were identified as belonging to three major lineages, and these lineages were almost allopatric in their distributions. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of G. orientalis were distributed south of the Yunkai Mountains, including on Hainan Island. The mtDNA data revealed a strong relationship between phylogeny and geography. In the microsatellite analysis, a total of 339 alleles with an average of 26 alleles per locus were observed across thirteen microsatellite loci. A clustering algorithm for microsatellite data revealed an admixture-like genetic structure. Although the mtDNA and microsatellite data sets displayed a discordant population structure, the results of an approximate Bayesian computation approach showed that these two markers revealed congruent historical signals. The population history of G. orientalis reflects vicariance events and dispersal related to the complex geological history of South China. Conclusion Our results (i) found that the discordances between mtDNA and microsatellite markers were accounted for by admixtures; (ii) showed that the Wuzhishan and Yinggeling mountain ranges and Qiongzhou Strait were important barriers limiting gene exchange between populations on both sides; (iii) indicated that during glaciation and inter-glacial periods, the strait and continental shelves were exposed and sank, which contributed with the dispersion and differentiation of populations; and (iv) displayed that the admixtures between lineages took place in coastal populations and then colonized the tributaries of the Pearl River.
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Affiliation(s)
- Jin-Quan Yang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, China
| | - Kui-Ching Hsu
- Department of Industrial Management, National Taiwan University of Science and Technology, 43 Keelung Road, Section 4, Taipei, 106, Taiwan
| | - Zhi-Zhi Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, China
| | - Li-Wei Su
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, China
| | - Po-Hsun Kuo
- Department of Industrial Management, National Taiwan University of Science and Technology, 43 Keelung Road, Section 4, Taipei, 106, Taiwan
| | - Wen-Qiao Tang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, China
| | - Zhuo-Cheng Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Dong Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, China
| | - Bao-Long Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, China
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, 701, Taiwan.
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Skovrind M, Olsen MT, Vieira FG, Pacheco G, Carl H, Gilbert MTP, Møller PR. Genomic population structure of freshwater-resident and anadromous ide (Leuciscus idus) in north-western Europe. Ecol Evol 2016; 6:1064-74. [PMID: 26941944 PMCID: PMC4761760 DOI: 10.1002/ece3.1909] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 11/12/2015] [Accepted: 11/23/2015] [Indexed: 11/28/2022] Open
Abstract
Climate change experts largely agree that future climate change and associated rises in oceanic water levels over the upcoming decades, will affect marine salinity levels. The subsequent effects on fish communities in estuarine ecosystems however, are less clear. One species that is likely to become increasingly affected by changes in salinity is the ide (Leuciscus idus). The ide is a stenohaline freshwater fish that primarily inhabits rivers, with frequent anadromous behavior when sea salinity does not exceed 15%. Unlike most other anadromous Baltic Sea fish species, the ide has yet to be subjected to large-scale stocking programs, and thus provides an excellent opportunity for studying the natural population structure across the current salinity gradient in the Danish Belts. To explore this, we used Genotyping-by-Sequencing to determine genomic population structure of both freshwater resident and anadromous ide populations in the western Baltic Sea region, and relate the results to the current salinity gradient and the demographic history of ide in the region. The sample sites separate into four clusters, with all anadromous populations in one cluster and the freshwater resident populations in the remaining three. Results demonstrate high level of differentiation between sites hosting freshwater resident populations, but little differentiation among anadromous populations. Thus ide exhibit the genomic population structure of both a typical freshwater species, and a typical anadromous species. In addition to providing a first insight into the population structure of north-western European ide, our data also (1) provide indications of a single illegal introduction by man; (2) suggest limited genetic effects of heavy pollution in the past; and (3) indicate possible historical anadromous behavior in a now isolated freshwater population.
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Affiliation(s)
- Mikkel Skovrind
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5‐71350Copenhagen KDenmark
| | - Morten Tange Olsen
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5‐71350Copenhagen KDenmark
| | - Filipe Garrett Vieira
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5‐71350Copenhagen KDenmark
| | - George Pacheco
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5‐71350Copenhagen KDenmark
| | - Henrik Carl
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5‐71350Copenhagen KDenmark
| | - M. Thomas P. Gilbert
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5‐71350Copenhagen KDenmark
| | - Peter Rask Møller
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5‐71350Copenhagen KDenmark
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Perdices A, Vasil'eva E, Vasil'ev V. From Asia to Europe across Siberia: phylogeography of the Siberian spined loach (Teleostei, Cobitidae). ZOOL SCR 2014. [DOI: 10.1111/zsc.12085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Anabel Perdices
- Dpto. Biodiversidad y Biología Evolutiva; Museo Nacional Ciencias Naturales (CSIC); C/José Gutiérrez Abascal, 2 28006 Madrid Spain
| | - Ekaterina Vasil'eva
- Zoological Museum of the Moscow State University; Bolshaya Nikitskaya 6 Moscow 125009 Russia
| | - Victor Vasil'ev
- A.N. Severtsov Institute of Ecology and Evolution; RAS, Leninskii prospect 33 Moscow 119071 Russia
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15
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Xu W, Yin W, Chen A, Li J, Lei G, Fu C. Phylogeographical analysis of a cold-temperate freshwater fish, the Amur sleeper (Perccottus glenii) in the Amur and Liaohe River basins of Northeast Asia. Zoolog Sci 2014; 31:671-9. [PMID: 25284386 DOI: 10.2108/zs130046] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Amur sleeper Perccottus glenii (Perciformes, Gobioidei, Odontobutidae) is well known as an invasive fish in the river basins of Eastern and Central Europe, but its genetic background is unavailable across its native habitats in northeast Asia. In this study, we used the mitochondrial cytochrome b gene by sampling 19 populations of P. glenii across its native distributional areas of Liaohe and Amur River basins to explore its evolutionary history. Phylogenetic analyses identified three major clades within P. glenii, among which Clade A and Clade B were co-distributed in the Liaohe and Amur River basins, and Clade C was restricted to the latter. Molecular dating showed that the splits of Clades A, B and C have happened in the late Early-early Middle Pleistocene and the most recent common ancestors of these clades have been presented in the late Middle-early Late Pleistocene. The P. glenii showed very high levels of genetic structure among populations (ΦST = 0.801), probably due to the characters of its life histories with very limited dispersal ability. The admixture of different clades in some populations of P. glenii probably reflects historical secondary contact. These findings indicate that Pleistocene climatic oscillation and river capture were major determinants for genetic variations and evolutionary history of the P. glenii.
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Affiliation(s)
- Wang Xu
- 1 Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Biodiversity Science, Fudan University, Shanghai 200433, China
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16
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Dufresne F, Stift M, Vergilino R, Mable BK. Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools. Mol Ecol 2013; 23:40-69. [DOI: 10.1111/mec.12581] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 12/19/2022]
Affiliation(s)
- France Dufresne
- Département de Biologie; Université du Québec à Rimouski; Québec QC Canada G5L 3A1
| | - Marc Stift
- Department of Biology; University of Konstanz; Konstanz D 78457 Germany
| | - Roland Vergilino
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Barbara K. Mable
- Institute of Biodiversity; Animal Health and Comparative Medicine; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow UK
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17
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Genetic and morphological analyses indicate high population mixing in the endangered cichlid Alcolapia flock of East Africa. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0551-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Bossu CM, Beaulieu JM, Ceas PA, Near TJ. Explicit tests of palaeodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae:Etheostoma:Ceasia). Mol Ecol 2013; 22:5397-417. [DOI: 10.1111/mec.12485] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 07/21/2013] [Accepted: 07/23/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Christen M. Bossu
- Department of Ecology and Evolutionary Biology; Yale University; New Haven CT 06520 USA
| | - Jeremy M. Beaulieu
- National Institute for Mathematical and Biological Synthesis (NIMBioS); University of Tennessee; Knoxville TN 37996 USA
| | | | - Thomas J. Near
- Department of Ecology and Evolutionary Biology; Yale University; New Haven CT 06520 USA
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Chiang TY, Lin HD, Zhao J, Kuo PH, Lee TW, Hsu KC. Diverse processes shape deep phylogeographical divergence in Cobitis sinensis
(Teleostei: Cobitidae) in East Asia. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12030] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tzen-Yuh Chiang
- Department of Life Sciences; Cheng Kung University; Tainan Taiwan
| | - Hung-Du Lin
- Department of Life Sciences; Cheng Kung University; Tainan Taiwan
| | - Jun Zhao
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture; Key Laboratory of Ecology and Environment Science in Guangdong Higher Education; College of Life Science; South China Normal University; Guangzhou China
| | - Po-Hsun Kuo
- Department of Industrial Management; Taiwan University of Science and Technology; Taipei Taiwan
| | - Teh-Wang Lee
- Endemic Species Research Institute; Nantou Taiwan
| | - Kui-Ching Hsu
- Department of Industrial Management; Taiwan University of Science and Technology; Taipei Taiwan
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20
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Brusentsov II, Katokhin AV, Brusentsova IV, Shekhovtsov SV, Borovikov SN, Goncharenko GG, Lider LA, Romashov BV, Rusinek OT, Shibitov SK, Suleymanov MM, Yevtushenko AV, Mordvinov VA. Low genetic diversity in wide-spread Eurasian liver fluke Opisthorchis felineus suggests special demographic history of this trematode species. PLoS One 2013; 8:e62453. [PMID: 23634228 PMCID: PMC3636034 DOI: 10.1371/journal.pone.0062453] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/21/2013] [Indexed: 01/09/2023] Open
Abstract
Opisthorchis felineus or Siberian liver fluke is a trematode parasite (Opisthorchiidae) that infects the hepato-biliary system of humans and other mammals. Despite its public health significance, this wide-spread Eurasian species is one of the most poorly studied human liver flukes and nothing is known about its population genetic structure and demographic history. In this paper, we attempt to fill this gap for the first time and to explore the genetic diversity in O. felineus populations from Eastern Europe (Ukraine, European part of Russia), Northern Asia (Siberia) and Central Asia (Northern Kazakhstan). Analysis of marker DNA fragments from O. felineus mitochondrial cytochrome c oxidase subunit 1 and 3 (cox1, cox3) and nuclear rDNA internal transcribed spacer 1 (ITS1) sequences revealed that genetic diversity is very low across the large geographic range of this species. Microevolutionary processes in populations of trematodes may well be influenced by their peculiar biology. Nevertheless, we suggest that lack of population genetics structure observed in O. felineus can be primarily explained by the Pleistocene glacial events and subsequent sudden population growth from a very limited group of founders. Rapid range expansion of O. felineus through Asian and European territories after severe bottleneck points to a high dispersal potential of this trematode species.
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Affiliation(s)
- Ilja I. Brusentsov
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey V. Katokhin
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Irina V. Brusentsova
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergei V. Shekhovtsov
- Laboratory of Molecular Biotechnology, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergei N. Borovikov
- Department of Animal Biotechnology, S.Seifullin Kazakh Agrotechnical University, Astana, Republic of Kazakhstan
| | | | - Lyudmila A. Lider
- Department of Veterinary Medicine, S.Seifullin Kazakh Agrotechnical University, Astana, Republic of Kazakhstan
| | - Boris V. Romashov
- Scientific Department, Voronezh State Biosphere Reserve, Voronezh, Russia
| | - Olga T. Rusinek
- Department of Parasitology, The Baikal Museum at the Irkutsk Scientific Center, Siberian Branch, Russian Academy of Sciences, Listvyanka, Irkutsk, Russia
| | - Samat K. Shibitov
- Department of Epizootological Problems, All-Russian K.I. Skryabin Institute of Helminthology, Moscow, Russia
| | - Marat M. Suleymanov
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Andrey V. Yevtushenko
- Department of Parasitology Ichthyopathology and Arachnology, National Scientific Center “Institute of Experimental and Clinical Veterinary Medicine”, Kharkov, Ukraine
| | - Viatcheslav A. Mordvinov
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Faria R, Weiss S, Alexandrino P. Comparative phylogeography and demographic history of European shads (Alosa alosa and A. fallax) inferred from mitochondrial DNA. BMC Evol Biol 2012; 12:194. [PMID: 23020523 PMCID: PMC3523006 DOI: 10.1186/1471-2148-12-194] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Accepted: 09/06/2012] [Indexed: 11/18/2022] Open
Abstract
Background Comparative broad-scale phylogeographic studies of aquatic organisms provide insights on biotic responses to the paleohydrological dynamics associated with climatic oscillations. These insights can be used to formulate a framework for understanding the evolutionary history of a species or closely related taxa as well as aid in predictive modeling of further responses to climate change. Anadromous fishes constitute interesting models for understanding the relative importance of environmental versus biological factors in shaping intraspecific genetic substructure on the interface between marine and freshwater realms. European shads, Alosa alosa and A. fallax are anadromous species that have persisted through historical large-scale environmental perturbations and now additionally face an array of anthropogenic challenges. A comprehensive phylogeographic investigation of these species is needed to provide insights on both the historical processes that have shaped their extant genetic structure and diversity, and the prospects for their future management and conservation. Results Despite introgressive hybridization, A. alosa and A. fallax are genetically divergent, congruent with previous studies. Three similarly divergent mtDNA clades were recognized within both A. fallax and A. alosa, most likely originating during common periods of isolation during the Pleistocene among the studied oceanographic regions. Periods of basin isolation apparently extended to the Black Sea as additional Alosa clades occur there. The present day geographic distribution of genetic diversity within European Alosa sp. suggests the existence of a strong but permeable barrier between the Atlantic and Mediterranean seas, as shown for a number of other aquatic species. Overall mtDNA diversity is considerably lower for A. alosa compared to A. fallax, suggesting that the former species is more sensitive to climatic as well as anthropogenic changes. For A. fallax, migration from the Mediterranean to the Atlantic was detected but not in the opposite direction, with colonization of the North Atlantic probably occurring after last glacial maximum. Conclusion The similar haplotype network topologies between the two species support a common intraspecific history of isolation. Despite these similarities, A. alosa and A. fallax have clearly responded differently to the hydrological dynamics of the Pleistocene, as reflected in their distinct demographic histories. As the species additionally occupy different ecological niches it should not be surprising that they differ in resilience to natural or human-mediated climatic changes. For A. fallax, it is further clear that its demographic response to large-scale hydrological events is not synchronized between the Atlantic and Mediterranean basins. These regional and species-specific differences should be incorporated into future predictive modeling of biological response to climate change as well as current management concepts.
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Affiliation(s)
- Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.
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Dynamic formation of asexual diploid and polyploid lineages: multilocus analysis of Cobitis reveals the mechanisms maintaining the diversity of clones. PLoS One 2012; 7:e45384. [PMID: 23028977 PMCID: PMC3447977 DOI: 10.1371/journal.pone.0045384] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 08/16/2012] [Indexed: 11/19/2022] Open
Abstract
Given the hybrid genomic constitutions and increased ploidy of many asexual animals, the identification of processes governing the origin and maintenance of clonal diversity provides useful information about the evolutionary consequences of interspecific hybridization, asexuality and polyploidy. In order to understand the processes driving observed diversity of biotypes and clones in the Cobitis taenia hybrid complex, we performed fine-scale genetic analysis of Central European hybrid zone between two sexual species using microsatellite genotyping and mtDNA sequencing. We found that the hybrid zone is populated by an assemblage of clonally (gynogenetically) reproducing di-, tri- and tetraploid hybrid lineages and that successful clones, which are able of spatial expansion, recruit from two ploidy levels, i.e. diploid and triploid. We further compared the distribution of observed estimates of clonal ages to theoretical distributions simulated under various assumptions and showed that new clones are most likely continuously recruited from ancestral populations. This suggests that the clonal diversity is maintained by dynamic equilibrium between origination and extinction of clonal lineages. On the other hand, an interclonal selection is implied by nonrandom spatial distribution of individual clones with respect to the coexisting sexual species. Importantly, there was no evidence for sexually reproducing hybrids or clonally reproducing non-hybrid forms. Together with previous successful laboratory synthesis of clonal Cobitis hybrids, our data thus provide the most compelling evidence that 1) the origin of asexuality is causally linked to interspecific hybridization; 2) successful establishment of clones is not restricted to one specific ploidy level and 3) the initiation of clonality and polyploidy may be dynamic and continuous in asexual complexes.
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23
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Wang B, Jiang J, Xie F, Li C. Postglacial colonization of the Qinling Mountains: phylogeography of the swelled vent frog (Feirana quadranus). PLoS One 2012; 7:e41579. [PMID: 22848532 PMCID: PMC3405020 DOI: 10.1371/journal.pone.0041579] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 06/22/2012] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The influence of Pleistocene climatic fluctuations on intraspecific diversification in the Qinling-Daba Mountains of East Asia remains poorly investigated. We tested hypotheses concerning refugia during the last glacial maximum (LGM) in this region by examining the phylogeography of the swelled vent frog (Feirana quadranus; Dicroglossidae, Anura, Amphibia). METHODOLOGY/PRINCIPAL FINDINGS We obtained complete mitochondrial ND2 gene sequences of 224 individuals from 34 populations of Feirana quadranus for phylogeographic analyses. Additionally, we obtained nuclear tyrosinase gene sequences of 68 F. quadranus, one F. kangxianensis and three F. taihangnica samples to test for mitochondrial introgression among them. Phylogenetic analyses based on all genes revealed no introgression among them. Phylogenetic analyses based on ND2 datasets revealed that F. quadranus was comprised of six lineages which were separated by deep valleys; the sole exception is that the Main Qinling and Micang-Western Qinling lineages overlap in distribution. Analyses of population structure indicated restricted gene flow among lineages. Coalescent simulations and divergence dating indicated that the basal diversification within F. quadranus may be associated with the dramatic uplifts of the Tibetan Plateau during the Pliocene. Coalescent simulations indicated that Wuling, Daba, and Western Qinling-Micang-Longmen Mountains were refugia for F. quadranus during the LGM. Demographic analyses indicated that the Daba lineage experienced population size increase prior to the LGM but the Main Qinling and the Micang-Western Qinling lineages expanded in population size and range after the LGM, and the other lineages almost have stable population size or slight slow population size decline. CONCLUSIONS/SIGNIFICANCE The Qinling-Daba Mountains hosted three refugia for F. quadranus during the LGM. Populations that originated in the Daba Mountains colonized the Main Qinling Mountains after the LGM. Recent sharp expansion of the Micang-Western Qinling and Main Qinling lineages probably contribute to their present-day secondary contact.
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Affiliation(s)
- Bin Wang
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
| | - Jianping Jiang
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
| | - Feng Xie
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
| | - Cheng Li
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
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Fijarczyk A, Nadachowska K, Hofman S, Litvinchuk SN, Babik W, Stuglik M, Gollmann G, Choleva L, Cogălniceanu D, Vukov T, Džukić G, Szymura JM. Nuclear and mitochondrial phylogeography of the European fire-bellied toads Bombina bombina and Bombina variegata supports their independent histories. Mol Ecol 2011; 20:3381-98. [PMID: 21749513 DOI: 10.1111/j.1365-294x.2011.05175.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Exact location and number of glacial refugia still remain unclear for many European cold-blooded terrestrial vertebrates. We performed a fine-scaled multilocus phylogeographic analysis of two Bombina species combining mitochondrial variation of 950 toads from 385 sites and nuclear genes (Rag-1, Ncx-1) from a subset of samples to reconstruct their colonization and contemporary variation patterns. We identified the lowlands northwest of the Black Sea and the Carpathians to be important refugial areas for B. bombina and B. variegata, respectively. This result emphasizes the importance of Central European refugia for ectothermic terrestrial species, far north of the Mediterranean areas regarded as exclusive glacial refugia for the animals. Additional refugia for B. variegata have been located in the southern Apennines and Balkans. In contrast, no evidence for the importance of other east European plains as refugial regions has been found. The distribution of mtDNA and Ncx-1 variation suggests the presence of local refugia near the Black Sea for B. bombina; however, coalescent simulations did not allow to distinguish whether one or two refugia were present in the region. Strong genetic drift apparently accompanied postglacial expansions reducing diversity in the colonization areas. Extended sampling, coupled with the multilocus isolation with migration analysis, revealed a limited and geographically restricted gene flow from the Balkan to Carpathian populations of B. variegata. However, despite proximity of inferred B. bombina and B. variegata refugia, gene exchange between them was not detected.
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Affiliation(s)
- Anna Fijarczyk
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
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Mezhzherin SV, Pavlenko LI. Genetic diversity, origin, and geographic distribution tendencies of biotypes of polyploid spined loaches (Cypriniformes, Cobitidae, Cobitis) in Ukraine. CYTOL GENET+ 2010. [DOI: 10.3103/s0095452710050105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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de Thoisy B, da Silva AG, Ruiz-García M, Tapia A, Ramirez O, Arana M, Quse V, Paz-y-Miño C, Tobler M, Pedraza C, Lavergne A. Population history, phylogeography, and conservation genetics of the last Neotropical mega-herbivore, the lowland tapir (Tapirus terrestris). BMC Evol Biol 2010; 10:278. [PMID: 20840756 PMCID: PMC2949869 DOI: 10.1186/1471-2148-10-278] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 09/14/2010] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Understanding the forces that shaped Neotropical diversity is central issue to explain tropical biodiversity and inform conservation action; yet few studies have examined large, widespread species. Lowland tapir (Tapirus terrrestris, Perissodactyla, Tapiridae) is the largest Neotropical herbivore whose ancestors arrived in South America during the Great American Biotic Interchange. A Pleistocene diversification is inferred for the genus Tapirus from the fossil record, but only two species survived the Pleistocene megafauna extinction. Here, we investigate the history of lowland tapir as revealed by variation at the mitochondrial gene Cytochrome b, compare it to the fossil data, and explore mechanisms that could have shaped the observed structure of current populations. RESULTS Separate methodological approaches found mutually exclusive divergence times for lowland tapir, either in the late or in the early Pleistocene, although a late Pleistocene divergence is more in tune with the fossil record. Bayesian analysis favored mountain tapir (T. pinchaque) paraphyly in relation to lowland tapir over reciprocal monophyly, corroborating the inferences from the fossil data these species are sister taxa. A coalescent-based analysis rejected a null hypothesis of allopatric divergence, suggesting a complex history. Based on the geographic distribution of haplotypes we propose (i) a central role for western Amazonia in tapir diversification, with a key role of the ecological gradient along the transition between Andean subcloud forests and Amazon lowland forest, and (ii) that the Amazon river acted as an barrier to gene flow. Finally, the branching patterns and estimates based on nucleotide diversity indicate a population expansion after the Last Glacial Maximum. CONCLUSIONS This study is the first examining lowland tapir phylogeography. Climatic events at the end of the Pleistocene, parapatric speciation, divergence along the Andean foothill, and role of the Amazon river, have similarly shaped the history of other taxa. Nevertheless further work with additional samples and loci is needed to improve our initial assessment. From a conservation perspective, we did not find a correspondence between genetic structure in lowland tapir and ecogeographic regions proposed to define conservation priorities in the Neotropics. This discrepancy sheds doubt into this scheme's ability to generate effective conservation planning for vagile species.
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Lohse K, Sharanowski B, Stone GN. QUANTIFYING THE PLEISTOCENE HISTORY OF THE OAK GALL PARASITOID CECIDOSTIBA FUNGOSA USING TWENTY INTRON LOCI. Evolution 2010; 64:2664-81. [PMID: 20455927 DOI: 10.1111/j.1558-5646.2010.01024.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, West Mains Road, United Kingdom.
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Perea S, Böhme M, Zupancic P, Freyhof J, Sanda R, Ozuluğ M, Abdoli A, Doadrio I. Phylogenetic relationships and biogeographical patterns in Circum-Mediterranean subfamily Leuciscinae (Teleostei, Cyprinidae) inferred from both mitochondrial and nuclear data. BMC Evol Biol 2010; 10:265. [PMID: 20807419 PMCID: PMC2940817 DOI: 10.1186/1471-2148-10-265] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 08/31/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leuciscinae is a subfamily belonging to the Cyprinidae fish family that is widely distributed in Circum-Mediterranean region. Many efforts have been carried out to deciphering the evolutionary history of this group. Thus, different biogeographical scenarios have tried to explain the colonization of Europe and Mediterranean area by cyprinids, such as the "north dispersal" or the "Lago Mare dispersal" models. Most recently, Pleistocene glaciations influenced the distribution of leuciscins, especially in North and Central Europe. Weighing up these biogeographical scenarios, this paper constitutes not only the first attempt at deciphering the mitochondrial and nuclear relationships of Mediterranean leuciscins but also a test of biogeographical hypotheses that could have determined the current distribution of Circum-Mediterranean leuciscins. RESULTS A total of 4439 characters (mitochondrial + nuclear) from 321 individuals of 176 leuciscine species rendered a well-supported phylogeny, showing fourteen main lineages. Analyses of independent mitochondrial and nuclear markers supported the same main lineages, but basal relationships were not concordant. Moreover, some incongruence was found among independent mitochondrial and nuclear phylogenies. The monophyly of some poorly known genera such as Pseudophoxinus and Petroleuciscus was rejected. Representatives of both genera belong to different evolutionary lineages. Timing of cladogenetic events among the main leuciscine lineages was gained using mitochondrial and all genes data set. CONCLUSIONS Adaptations to a predatory lifestyle or miniaturization have superimposed the morphology of some species. These species have been separated into different genera, which are not supported by a phylogenetic framework. Such is the case of the genera Pseudophoxinus and Petroleuciscus, which real taxonomy is not well known. The diversification of leuciscine lineages has been determined by intense vicariant events following the paleoclimatological and hydrogeological history of Mediterranean region. We propose different colonization models of Mediterranean region during the early Oligocene. Later vicariance events promoted Leuciscinae diversification during Oligocene and Miocene periods. Our data corroborate the presence of leuciscins in North Africa before the Messinian salinity crisis. Indeed, Messinian period appears as a stage of gradually Leuciscinae diversification. The rise of humidity at the beginning of the Pliocene promoted the colonization and posterior isolation of newly established freshwater populations. Finally, Pleistocene glaciations determined the current European distribution of some leuciscine species.
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Affiliation(s)
- Silvia Perea
- Museo Nacional de Ciencias Naturales-CSIC, Department of Biodiversity and Evolutionary Biology, José Gutiérrez Abascal 2, 28006 Madrid, Spain.
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Sousa V, Penha F, Pala I, Chikhi L, Coelho MM. Conservation genetics of a critically endangered Iberian minnow: evidence of population decline and extirpations. Anim Conserv 2010. [DOI: 10.1111/j.1469-1795.2009.00317.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Chiang TY, Lin HD, Shao KT, Hsu KC. Multiple factors have shaped the phylogeography of Chinese spiny loach Cobitis sinensis in Taiwan as inferred from mitochondrial DNA variation. JOURNAL OF FISH BIOLOGY 2010; 76:1173-1189. [PMID: 20409169 DOI: 10.1111/j.1095-8649.2010.02589.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Mitochondrial DNA cytochrome b sequences (1140 bp) in 61 specimens of Chinese spiny loach Cobitis sinensis from 12 drainages in Taiwan were identified as two major clades, exhibiting a southern and a northern distribution, north of TzengWen and south of TzengWen (including TzengWen), respectively. The divergence time between these two phylogroups was estimated at 7.34-9.06 million years before present (B.P.), but these two phylogroups were formed c. 3.41-4.23 and 2.22-2.75 M B.P., respectively. Moreover, geological events have been recalculated that Taiwan Island emerged above sea level at an estimate of c. 4-5 M B.P., and quickly became its present shape at c. 2 M B.P. through mountain building. These results suggest that these two major clades of C. sinensis in Taiwan might originate from two different continental populations, since the island's initial isolation in the Pliocene. Within southern Taiwan, the initial colonization was hypothesized to be in KaoPing River, followed by its northward dispersal. The high divergence between KaoPing and TzengWen was influenced by glaciations and landforms. Within north Taiwan, the colonization was from the Miaoli Plateau through western Taiwan to north-eastern and northern Taiwan. This dispersal pattern is concordant with the previously proposed hypothesis. Apparently, both geological and phylogeographic evidence suggested that river capture of the upper Takia River by the LanYang River promoted range expansion in freshwater fishes and also indicated that the Central Range within Taiwan did not act as a barrier to the dispersal of C. sinensis.
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Affiliation(s)
- T-Y Chiang
- Department of Life Sciences, Cheng Kung University, Tainan, Taiwan
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Janko K, Eisner J. Sperm-dependent parthenogens delay the spatial expansion of their sexual hosts. J Theor Biol 2009; 261:431-40. [DOI: 10.1016/j.jtbi.2009.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 08/01/2009] [Accepted: 08/10/2009] [Indexed: 11/26/2022]
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Hänfling B, Dümpelmann C, Bogutskaya NG, Brandl R, Brändle M. Shallow phylogeographic structuring of Vimba vimba across Europe suggests two distinct refugia during the last glaciation. JOURNAL OF FISH BIOLOGY 2009; 75:2269-2286. [PMID: 20738686 DOI: 10.1111/j.1095-8649.2009.02415.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Genetic variation and geographical structuring of vimba Vimba vimba were analysed across 26 sites (80 individuals) by means of mtDNA sequences (cyt b gene, mitochondrial control region) to localize hypothesized glacial refugia and to reconstruct postglacial recoloniation routes. Although genetic diversity among sequenced individuals was low, a combined analysis of the two sequenced fragments revealed a western (central and northern Europe: Danube, Elbe and lakes of Sweden) and an eastern clade (eastern Europe: Dnieper-South Bug, Don, Neman). Furthermore, a number of divergent ancestral haplotypes distributed around the Black and Caspian Seas became apparent. Mismatch analyses supported a sudden expansion model for the populations of the western clade between 50 and 10 000 bp. Overall, the study provides strong evidence for a northward and westward expansion of V. vimba from two refugial regions located in the Danubian drainage and the northern Pontic regions respectively.
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Affiliation(s)
- B Hänfling
- Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
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Larmuseau MHD, Freyhof J, Volckaert FAM, Van Houdt JKJ. Matrilinear phylogeography and demographical patterns of Rutilus rutilus: implications for taxonomy and conservation. JOURNAL OF FISH BIOLOGY 2009; 75:332-53. [PMID: 20738542 DOI: 10.1111/j.1095-8649.2009.02322.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A phylogeographic analysis of mitochondrial DNA sequence variation was carried out to infer the geographical distribution of the genealogical lineages and the historical demography of roach Rutilus rutilus (L.). A total of 265 individuals from 52 sites covering most of the Eurasian distribution range were sequenced for a 475 bp fragment of the mitochondrial cytochrome b gene. The monophyletic roach contained two deep clades that dated back to the Pliocene. The Ponto-Caspian clade comprised populations from Greece to Siberia with a likely palaeorefugium at the west coast of the Caspian Sea. This clade largely corresponds to individuals with morphological features described as Rutilus heckelii. The west European clade included individuals from central and western Europe with the Danube and Dniester basins as possible palaeorefugia. This clade largely corresponds to individuals with morphological features described as R. rutilus. A suture-zone of the two main lineages was observed along the coastal region of the Black Sea. The neutrality tests and the mismatch distributions indicated a demographic expansion during the Middle-Pleistocene for both clades.
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Affiliation(s)
- M H D Larmuseau
- Laboratory of Animal Diversity & Systematics, Katholieke Universiteit Leuven, Deberiotstraat 32, B-3000 Leuven, Belgium.
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Zhang DX, Yan LN, Ji YJ, Hewitt GM, Huang ZS. Unexpected relationships of substructured populations in Chinese Locusta migratoria. BMC Evol Biol 2009; 9:144. [PMID: 19558707 PMCID: PMC2718889 DOI: 10.1186/1471-2148-9-144] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 06/28/2009] [Indexed: 11/16/2022] Open
Abstract
Background Highly migratory species are usually expected to have minimal population substructure because strong gene flow has the effect of homogenizing genetic variation over geographical populations, counteracting random drift, selection and mutation. The migratory locust Locusta migratoria belongs to a monotypic genus, and is an infamous pest insect with exceptional migratory ability – with dispersal documented over a thousand kilometers. Its distributional area is greater than that of any other locust or grasshopper, occurring in practically all the temperate and tropical regions of the eastern hemisphere. Consequently, minimal population substructuring is expected. However, in marked contrast to its high dispersal ability, three geographical subspecies have been distinguished in China, with more than nine being biologically and morphologically identified in the world. Such subspecies status has been under considerable debate. Results By multilocus microsatellite genotyping analysis, we provide ample genetic evidence for strong population substructure in this highly migratory insect that conforms to geography. More importantly, our genetic data identified an unexpected cryptic subdivision and demonstrated a strong affiliation of the East China locusts to those in Northwest/Northern China. The migratory locusts in China formed three distinct groups, viz. (1) the Tibetan group, comprising locusts from Tibet and nearby West China high mountain regions; this is congruent with the previously recognized Tibetan subspecies, L. m. tibetensis; (2) the South China group, containing locusts from the Hainan islands; this corresponds to the Southeast Asia oriental tropical subspecies L. m. manilensis; (3) the North China group, including locusts from the Northwest and Northern China (the Asiatic subspecies L. m. migratoria), Central China and Eastern China regions. Therefore, the traditional concept on Locusta subspecies status established from Uvarov in 1930s needs to be revised. The three groups of locusts probably have separate evolutionary histories that were most likely linked to Quaternary glaciations events, and derived from different ancestral refugial populations following postglacial expansions. Conclusion The migratory locust populations in China have differentiated into three genetically distinct groups despite high dispersal capability. While this clarified long-standing suspicions on the subspecific diversification of this species in China, it also revealed that the locusts in the vast area of East China are not the oriental subspecies but the Asiatic subspecies, an unexpected substructuring pattern. The distribution pattern of the three locust groups in China may be primarily defined by adaptive differentiation coupled to Quaternary glaciations events. Our results are of general significance both for locust research and for phylogeographical study of flora and fauna in China, illustrating the potential importance of phylogeographical history in shaping the divergence and distribution patterns of widespread species with strong dispersal ability.
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Affiliation(s)
- De-Xing Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China.
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Flanders J, Jones G, Benda P, Dietz C, Zhang S, Li G, Sharifi M, Rossiter SJ. Phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum: contrasting results from mitochondrial and microsatellite data. Mol Ecol 2009; 18:306-18. [PMID: 19192181 DOI: 10.1111/j.1365-294x.2008.04021.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phylogeographical studies are typically based on haplotype data, occasionally on nuclear markers such as microsatellites, but rarely combine both. This is unfortunate because the use of markers with contrasting modes of inheritance and rates of evolution might provide a more accurate and comprehensive understanding of a species' history. Here we present a detailed study of the phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum, using 1098 bp of the mitochondrial ND2 gene from 45 localities from across its Palaearctic range to infer population history. In addition, we re-analysed a large microsatellite data set available for this species and compared the results of both markers to infer population relationships and the historical processes influencing them. We show that mtDNA, the most popular marker in phylogeography studies, yielded a misleading result, and would have led us to conclude erroneously that a single expansion had taken place in Europe. Only by combining the mitochondrial and microsatellite data sets are we able to reconstruct the species' history and show two colonization events in Europe, one before the Last Glacial Maximum (LGM) and one after it. Combining markers also revealed the importance of Asia Minor as an ancient refugium for this species and a source population for the expansion of the greater horseshoe bat into Europe before the LGM.
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Affiliation(s)
- Jon Flanders
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
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DUBEY SYLVAIN, DIKER EBRU, KURTONUR CENGIZ, VOGEL PETER. Secondary contact zones and hybridizations: the case of the lesser white-toothed shrew (Crocidura suaveolens group, Soricidae). Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.01070.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Choleva L, Apostolou A, Rab P, Janko K. Making it on their own: sperm-dependent hybrid fishes (Cobitis) switch the sexual hosts and expand beyond the ranges of their original sperm donors. Philos Trans R Soc Lond B Biol Sci 2008; 363:2911-9. [PMID: 18508748 DOI: 10.1098/rstb.2008.0059] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Interspecific hybridization may result in asexual hybrid lineages that reproduce via parthenogenesis. Contrary to true parthenogens, sperm-dependent asexuals (gynogens and hybridogens) are restricted to the range of bisexual species, generally the parental taxa, by their need for a sperm donor. It has been documented that asexual lineages may rarely use sperm from a non-parental species or even switch a host. The available literature reports do not allow distinguishing, between whether such host switches arise by the expansion of asexuals out of their parental's range (and into that of another's) or by the local extinction of a parental population followed by a host switch. The present study combines new and previously collected data on the distribution and history of gynogenetic spined loaches (Cobitis) of hybrid origin. We identified at least three clonal lineages that have independently switched their sperm dependency to different non-parental Cobitis species, and in cases incorporated their genomes. Our current knowledge of European Cobitis species and their hybrids suggests that this pattern most probably results from the expansion of gynogenetic lineages into new areas. Such expansion was independent of the original parental species. This suggests that sperm dependence is not as restrictive to geographical expansion when compared with true parthenogenesis as previously thought.
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Affiliation(s)
- Lukás Choleva
- Department of Vertebrate Evolutionary Biology and Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov 277 21, Czech Republic.
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DE Gelas K, Janko K, Volckaert FAM, DE Charleroy D, VAN Houdt JKJ. Development of nine polymorphic microsatellite loci in the spined loach, Cobitis taenia, and cross-species amplification in the related species C. elongatoides, C. taurica and C. tanaitica. Mol Ecol Resour 2008; 8:1001-3. [PMID: 21585954 DOI: 10.1111/j.1755-0998.2008.02135.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Nine polymorphic microsatellite loci were developed for the spined loach, Cobitis taenia (Teleostei: Cobitidae). The loci were validated using 50 individuals from a population in Belgium. Moderate to high levels of polymorphism were detected (two to 11 alleles). In addition, most markers amplified successfully in three closely related taxa that are known to hybridize with C. taenia: C. elongatoides, C. taurica and C. tanaitica. Some of the loci are most likely diagnostic among species. These markers will be valuable for the study of the historical and contemporary interactions within C. taenia and the Cobitis species complex.
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Affiliation(s)
- K DE Gelas
- Research Institute for Nature and Forest, Dwersbos 28, B-1630 Linkebeek, Belgium, Laboratory of Animal Diversity and Systematics, K.U. Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium, Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 277 21 Libéchov, Czech Republic
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Brown JE, Stepien CA. Ancient divisions, recent expansions: phylogeography and population genetics of the round goby Apollonia melanostoma. Mol Ecol 2008; 17:2598-615. [PMID: 18466236 DOI: 10.1111/j.1365-294x.2008.03777.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
During the past two decades, the round goby Apollonia melanostoma (=Neogobius melanostomus) has expanded its range via shipping transport and canals, extending north and west from the Ponto-Caspian region of Eurasia and to the North American Great Lakes. Exotic populations of the round goby have been very successful in the Baltic Sea and the Great Lakes regions, exerting significant ecological changes. Our study evaluates the population genetic and biogeographical structure of the round goby across its native and nonindigenous ranges, in light of geological history and its expansion pathways. We analyzed seven new nuclear microsatellite loci and mitochondrial DNA cytochrome b gene sequences from 432 individuals in 22 locations. Population structure was tested using F(ST)-analogs, phylogenetic trees, clustering diagrams, Bayesian assignment tests and nested clade analyses. Results show that native populations in the Black vs. the Caspian Sea basins diverge by 1.4% and c. 350,000 years, corresponding to closure of their prior connections and supporting the taxonomic separation of the Black Sea A. m. melanostoma from the Caspian Sea A. m. affinis. Their within-basin populations diverge by approximately 0.4% and 100,000 years. Nonindigenous populations in the Baltic Sea and Danube and Dnieper Rivers trace to separate northern Black Sea origins, whereas the upper Volga River system houses mixed populations of A. m. melanostoma and A. m. affinis. Native populations average twice the genetic diversity of most exotic sites; however, sites in the Volga River system have high diversity due to mixing of the two taxa. Our results highlight how vicariance and anthropogenic disturbances have shaped a rapidly expanding species' genetic heritage.
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Affiliation(s)
- Joshua E Brown
- Great Lakes Genetics Laboratory, Lake Erie Center and Department of Environmental Sciences, University of Toledo, 6200 Bayshore Road, Toledo, OH 43618, USA
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ŠEDIVÁ ALENA, JANKO KAREL, ŠLECHTOVÁ VENDULA, KOTLÍK PETR, SIMONOVIĆ PREDRAG, DELIC ANTUN, VASSILEV MILEN. Around or across the Carpathians: colonization model of the Danube basin inferred from genetic diversification of stone loach (Barbatula barbatula) populations. Mol Ecol 2008; 17:1277-92. [DOI: 10.1111/j.1365-294x.2007.03656.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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41
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Thornton HEB, Roncal J, Lewis CE, Maschinski J, Francisco-Ortega J. Conservation Genetics of Jacquemontia reclinata (Convolvulaceae), an Endangered Species from Southern Florida: Implications for Restoration Management. Biotropica 2008. [DOI: 10.1111/j.1744-7429.2008.00399.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Challis RJ, Mutun S, Nieves-Aldrey JL, Preuss S, Rokas A, Aebi A, Sadeghi E, Tavakoli M, Stone GN. Longitudinal range expansion and cryptic eastern species in the western Palaearctic oak gallwasp, Andricus coriarius. Mol Ecol 2008; 16:2103-14. [PMID: 17498235 DOI: 10.1111/j.1365-294x.2006.03210.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The oak gallwasp Andricus coriarius is distributed across the Western Palaearctic from Morocco to Iran. It belongs to a clade of host-alternating Andricus species that requires host oaks in two sections of Quercus subgenus Quercus to complete its lifecycle, a requirement that has restricted the historic distribution and dispersal of members of this clade. Here we present nuclear and mitochondrial sequence evidence from the entire geographic range of A. coriarius to investigate the genetic legacy of longitudinal range expansion. We show A. coriarius as currently understood to be para- or polyphyletic, with three evolutionarily independent (but partially sympatric) lineages that diverged c. 10 million years ago (mya). The similarities in gall structure that have justified recognition of single species to date thus represent either strong conservation of an ancestral state or striking convergence. All three lineages originated in areas to the east of Europe, underlining the significance of Turkey, Iran and the Levant as 'cradles' of gallwasp evolution. One of the three lineages gave rise to all European populations, and range expansion from a putative Eastern origin to the present distribution is predicted to have occurred around 1.6 mya.
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Affiliation(s)
- Richard J Challis
- Institute of Evolutionary Biology, University of Edinburgh, School of Biological Sciences, The King's Buildings, West Mains Road, Edinburgh, EH9 3JT, UK.
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Perdices A, Bohlen J, Doadrio I. The molecular diversity of adriatic spined loaches (Teleostei, Cobitidae). Mol Phylogenet Evol 2008; 46:382-90. [PMID: 17625922 DOI: 10.1016/j.ympev.2007.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Accepted: 05/08/2007] [Indexed: 10/23/2022]
Affiliation(s)
- Anabel Perdices
- National Museum of Natural History, Department of Biodiversity and Evolutionary Biology, C/José Gutiérrez Abascal 2, 28006 Madrid, Spain.
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ROSSITER STEPHENJ, BENDA PETR, DIETZ CHRISTIAN, ZHANG SHUYI, JONES GARETH. Rangewide phylogeography in the greater horseshoe bat inferred from microsatellites: implications for population history, taxonomy and conservation. Mol Ecol 2007; 16:4699-714. [DOI: 10.1111/j.1365-294x.2007.03546.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Amato ML, Brooks RJ, Fu J. A phylogeographic analysis of populations of the wood turtle (Glyptemys insculpta) throughout its range. Mol Ecol 2007; 17:570-81. [PMID: 17971089 DOI: 10.1111/j.1365-294x.2007.03580.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigated the phylogeography of wood turtles, Glyptemys insculpta, in North America using 750 bp of the mitochondrial control region from 117 individuals sampled at 29 localities across the species' range. A total of 21 haplotypes were identified and little genetic variation was found. The highest pairwise difference was 2%. From nested clade analysis (NCA), one main postglacial dispersal route was inferred along the east coast, with subsequent westward dispersal. NCA further revealed some patterns of restricted gene flow/dispersal. We propose that wood turtles experienced a combined effect of bottleneck during the Pleistocene as well as of selective sweep, which produced the low level of variation observed. Following the Pleistocene, wood turtles would have undergone a rapid northward expansion from a common southern refugium as glaciers retreated. These findings shed light on where to direct conservation priorities, on conservation strategies needed, and on the potential effects of interpopulation transfers for this vulnerable species.
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Affiliation(s)
- Marina L Amato
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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46
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Sousa V, Penha F, Collares-Pereira MJ, Chikhi L, Coelho MM. Genetic structure and signature of population decrease in the critically endangered freshwater cyprinid Chondrostoma lusitanicum. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9399-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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Mezhzherin SV, Pavlenko LI. A case of hybridization in loaches (osteichthies: Cobitidae: Cobitis) determining genetic instability and expansion. CYTOL GENET+ 2007. [DOI: 10.3103/s0095452707040056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Dubey S, Cosson JF, Vohralík V, Krystufek B, Diker E, Vogel P. Molecular evidence of Pleistocene bidirectional faunal exchange between Europe and the Near East: the case of the bicoloured shrew (Crocidura leucodon, Soricidae). J Evol Biol 2007; 20:1799-808. [PMID: 17714297 DOI: 10.1111/j.1420-9101.2007.01382.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We sequenced 1077 bp of the mitochondrial cytochrome b gene and 511 bp of the nuclear Apolipoprotein B gene in bicoloured shrew (Crocidura leucodon, Soricidae) populations ranging from France to Georgia. The aims of the study were to identify the main genetic clades within this species and the influence of Pleistocene climatic variations on the respective clades. The mitochondrial analyses revealed a European clade distributed from France eastwards to north-western Turkey and a Near East clade distributed from Georgia to Romania; the two clades separated during the Middle Pleistocene. We clearly identified a population expansion after a bottleneck for the European clade based on mitochondrial and nuclear sequencing data; this expansion was not observed for the eastern clade. We hypothesize that the western population was confined to a small Italo-Balkanic refugium, whereas the eastern population subsisted in several refugia along the southern coast of the Black Sea.
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Affiliation(s)
- S Dubey
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
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Waters JM, Rowe DL, Apte S, King TM, Wallis GP, Anderson L, Norris RJ, Craw D, Burridge CP. Geological Dates and Molecular Rates: Rapid Divergence of Rivers and Their Biotas. Syst Biol 2007; 56:271-82. [PMID: 17464882 DOI: 10.1080/10635150701313855] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
We highlight a novel molecular clock calibration system based on geologically dated river reversal and river capture events. Changes in drainage pattern may effect vicariant isolation of freshwater taxa, and thus provide a predictive framework for associated phylogeographic study. As a case in point, New Zealand's Pelorus and Kaituna rivers became geologically isolated from the larger Wairau River system 70 to 130 kyr BP. We conducted mitochondrial DNA phylogeographic analyses of two unrelated freshwater-limited fish taxa native to these river systems (Gobiomorphus breviceps, n = 63; Galaxias divergens, n = 95). Phylogenetic analysis of combined control region and cytochrome b sequences yielded reciprocally monophyletic clades of Pelorus-Kaituna and Wairau haplotypes for each species. Calibrated rates of molecular change based on this freshwater vicariant event are substantially faster than traditionally accepted rates for fishes but consistent with other recent inferences based on geologically young calibration points. A survey of freshwater phylogeographic literature reveals numerous examples in which the ages of recent evolutionary events may have been substantially overestimated through the use of "accepted" calibrations. We recommend that--wherever possible--biologists should start to reassess the conclusions of such studies by using more appropriate molecular calibrations derived from recent geological events.
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Affiliation(s)
- Jonathan M Waters
- Department of Zoology, University of Otago, PO Box 56, Dunedin, New Zealand.
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50
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Mezhzherin SV, Pavlenko LI. Genetic structure of diploid-polyploid complex of spined loach genus Cobitis (Cypriniformes, Cobitidae) in the Lower Danube. CYTOL GENET+ 2007. [DOI: 10.3103/s0095452707010070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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