Nuclear and mitochondrial DNA sequence data reveal the evolutionary history of Barbus (Cyprinidae) in the ancient lake systems of the Balkans

Albrecht, 2008, Ancient Lake Ohrid: biodiversity and evolution, Hydrobiologia, 615, 103, 10.1007/s10750-008-9558-y Albrecht, 2008, Concurrent evolution of ancient sister lakes and sister species. The freshwater gastropod genus Radix in lakes Ohrid and Prespa, Hydrobiologia, 615, 157, 10.1007/s10750-008-9555-1 Anisimova, 2006, Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative, Syst. Biol., 55, 539, 10.1080/10635150600755453 Atarhouch, 2003, Primers for EPIC amplification of intron sequences for fish and other vertebrate population genetic studies, Biotechniques, 35, 676, 10.2144/03354bm02 Avise, 2000 Avise, 2008, Hemiplasy: a new term in the lexicon of phylogenetics, Syst. Biol., 57, 503, 10.1080/10635150802164587 Barluenga, 2006, Sympatric speciation in Nicaraguan crater lake cichlid fish, Nature, 439, 719, 10.1038/nature04325 Bianco, 1998, Diversity of Barbinae fishes in southern Europe with description of a new genus and a new species (Cyprinidae), Ital. J. Zool., 65, 125, 10.1080/11250009809386804 Berrebi, 1996, Systematic of Barbus: state of the art and heuristic comments, Folia Zool., 45, 5 Bordon, 2009, Pollen-inferred Late-Glacial and Holocene climate in southern Balkans (Lake Maliq), Quat. Int., 200, 19, 10.1016/j.quaint.2008.05.014 Bryant, 2004, Neighbor-Net: an agglomerative method for the construction of phylogenetic networks, Mol. Biol. Evol., 21, 255, 10.1093/molbev/msh018 Burridge, 2006, River capture, range expansion, and cladogenesis: the genetic signature of freshwater vicariance, Evolution, 60, 1038, 10.1111/j.0014-3820.2006.tb01181.x Carstens, 2007, Shifting distributions and speciation: species divergence during rapid climate change, Mol. Ecol., 16, 619, 10.1111/j.1365-294X.2006.03167.x Cheynier, 2001, Insertion/deletion frequencies match those of point mutations in the hypervariable regions of the simian immunodeficiency virus surface envelope gene, J. Gen. Virol., 82, 1613, 10.1099/0022-1317-82-7-1613 Cowling, 1996, Plant diversity in Mediterranean-climate regions, Trends Ecol. Evol., 11, 362, 10.1016/0169-5347(96)10044-6 Craw, 2007, Geological and biological evidence for drainage reorientation during uplift of alluvial basins, central Otago, New Zealand, NZ J. Geol. Geophys., 50, 367, 10.1080/00288300709509844 Crivelli, 1996, The Prespa barbel, Barbus prespensis, a fish species endemic to the Prespa Lakes (North-western Greece), Folia Zool., 45, 21 Crivelli, 1997, Fish and fisheries of the Prespa lakes, Hydrobiologia, 351, 107, 10.1023/A:1003064509018 Cvijić, 1911 Degnan, 2009, Gene tree discordance, phylogenetic inference and the multispecies coalescent, Trend Ecol. Evol., 24, 332, 10.1016/j.tree.2009.01.009 Doadrio, 1990, Phylogenetic relationships and classification of western palaearctic species of the genus Barbus (Osteichthyes, Cyprinidae), Aquat. Living Resour., 3, 265, 10.1051/alr:1990028 Economidis, P.S., Daoulas, C., 2003. Barbus prespensis Karaman, 1924. In: Banarescu, P.M., Bogutskaya, N.G. (Eds.), The Freshwater Fishes of Europe. Aula-Verlag, Wiebelsheim, Germany. Cyprinidae 5/II, part II, Barbus, 365–376. Economidis, P.S., Sorič, V.M., Banarescu, P.M., 2003. Barbus peloponnesius Valenciennes, 1842. In: Banarescu, P.M., Bogutskaya, N.G. (Eds.), The Freshwater Fishes of Europe. Aula-Verlag, Wiebelsheim, Germany. Cyprinidae 5/II, part II, Barbus, 301–337. Elmer, 2009, Pleistocene desiccation in East Africa bottlenecked but did not extirpate the adaptive radiation of Lake Victoria haplochromine cichlid fishes, PNAS, 106, 13404, 10.1073/pnas.0902299106 Excoffier, 1992, Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data, Genetics, 131, 479, 10.1093/genetics/131.2.479 Excoffier, 2005, Arlequin ver. 3.0: an integrated software package for population genetics data analysis, Evol. Bioinform. Online, 1, 47, 10.1177/117693430500100003 Felsenstein, 1985, Confidence limits on phylogenies: an approach using bootstrap, Evolution, 39, 783, 10.1111/j.1558-5646.1985.tb00420.x Flot, 2006, Phase determination from direct sequencing of length-variable DNA regions, Mol. Ecol. Notes, 6, 627, 10.1111/j.1471-8286.2006.01355.x Fu, 1997, Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection, Genetics, 147, 915, 10.1093/genetics/147.2.915 Gamble, 2008, Species limits and phylogeography of North American cricket frogs (Acris: Hylidae), Mol. Phylogenet. Evol., 48, 112, 10.1016/j.ympev.2008.03.015 de Graaf, 2010, Preliminary insight into the age and origin of the Labeobarbus fish species flock from Lake Tana (Ethiopia) using the mtDNA cytochrome b gene, Mol. Phylogenet. Evol., 54, 336, 10.1016/j.ympev.2009.10.029 Guindon, 2003, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst. Biol., 52, 696, 10.1080/10635150390235520 Hare, 1999, The accuracy of heterozygous base calling from diploid sequence and resolution of haplotypes using allele-specific sequencing, Mol. Ecol., 8, 1749, 10.1046/j.1365-294x.1999.00738-1.x Hey, 2004, Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis, Genetics, 167, 747, 10.1534/genetics.103.024182 Hey, 2007, Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics, Proc. Natl. Acad. Sci. USA, 104, 2785, 10.1073/pnas.0611164104 Hrbek, 2003, Closing of the Tethys Sea and the phylogeny of Eurasian killifishes (Cyprinodontiformes: Cyprinodontidae), J. Evol. Biol., 16, 17, 10.1046/j.1420-9101.2003.00475.x Hudson, 1985, Statistical properties of the number of recombination events in the history of a sample of DNA sequences, Genetics, 111, 147, 10.1093/genetics/111.1.147 Huson, 2006, Application of phylogenetic networks in evolutionary studies, Mol. Biol. Evol., 23, 254, 10.1093/molbev/msj030 Karaman, 1971, Susswasserfische der Türkei, 8 Teil. Revision der Barben Europas, Vorderasiens und Nordafrikas, Mitt. Hamburg Zool. Mus. Inst., 67, 175 Ketmaier, 2008, Molecular systematics, phylogeny and biogeography of roaches (Rutilus, Teleostei, Cyprinidae), Mol. Phylogenet. Evol., 49, 362, 10.1016/j.ympev.2008.07.012 Klossa-Kilia, 2002, Mitochondrial DNA diversity in Atherina boyeri populations as determined by RFLP analysis of three mtDNA segments, Heredity, 89, 363, 10.1038/sj.hdy.6800144 Kotlík, 2002, Genetic subdivision and biogeography of the Danubian rheophilic barb Barbus petenyi inferred from phylogenetic analysis of mitochondrial DNA variation, Mol. Phylogenet. Evol., 24, 10, 10.1016/S1055-7903(02)00264-6 Kotlík, 2004, Circum Black Sea phylogeography of Barbus freshwater fishes: divergence in the Pontic glacial refugium, Mol. Ecol., 13, 87, 10.1046/j.1365-294X.2003.02021.x Kotlík, 2008, Divergence with gene flow between Ponto-Caspian refugia in an anadromous cyprinid Rutilus frisii revealed by multiple gene phylogeography, Mol. Ecol., 17, 1076, 10.1111/j.1365-294X.2007.03638.x Kottelat, 1997, European freshwater fishes. An heuristic checklist of the freshwater fishes of Europe (exclusive of former USSR), with an introduction for non-systematists and comments on nomenclature and conservation, Biologia, 52, S1 Kottelat, 2007 Lajbner, 2009, Rare and asymmetrical hybridization of the endemic Barbus carpathicus with its widespread congener Barbus barbus, J. Fish. Biol., 74, 418, 10.1111/j.1095-8649.2008.02098.x Machordom, 2001, Evolutionary history and speciation modes in the cyprinid genus Barbus, Proc. R. Soc. Lond. Biol., 268, 1297, 10.1098/rspb.2001.1654 Martens, 1997, Speciation in ancient lakes, Trends Ecol. Evol., 12, 177, 10.1016/S0169-5347(97)01039-2 Nei, 1987 Nielsen, 2001, Distinguishing migration from isolation: a Markov chain Monte Carlo approach, Genetics, 158, 885, 10.1093/genetics/158.2.885 Oosterbroek, 1992, Area-cladograms of Circum-Mediterranean taxa in relation to Mediterranean palaeogeography, J. Biogeogr., 19, 3, 10.2307/2845616 Palumbi, 2001, Predicting nuclear gene coalescence from mitochondrial data: the three-times rule, Evolution, 55, 859, 10.1554/0014-3820(2001)055[0859:PNGCFM]2.0.CO;2 Perdices, 2008, The molecular diversity of adriatic spined loaches (Teleostei, Cobitidae), Mol. Phylogenet. Evol., 46, 382, 10.1016/j.ympev.2007.05.007 Posada, 2003, Using Modeltest and PAUP∗ to select a model of nucleotide substitution Posada, 2008, JModelTest: Phylogenetic Model Averaging, Mol. Biol. Evol., 25, 1253, 10.1093/molbev/msn083 Rakaj, 1995, Conservation status of freshwater fish of Albania, Biol. Conserv., 72, 195, 10.1016/0006-3207(94)00082-2 Ramírez-Soriano, 2008, Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination, Genetics, 179, 555, 10.1534/genetics.107.083006 Ramos-Onsins, 2002, Statistical properties of new neutrality tests against population growth, Mol. Biol. Evol., 19, 2092, 10.1093/oxfordjournals.molbev.a004034 Rozas, 2003, DnaSP, DNA polymorphism analyses by the coalescent and other methods, Bioinformatics, 19, 2496, 10.1093/bioinformatics/btg359 Saitoh, 2000, Complete nucleotide sequence of Japanese flounder (Paralichthys olivaceus) mitochondrial genome: structural properties and cue for resolving teleostean relationships, J. Hered., 91, 271, 10.1093/jhered/91.4.271 Šanda, 2008, Distribution of loach fishes (Cobitidae, Nemacheilidae) in Albania, with genetic analysis of populations of Cobitis ohridana, Folia Zool., 57, 42 Sauquet, 2009, Contrasted patterns of hyperdiversification in Mediterranean hotspots, Proc. Natl. Acad. Sci. USA, 106, 221, 10.1073/pnas.0805607106 Schultheiss, 2008, The neglected side of speciation in ancient lakes: phylogeography of an inconspicuous mollusc taxon in lakes Ohrid and Prespa, Hydrobiologia, 615, 141, 10.1007/s10750-008-9553-3 Sousa-Santos, 2005, Heterozygous indels as useful tools in the reconstruction of DNA sequences and in the assessment of ploidy level and genomic constitution of hybrid organisms, DNA Seq., 16, 462, 10.1080/10425170500356065 Stanković, S., 1960. The Balkan Lake Ohrid and its Living World. Monographiae Biologicae, vol. 9. Dr. W. Junk, Den Haag, The Netherlands. Stephens, 2005, Accounting for decay of linkage disequilibrium in haplotype inference and missing data imputation, Am. J. Hum. Genet., 76, 449, 10.1086/428594 Stephens, 2001, A new statistical method for haplotype reconstruction from population data, Am. J. Hum. Genet., 68, 978, 10.1086/319501 Strasburg, 2009, How robust are “Isolation with Migration” analyses to violations of the IM model? A simulation study, Mol. Biol. Evol., 27, 297, 10.1093/molbev/msp233 Sušnik, 2007, Historical demography of brown trout (Salmo trutta) in the Adriatic drainage including the putative S. letnica endemic to lake Ohrid, Mol. Phylogenet. Evol., 44, 63, 10.1016/j.ympev.2006.08.021 Swofford, 2003 Tajima, 1989, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, 123, 585, 10.1093/genetics/123.3.585 Tamura, 2007, MEGA 4: molecular evolutionary genetics analysis (MEGA) software version 4.0, Mol. Biol. Evol., 24, 1596, 10.1093/molbev/msm092 Triantis, 2005, Species richness, environmental heterogeneity and area: a case study based on land snails in Skyros archipelago (Aegean Sea, Greece), J. Biogeogr., 32, 1727, 10.1111/j.1365-2699.2005.01322.x Tsigenopoulos, 2000, Molecular phylogeny of North Mediterranean freshwater barbs (genus Barbus: Cyprinidae) inferred from cytochrome b sequences: biogeographic and systematic implications, Mol. Phylogenet. Evol., 14, 165, 10.1006/mpev.1999.0702 Tsigenopoulos, 1999, The North Mediterranean Barbus lineage: phylogenetic hypotheses and taxonomic implications based on allozyme data, J. Fish Biol., 54, 267 Tsigenopoulos, 2002, Biogeography and pattern of gene flow among Barbus species (Teleostei: Cyprinidae) inhabiting the Italian Peninsula and neighboring Adriatic drainages as revealed by allozyme and mitochondrial sequence data, Biol. J. Linn. Soc., 75, 83, 10.1046/j.1095-8312.2002.00007.x Wiley, 2000, The evolutionary species concept, 70 Winkworth, 2005, Biogeographic interpretation of split graphs: least squares optimization of branch lengths, Syst. Biol., 54, 56, 10.1080/10635150590906046 Woerner, 2007, Recombination-filtered genomic datasets by information maximization, Bioinformatics, 23, 1851, 10.1093/bioinformatics/btm253 Zárate, 2007, Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1, J. Virol., 81, 6643, 10.1128/JVI.02268-06 Zardoya, 1999, Molecular evidence on the evolutionary and biogeographical patterns of European cyprinids, J. Mol. Evol., 49, 227, 10.1007/PL00006545 Zardoya, 1999, Phylogenetic relationships of Greek Cyprinidae: molecular evidence for the origin for at least two origins of the Greek cyprinid fauna, Mol. Phylogenet. Evol., 13, 122, 10.1006/mpev.1999.0630