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Nakamura H, Aibara M, Nikaido M. Ancient standing genetic variation facilitated the adaptive radiation of Lake Victoria cichlids. Genes Genet Syst 2023; 98:93-99. [PMID: 37495512 DOI: 10.1266/ggs.23-00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023] Open
Abstract
Cichlid fishes are textbook examples of explosive speciation and adaptive radiation, providing a great opportunity to understand how the genomic substrate yields extraordinary species diversity. Recently, we performed comparative genomic analyses of three Lake Victoria cichlids to reveal the genomic substrates underlying their rapid speciation and adaptation. We found that long divergent haplotypes derived from large-scale standing genetic variation, which originated before the adaptive radiation of Lake Victoria cichlids, may have contributed to their rapid diversification. In addition, the present study on genomic data from other East African cichlids suggested the reuse of alleles that may have originated in the ancestral lineages of Lake Tanganyika cichlids during cichlid evolution. Therefore, our results highlight that the primary factor that could drive repeated adaptive radiation across East African cichlids was allelic reuse from standing genetic variation to adapt to their own specific environment. In this report, we summarize the main results and discuss the evolutionary mechanisms of cichlids, based on our latest findings.
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Affiliation(s)
- Haruna Nakamura
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies
| | - Mitsuto Aibara
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology
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2
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Astudillo-Clavijo V, Stiassny MLJ, Ilves KL, Musilova Z, Salzburger W, López-Fernández H. Exon-based phylogenomics and the relationships of African cichlid fishes: tackling the challenges of reconstructing phylogenies with repeated rapid radiations. Syst Biol 2022; 72:134-149. [PMID: 35880863 DOI: 10.1093/sysbio/syac051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae, and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system.
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Affiliation(s)
- Viviana Astudillo-Clavijo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, 10024-5102, USA
| | - Katriina L Ilves
- Research & Collections, Zoology, Canadian Museum of Nature, Ottawa, K1P 6P4, Canada
| | - Zuzana Musilova
- Department of Zoology, Charles University in Prague, Vinicna 7, Prague, CZ-128 44, Czech Republic
| | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Hernán López-Fernández
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
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3
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van der Merwe PDW, Cotterill FPD, Kandziora M, Watters BR, Nagy B, Genade T, Flügel TJ, Svendsen DS, Bellstedt DU. Genomic fingerprints of palaeogeographic history: The tempo and mode of rift tectonics across tropical Africa has shaped the diversification of the killifish genus Nothobranchius (Teleostei: Cyprinodontiformes). Mol Phylogenet Evol 2020; 158:106988. [PMID: 33059071 DOI: 10.1016/j.ympev.2020.106988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/16/2020] [Accepted: 10/07/2020] [Indexed: 01/04/2023]
Abstract
This paper reports a phylogeny of the African killifishes (Genus Nothobranchius, Order Cyprinodontiformes) informed by five genetic markers (three nuclear, two mitochondrial) of 80 taxa (seven undescribed and 73 of the 92 recognized species). These short-lived annual fishes occupy seasonally wet habitats in central and eastern Africa, and their distribution coincides largely with the East African Rift System (EARS). The fossil dates of sister clades used to constrain a chronometric tree of all sampled Nothobranchius recovered the origin of the genus at ~13.27 Mya. It was followed by the radiations of six principal clades through the Neogene. An ancestral area estimation tested competing biogeographical hypotheses to constrain the ancestral origin of the genus to the Nilo-Sudan Ecoregion, which seeded a mid-Miocene dispersal event into the Coastal ecoregion, followed closely (~10 Mya) by dispersals southward across the Mozambique coastal plain into the Limpopo Ecoregion. Extending westwards across the Tanzanian plateau, a pulse of radiations through the Pliocene were associated with dispersals and fragmentation of wetlands across the Kalahari and Uganda Ecoregions. We interpret this congruence of drainage rearrangements with dispersals and cladogenic events of Nothobranchius to reflect congruent responses to recurrent uplift and rifting. The coevolution of these freshwater fishes and wetlands is attributed to ultimate control by tectonics, as the EARS extended southwards during the Neogene. Geobiological consilience of the combined evidence supports a tectonic hypothesis for the evolution of Nothobranchius.
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Affiliation(s)
| | | | - Martha Kandziora
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Brian R Watters
- 6141 Parkwood Drive, Nanaimo, British Columbia V9T6A2, Canada
| | - Béla Nagy
- 30, Rue du Mont Ussy, 77300 Fontainebleau, France
| | - Tyrone Genade
- Biomedical Sciences, East Tennessee State University, USA
| | - Tyrel J Flügel
- Department of Geography and Environmental Studies, Stellenbosch University, South Africa
| | - David S Svendsen
- Department of Geography and Environmental Studies, Stellenbosch University, South Africa
| | - Dirk U Bellstedt
- Department of Biochemistry, Stellenbosch University, South Africa.
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Altner M, Ruthensteiner B, Reichenbacher B. New haplochromine cichlid from the upper Miocene (9-10 MYA) of Central Kenya. BMC Evol Biol 2020; 20:65. [PMID: 32503417 PMCID: PMC7275555 DOI: 10.1186/s12862-020-01602-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/06/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The diversification process known as the Lake Tanganyika Radiation has given rise to the most speciose clade of African cichlids. Almost all cichlid species found in the lakes Tanganyika, Malawi and Victoria, comprising a total of 12-16 tribes, belong to this clade. Strikingly, all the species in the latter two lakes are members of the tribe Haplochromini, whose origin remains unclear. The 'out of Tanganyika' hypothesis argues that the Haplochromini emerged simultaneously with other cichlid tribes and lineages in Lake Tanganyika, presumably about 5-6 million years ago (MYA), and that their presence in the lakes Malawi and Victoria and elsewhere in Africa today is due to later migrations. In contrast, the 'melting pot Tanganyika hypothesis' postulates that Haplochromini emerged in Africa prior to the formation of Lake Tanganyika, and that their divergence could have begun about 17 MYA. Haplochromine fossils could potentially resolve this debate, but such fossils are extremely rare. RESULTS Here we present a new fossil haplochromine from the upper Miocene site Waril (9-10 million years) in Central Kenya. Comparative morphology, supported by Micro-CT imaging, reveals that it bears a unique combination of characters relating to dentition, cranial bones, caudal skeleton and meristic traits. Its most prominent feature is the presence of exclusively unicuspid teeth, with canines in the outer tooth row. †Warilochromis unicuspidatus gen. et sp. nov. shares this combination of characters solely with members of the Haplochromini and its lacrimal morphology indicates a possible relation to the riverine genus Pseudocrenilabrus. Due to its fang-like dentition and non-fusiform body, †W. unicuspidatus gen. et sp. nov. might have employed either a sit-and-pursue or sit-and-wait hunting strategy, which has not been reported for any other fossil haplochromine cichlid. CONCLUSIONS The age of the fossil (9-10 MYA) is incompatible with the 'out of Tanganyika' hypothesis, which postulates that the divergence of the Haplochromini began only 5-6 MYA. The presence of this fossil in an upper Miocene palaeolake in the Central Kenya Rift, as well as its predatory lifestyle, indicate that Haplochromini were already an important component of freshwater drainages in East Africa at that time.
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Affiliation(s)
- Melanie Altner
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333 Munich, DE Germany
| | - Bernhard Ruthensteiner
- Section Evertebrata Varia, SNSB – ZSM Bavarian State Collection of Zoology, Münchhausen-Strasse 21, 81247 Munich, DE Germany
| | - Bettina Reichenbacher
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333 Munich, DE Germany
- GeoBio-Center at Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333 Munich, DE Germany
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Meier JI, Stelkens RB, Joyce DA, Mwaiko S, Phiri N, Schliewen UK, Selz OM, Wagner CE, Katongo C, Seehausen O. The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlid fishes. Nat Commun 2019; 10:5391. [PMID: 31796733 PMCID: PMC6890737 DOI: 10.1038/s41467-019-13278-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 10/22/2019] [Indexed: 01/26/2023] Open
Abstract
The process of adaptive radiation was classically hypothesized to require isolation of a lineage from its source (no gene flow) and from related species (no competition). Alternatively, hybridization between species may generate genetic variation that facilitates adaptive radiation. Here we study haplochromine cichlid assemblages in two African Great Lakes to test these hypotheses. Greater biotic isolation (fewer lineages) predicts fewer constraints by competition and hence more ecological opportunity in Lake Bangweulu, whereas opportunity for hybridization predicts increased genetic potential in Lake Mweru. In Lake Bangweulu, we find no evidence for hybridization but also no adaptive radiation. We show that the Bangweulu lineages also colonized Lake Mweru, where they hybridized with Congolese lineages and then underwent multiple adaptive radiations that are strikingly complementary in ecology and morphology. Our data suggest that the presence of several related lineages does not necessarily prevent adaptive radiation, although it constrains the trajectories of morphological diversification. It might instead facilitate adaptive radiation when hybridization generates genetic variation, without which radiation may start much later, progress more slowly or never occur.
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Affiliation(s)
- Joana I Meier
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street, Cambridge, CB2 1TP, UK
| | - Rike B Stelkens
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
- Division of Population Genetics, Department of Zoology, Stockholm University, Svante Arrheniusväg 18 B, 106 91, Stockholm, Sweden
| | - Domino A Joyce
- Evolutionary and Ecological Genomics Group, Department of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Salome Mwaiko
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Numel Phiri
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Ulrich K Schliewen
- SNSB-Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, Munich, Germany
| | - Oliver M Selz
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Catherine E Wagner
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
- Biodiversity Institute and Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Cyprian Katongo
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Ole Seehausen
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland.
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.
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6
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Penk SBR, Altner M, F Cerwenka A, Schliewen UK, Reichenbacher B. New fossil cichlid from the middle Miocene of East Africa revealed as oldest known member of the Oreochromini. Sci Rep 2019; 9:10198. [PMID: 31308387 PMCID: PMC6629881 DOI: 10.1038/s41598-019-46392-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/28/2019] [Indexed: 11/09/2022] Open
Abstract
A new genus and species of fossil cichlid fishes of middle Miocene age (12.5 Ma) is described from the Ngorora fish Lagerstätte (Tugen Hills, Kenya) in the East African Rift Valley. Parsimony analysis of morphological characters using published phylogenetic frameworks for extant cichlids combined with the application of a comprehensive best-fit approach based on morphology was employed to place the new fossil taxon in the phylogenetic context of the African cichlids. The data reveal that the fossil specimens can be assigned to the tribe Oreochromini within the haplotilapiines. †Oreochromimos kabchorensis gen. et sp. nov. shows a mosaic set of characters bearing many similarities to the almost pan-African Oreochromis and the East African lake-endemic Alcolapia. As the striking diversity of present-day African cichlids, with 1100 recognised species, has remained largely invisible in the fossil record, the material described here adds significantly to our knowledge of the Miocene diversity of the group. It effectively doubles the age of a fossil calibration point, which has hitherto been used to calibrate divergence times of the East African cichlids in molecular phylogenetic investigations. Furthermore, the comparative dataset derived from extant cichlids presented here will greatly facilitate the classification of fossil cichlids in future studies.
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Affiliation(s)
- Stefanie B R Penk
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany.
| | - Melanie Altner
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany
| | - Alexander F Cerwenka
- Section Evertebrata varia, SNSB Bavarian State Collection of Zoology, 81247, Munich, Germany
| | - Ulrich K Schliewen
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333, Munich, Germany
- Department of Ichthyology, SNSB Bavarian State Collection of Zoology, 81247, Munich, Germany
| | - Bettina Reichenbacher
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany.
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333, Munich, Germany.
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7
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Schedel FDB, Musilova Z, Schliewen UK. East African cichlid lineages (Teleostei: Cichlidae) might be older than their ancient host lakes: new divergence estimates for the east African cichlid radiation. BMC Evol Biol 2019; 19:94. [PMID: 31023223 PMCID: PMC6482553 DOI: 10.1186/s12862-019-1417-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/31/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Cichlids are a prime model system in evolutionary research and several of the most prominent examples of adaptive radiations are found in the East African Lakes Tanganyika, Malawi and Victoria, all part of the East African cichlid radiation (EAR). In the past, great effort has been invested in reconstructing the evolutionary and biogeographic history of cichlids (Teleostei: Cichlidae). In this study, we present new divergence age estimates for the major cichlid lineages with the main focus on the EAR based on a dataset encompassing representative taxa of almost all recognized cichlid tribes and ten mitochondrial protein genes. We have thoroughly re-evaluated both fossil and geological calibration points, and we included the recently described fossil †Tugenchromis pickfordi in the cichlid divergence age estimates. RESULTS Our results estimate the origin of the EAR to Late Eocene/Early Oligocene (28.71 Ma; 95% HPD: 24.43-33.15 Ma). More importantly divergence ages of the most recent common ancestor (MRCA) of several Tanganyika cichlid tribes were estimated to be substantially older than the oldest estimated maximum age of the Lake Tanganyika: Trematocarini (16.13 Ma, 95% HPD: 11.89-20.46 Ma), Bathybatini (20.62 Ma, 95% HPD: 16.88-25.34 Ma), Lamprologini (15.27 Ma; 95% HPD: 12.23-18.49 Ma). The divergence age of the crown haplochromine H-lineage is estimated to 22.8 Ma (95% HPD: 14.40-26.32 Ma) and of the Lake Malawi radiation to 4.07 Ma (95% HDP: 2.93-5.26 Ma). In addition, we recovered a novel lineage within the Lamprologini tribe encompassing only Lamprologus of the lower and central Congo drainage with its divergence estimated to the Late Miocene or early Pliocene. Furthermore we recovered two novel mitochondrial haplotype lineages within the Haplochromini tribe: 'Orthochromis' indermauri and 'Haplochormis' vanheusdeni. CONCLUSIONS Divergence time estimates of the MRCA of several Tanganyika cichlid tribes predate the age of the extant Lake Tanganyika basin, and hence are in line with the recently formulated "Melting-Pot Tanganyika" hypothesis. The radiation of the 'Lower Congo Lamprologus clade' might be linked with the Pliocene origin of the modern lower Congo rapids as has been shown for other Lower Congo cichlid assemblages. Finally, the age of origin of the Lake Malawi cichlid flock agrees well with the oldest age estimate for lacustrine conditions in Lake Malawi.
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Affiliation(s)
| | - Zuzana Musilova
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, CZ-128 44 Prague, Czech Republic
| | - Ulrich Kurt Schliewen
- Department of Ichthyology, SNSB - Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
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8
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Multigene fossil-calibrated analysis of the African lampeyes (Cyprinodontoidei: Procatopodidae) reveals an early Oligocene origin and Neogene diversification driven by palaeogeographic and palaeoclimatic events. ORG DIVERS EVOL 2019. [DOI: 10.1007/s13127-019-00396-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Malinsky M, Svardal H, Tyers AM, Miska EA, Genner MJ, Turner GF, Durbin R. Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. Nat Ecol Evol 2018; 2:1940-1955. [PMID: 30455444 PMCID: PMC6443041 DOI: 10.1038/s41559-018-0717-x] [Citation(s) in RCA: 263] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/10/2018] [Indexed: 12/30/2022]
Abstract
The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. The average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalist Astatotilapia-like ancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep-water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation.
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Affiliation(s)
- Milan Malinsky
- Wellcome Sanger Institute, Cambridge, UK.
- Zoological Institute, University of Basel, Basel, Switzerland.
| | - Hannes Svardal
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Alexandra M Tyers
- School of Natural Sciences, Bangor University, Bangor, UK
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Eric A Miska
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Richard Durbin
- Wellcome Sanger Institute, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
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10
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Vreven EJWMN, Musschoot T, Decru E, Wamuini Lunkayilakio S, Obiero K, Cerwenka AF, Schliewen UK. The complex origins of mouth polymorphism in the Labeobarbus (Cypriniformes: Cyprinidae) of the Inkisi River basin (Lower Congo, DRC, Africa): insights from an integrative approach. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Emmanuel J W M N Vreven
- Vertebrate Section, Ichthyology, Royal Museum for Central Africa, RMCA, Leuvensesteenweg, Tervuren, Belgium
- KU Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Charles Deberiotstraat, Leuven, Belgium
| | - Tobias Musschoot
- Vertebrate Section, Ichthyology, Royal Museum for Central Africa, RMCA, Leuvensesteenweg, Tervuren, Belgium
| | - Eva Decru
- Vertebrate Section, Ichthyology, Royal Museum for Central Africa, RMCA, Leuvensesteenweg, Tervuren, Belgium
- KU Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Charles Deberiotstraat, Leuven, Belgium
| | | | - Kevin Obiero
- Kenya Marine and Fisheries Research Institute, Lake Turkana Research Station, Lodwar, Kenya
| | - Alexander F Cerwenka
- SNSB Bavarian Natural History Collections, Bavarian State Collection of Zoology, Department of Ichthyology, Münchhausenstrasse, München, Germany
| | - Ulrich K Schliewen
- SNSB Bavarian Natural History Collections, Bavarian State Collection of Zoology, Department of Ichthyology, Münchhausenstrasse, München, Germany
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11
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Salzburger W. Understanding explosive diversification through cichlid fish genomics. Nat Rev Genet 2018; 19:705-717. [DOI: 10.1038/s41576-018-0043-9] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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12
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Irisarri I, Singh P, Koblmüller S, Torres-Dowdall J, Henning F, Franchini P, Fischer C, Lemmon AR, Lemmon EM, Thallinger GG, Sturmbauer C, Meyer A. Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes. Nat Commun 2018; 9:3159. [PMID: 30089797 PMCID: PMC6082878 DOI: 10.1038/s41467-018-05479-9] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/30/2018] [Indexed: 11/21/2022] Open
Abstract
Lake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using anchored phylogenomics and uncover hybridization at its base, as well as early in the haplochromine radiation. This suggests that hybridization might have facilitated these speciation bursts. Time-calibrated trees support that the radiation of Tanganyika cichlids coincided with lake formation and that Gondwanan vicariance concurred with the earliest splits in the cichlid family tree. Genes linked to key innovations show signals of introgression or positive selection following colonization of lake habitats and species' dietary adaptations are revealed as major drivers of colour vision evolution. These findings shed light onto the processes shaping the evolution of adaptive radiations.
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Affiliation(s)
- Iker Irisarri
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, Madrid, 28006, Spain
| | - Pooja Singh
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Julián Torres-Dowdall
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
| | - Frederico Henning
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Ilha do Fundão, Rio de Janeiro, 21944-970, Brazil
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
| | - Christoph Fischer
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, Graz, 8010, Austria
- OMICS Center Graz, BioTechMed Graz, Stiftingtalstraße 24, Graz, 8010, Austria
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, FL, 32306, USA
| | - Gerhard G Thallinger
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, Graz, 8010, Austria
- OMICS Center Graz, BioTechMed Graz, Stiftingtalstraße 24, Graz, 8010, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria.
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany.
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, 02138, MA, USA.
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13
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Meyer BS, Matschiner M, Salzburger W. Disentangling Incomplete Lineage Sorting and Introgression to Refine Species-Tree Estimates for Lake Tanganyika Cichlid Fishes. Syst Biol 2018; 66:531-550. [PMID: 27539485 DOI: 10.1093/sysbio/syw069] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/27/2016] [Indexed: 12/19/2022] Open
Abstract
Adaptive radiation is thought to be responsible for the evolution of a great portion of the past and present diversity of life. Instances of adaptive radiation, characterized by the rapid emergence of an array of species as a consequence to their adaptation to distinct ecological niches, are important study systems in evolutionary biology. However, because of the rapid lineage formation in these groups, and occasional gene flow between the participating species, it is often difficult to reconstruct the phylogenetic history of species that underwent an adaptive radiation. In this study, we present a novel approach for species-tree estimation in rapidly diversifying lineages, where introgression is known to occur, and apply it to a multimarker data set containing up to 16 specimens per species for a set of 45 species of East African cichlid fishes (522 individuals in total), with a main focus on the cichlid species flock of Lake Tanganyika. We first identified, using age distributions of most recent common ancestors in individual gene trees, those lineages in our data set that show strong signatures of past introgression. This led us to formulate three hypotheses of introgression between different lineages of Tanganyika cichlids: the ancestor of Boulengerochromini (or of Boulengerochromini and Bathybatini) received genomic material from the derived H-lineage; the common ancestor of Cyprichromini and Perissodini experienced, in turn, introgression from Boulengerochromini and/or Bathybatini; and the Lake Tanganyika Haplochromini and closely related riverine lineages received genetic material from Cyphotilapiini. We then applied the multispecies coalescent model to estimate the species tree of Lake Tanganyika cichlids, but excluded the lineages involved in these introgression events, as the multispecies coalescent model does not incorporate introgression. This resulted in a robust species tree, in which the Lamprologini were placed as sister lineage to the H-lineage (including the Eretmodini), and we identify a series of rapid splitting events at the base of the H-lineage. Divergence ages estimated with the multispecies coalescent model were substantially younger than age estimates based on concatenation, and agree with the geological history of the Great Lakes of East Africa. Finally, we formally tested the three hypotheses of introgression using a likelihood framework, and find strong support for introgression between some of the cichlid tribes of Lake Tanganyika.
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Affiliation(s)
- Britta S Meyer
- Zoological Institute, University of Basel, Basel, Switzerland.,Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Michael Matschiner
- Zoological Institute, University of Basel, Basel, Switzerland.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Walter Salzburger
- Zoological Institute, University of Basel, Basel, Switzerland.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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14
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Faulkes CG, Mgode GF, Archer EK, Bennett NC. Relic populations of Fukomys mole-rats in Tanzania: description of two new species F. livingstoni sp. nov. and F. hanangensis sp. nov. PeerJ 2017; 5:e3214. [PMID: 28462027 PMCID: PMC5410139 DOI: 10.7717/peerj.3214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/21/2017] [Indexed: 11/22/2022] Open
Abstract
Previous studies of African mole-rats of the genera Heliophobius and Fukomys (Bathyergidae) in the regions of East and south central Africa have revealed a diversity of species and vicariant populations, with patterns of distribution having been influenced by the geological process of rifting and changing patterns of drainage of major river systems. This has resulted in most of the extant members of the genus Fukomys being distributed west of the main Rift Valley. However, a small number of isolated populations are known to occur east of the African Rift Valley in Tanzania, where Heliophobius is the most common bathyergid rodent. We conducted morphological, craniometric and phylogenetic analysis of mitochondrial cytochrome b (cyt b) sequences of two allopatric populations of Tanzanian mole-rats (genus Fukomys) at Ujiji and around Mount Hanang, in comparison with both geographically adjacent and more distant populations of Fukomys. Our results reveal two distinct evolutionary lineages, forming clades that constitute previously unnamed species. Here, we formally describe and designate these new species F. livingstoni and F. hanangensis respectively. Molecular clock-based estimates of divergence times, together with maximum likelihood inference of biogeographic range evolution, offers strong support for the hypothesis that vicariance in the Western Rift Valley and the drainage patterns of major river systems has subdivided populations of mole-rats. More recent climatic changes and tectonic activity in the “Mbeya triple junction” and Rungwe volcanic province between Lakes Rukwa and Nyasa have played a role in further isolation of these extra-limital populations of Fukomys in Tanzania.
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Affiliation(s)
- Chris G Faulkes
- School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
| | - Georgies F Mgode
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Elizabeth K Archer
- School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
| | - Nigel C Bennett
- Department of Zoology & Entomology, University of Pretoria, Pretoria, Gauteng, South Africa
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15
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Meier JI, Marques DA, Mwaiko S, Wagner CE, Excoffier L, Seehausen O. Ancient hybridization fuels rapid cichlid fish adaptive radiations. Nat Commun 2017; 8:14363. [PMID: 28186104 PMCID: PMC5309898 DOI: 10.1038/ncomms14363] [Citation(s) in RCA: 357] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 12/20/2016] [Indexed: 01/01/2023] Open
Abstract
Understanding why some evolutionary lineages generate exceptionally high species diversity is an important goal in evolutionary biology. Haplochromine cichlid fishes of Africa's Lake Victoria region encompass >700 diverse species that all evolved in the last 150,000 years. How this 'Lake Victoria Region Superflock' could evolve on such rapid timescales is an enduring question. Here, we demonstrate that hybridization between two divergent lineages facilitated this process by providing genetic variation that subsequently became recombined and sorted into many new species. Notably, the hybridization event generated exceptional allelic variation at an opsin gene known to be involved in adaptation and speciation. More generally, differentiation between new species is accentuated around variants that were fixed differences between the parental lineages, and that now appear in many new combinations in the radiation species. We conclude that hybridization between divergent lineages, when coincident with ecological opportunity, may facilitate rapid and extensive adaptive radiation.
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Affiliation(s)
- Joana I. Meier
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - David A. Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Salome Mwaiko
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Catherine E. Wagner
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Biodiversity Institute & Department of Botany, University of Wyoming, Laramie Wyoming 82071, USA
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
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16
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Naumenko SA, Logacheva MD, Popova NV, Klepikova AV, Penin AA, Bazykin GA, Etingova AE, Mugue NS, Kondrashov AS, Yampolsky LY. Transcriptome‐based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection. Mol Ecol 2017; 26:536-553. [DOI: 10.1111/mec.13927] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Sergey A. Naumenko
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia
- Genetics and Genome Biology Program The Hospital For Sick Children Toronto ON Canada
| | - Maria D. Logacheva
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia
- Pirogov Russian National Research Medical University Moscow Russia
| | - Nina V. Popova
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
| | - Anna V. Klepikova
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia
| | - Aleksey A. Penin
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia
| | - Georgii A. Bazykin
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia
- Pirogov Russian National Research Medical University Moscow Russia
- Skolkovo Institute of Science and Technology Skolkovo Russia
| | - Anna E. Etingova
- Baikal Museum Irkutsk Research Center Russian Academy of Sciences Listvyanka, Irkutsk region Russia
| | - Nikolai S. Mugue
- Laboratory of Molecular Genetics Russian Institute for Fisheries and Oceanography (VNIRO) Moscow Russia
- Laboratory of Experimental Embryology Koltsov Institute of Developmental Biology Moscow Russia
| | - Alexey S. Kondrashov
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Department of Ecology and Evolution University of Michigan Ann Arbor MI USA
| | - Lev Y. Yampolsky
- Department of Biological Sciences East Tennessee State University Johnson City TN USA
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17
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Meier JI, Sousa VC, Marques DA, Selz OM, Wagner CE, Excoffier L, Seehausen O. Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization. Mol Ecol 2016; 26:123-141. [PMID: 27613570 DOI: 10.1111/mec.13838] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 08/15/2016] [Accepted: 08/22/2016] [Indexed: 01/15/2023]
Abstract
Modes and mechanisms of speciation are best studied in young species pairs. In older taxa, it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pundamilia and P. nyererei, is particularly well suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive isolation at different rocky islands within the lake. Genetic distances between allopatric island populations of the same nominal species often exceed those between the sympatric species. It thus remained unresolved whether speciation into P. nyererei and P. pundamilia occurred once, followed by geographical range expansion and interspecific gene flow in local sympatry, or if the species pair arose repeatedly by parallel speciation. Here, we use genomic data and demographic modelling to test these alternative evolutionary scenarios. We demonstrate that gene flow plays a strong role in shaping the observed patterns of genetic similarity, including both gene flow between sympatric species and gene flow between allopatric populations, as well as recent and early gene flow. The best supported model for the origin of P. pundamilia and P. nyererei population pairs at two different islands is one where speciation happened twice, whereby the second speciation event follows shortly after introgression from an allopatric P. nyererei population that arose earlier. Our findings support the hypothesis that very similar species may arise repeatedly, potentially facilitated by introgressed genetic variation.
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Affiliation(s)
- Joana I Meier
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,CMPG, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Vitor C Sousa
- CMPG, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland
| | - David A Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,CMPG, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Oliver M Selz
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Catherine E Wagner
- Biodiversity Institute & Department of Botany, University of Wyoming, Berry Center, 1000 E. University Ave, Laramie, WY, 82071, USA
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
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18
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Vanhove MPM, Hablützel PI, Pariselle A, Šimková A, Huyse T, Raeymaekers JAM. Cichlids: A Host of Opportunities for Evolutionary Parasitology. Trends Parasitol 2016; 32:820-832. [PMID: 27595383 DOI: 10.1016/j.pt.2016.07.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/31/2016] [Accepted: 07/14/2016] [Indexed: 01/07/2023]
Abstract
Thanks to high species diversity and a broad range of speciation mechanisms, cichlid fishes represent a textbook model in evolutionary biology. They are also of substantial economic value. Despite this importance, cichlid parasites remain understudied, although some are more diverse than their hosts. They may offer important insights into cichlid evolution and the evolution of host-parasite interactions. We review five major lines of research conducted on cichlid parasites so far: the study of parasite diversity and speciation; the role of parasites in cichlid diversification; the evolutionary ecology of host specificity; historical biogeography; and biological invasions. We call for more research in these areas and suggest approaches to valorise the potential that cichlid parasites hold for the study of evolutionary parasitology.
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Affiliation(s)
- Maarten P M Vanhove
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium; Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic.
| | - Pascal I Hablützel
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Antoine Pariselle
- Institut des Sciences de l'Évolution, IRD-CNRS-Université de Montpellier, CC 063, Place Eugène Bataillon, F-34095 Montpellier cedex 05, France
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
| | - Tine Huyse
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium; Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
| | - Joost A M Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium; Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
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19
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Kmentová N, Gelnar M, Koblmüller S, Vanhove MPM. Deep-water parasite diversity in Lake Tanganyika: description of two new monogenean species from benthopelagic cichlid fishes. Parasit Vectors 2016; 9:426. [PMID: 27488497 PMCID: PMC4972994 DOI: 10.1186/s13071-016-1696-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 07/13/2016] [Indexed: 11/10/2022] Open
Abstract
Background Lake Tanganyika is the world’s second deepest lake. Its diverse cichlid assemblage offers a unique opportunity for studying a deep-water host-parasite model in freshwater. Low host specificity and a broad host range including representatives of the Bathybatini tribe in the only monogenean parasite described from this habitat, Cichlidogyrus casuarinus Pariselle, Muterezi Bukinga & Vanhove, 2015 suggest a link between lower specificity and lower host density. Conversely, high host specificity and species richness are reported for monogeneans of the lake’s littoral cichlids. We further investigated whether the deep-water environment in Lake Tanganyika is really monogenean species-depauperate by investigating the monogenean fauna of Trematocara unimaculatum (a representative of the tribe Trematocarini, the sister lineage of the Bathybatini) and Benthochromis horii, a member of the tribe Benthochromini, found in the same deep-water habitat as the already known hosts of C. casuarinus. Methods Sclerotised structures of the collected monogenean individuals were characterised morphologically using light microscopy and morphometrics. Results Both examined cichlid species are infected by a single monogenean species each, which are new to science. They are described as Cichlidogyrus brunnensis n. sp., infecting T. unimaculatum, and Cichlidogyrus attenboroughi n. sp., parasitising on B. horii. Diagnostic characteristics include the distal bifurcation of the accessory piece in C. brunnensis n. sp. and the combination of long auricles and no heel in C. attenboroughi n. sp. In addition C. brunnensis n. sp. does not resemble C. casuarinus, the only species of Cichlidogyrus thus far reported from the Bathybatini. Also Cichlidogyrus attenboroughi n. sp. does not resemble any of the monogenean species documented from the pelagic zone of the lake and is among the few described species of Cichlidogyrus without heel. Conclusions As two new and non-resembling Cichlidogyrus species are described from T. unimaculatum and B. horii, colonisation of the deep-water habitat by more than one morphotype of Cichlidogyrus is evident. Based on morphological comparisons with previously described monogenean species, parasite transfers with the littoral zone are possible. Therefore, parasites of pelagic cichlids in the lake do not seem to only mirror host phylogeny and the evolutionary history of this host-parasite system merits further attention.
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Affiliation(s)
- Nikol Kmentová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
| | - Milan Gelnar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Stephan Koblmüller
- Institute of Zoology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria.,Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65, Brno, Czech Republic
| | - Maarten P M Vanhove
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.,Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080, Tervuren, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000, Leuven, Belgium.,Present address: Capacities for Biodiversity and Sustainable Development, Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000, Brussels, Belgium
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20
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Takahashi T, Sota T. A robust phylogeny among major lineages of the East African cichlids. Mol Phylogenet Evol 2016; 100:234-242. [PMID: 27068840 DOI: 10.1016/j.ympev.2016.04.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/16/2016] [Accepted: 04/07/2016] [Indexed: 11/30/2022]
Abstract
The huge monophyletic group of the East African cichlid radiations (EAR) consists of thousands of species belonging to 12-14 tribes; the number of tribes differs among studies. Many studies have inferred phylogenies of EAR tribes using various genetic markers. However, these phylogenies partly contradict one another and can have weak statistic support. In this study, we conducted maximum-likelihood (ML) phylogenetic analyses using restriction site-associated DNA (RAD) sequences and propose a new robust phylogenetic hypothesis among Lake Tanganyika cichlid fishes, which cover most EAR tribes. Data matrices can vary in size and contents depending on the strategies used to process RAD sequences. Therefore, we prepared 23 data matrices with various processing strategies. The ML phylogenies inferred from 15 large matrices (2.0×10(6) to 1.1×10(7) base pairs) resolved every tribe as a monophyletic group with 100% bootstrap support and shared the same topology regarding relationships among the tribes. Most nodes among the tribes were supported by 100% bootstrap values, and the bootstrap support for the other node varied among the 15 ML trees from 70% to 100%. These robust ML trees differ partly in topology from those in earlier studies, and these phylogenetic relationships have important implications for the tribal classification of EAR.
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Affiliation(s)
- Tetsumi Takahashi
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; National Institute of Genetics, Yata, Mishima, Shizuoka 411-8540, Japan.
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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21
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Breman FC, Loix S, Jordaens K, Snoeks J, Van Steenberge M. Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika. Mol Ecol Resour 2016; 16:1455-1464. [DOI: 10.1111/1755-0998.12523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Floris C. Breman
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
| | - Sara Loix
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
| | - Kurt Jordaens
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
| | - Jos Snoeks
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
| | - Maarten Van Steenberge
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
- Institute of Zoology; University of Graz; Universitätsplatz 2 8010 Graz Austria
- Operational Directorate Taxonomy and Phylogeny; Royal Belgian Institute of Natural Sciences; Vautierstraat 29 1000 Brussels Belgium
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Schneider K, Koblmüller S, Sefc KM. HEXT, a software supporting tree-based screens for hybrid taxa in multilocus data sets, and an evaluation of the homoplasy excess test. Methods Ecol Evol 2015; 7:358-368. [PMID: 27066216 PMCID: PMC4824276 DOI: 10.1111/2041-210x.12490] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/27/2015] [Indexed: 12/01/2022]
Abstract
The homoplasy excess test (HET) is a tree-based screen for hybrid taxa in multilocus nuclear phylogenies. Homoplasy between a hybrid taxon and the clades containing the parental taxa reduces bootstrap support in the tree. The HET is based on the expectation that excluding the hybrid taxon from the data set increases the bootstrap support for the parental clades, whereas excluding non-hybrid taxa has little effect on statistical node support. To carry out a HET, bootstrap trees are calculated with taxon-jackknife data sets, that is excluding one taxon (species, population) at a time. Excess increase in bootstrap support for certain nodes upon exclusion of a particular taxon indicates the hybrid (the excluded taxon) and its parents (the clades with increased support).We introduce a new software program, hext, which generates the taxon-jackknife data sets, runs the bootstrap tree calculations, and identifies excess bootstrap increases as outlier values in boxplot graphs. hext is written in r language and accepts binary data (0/1; e.g. AFLP) as well as co-dominant SNP and genotype data.We demonstrate the usefulness of hext in large SNP data sets containing putative hybrids and their parents. For instance, using published data of the genus Vitis (~6,000 SNP loci), hext output supports V. × champinii as a hybrid between V. rupestris and V. mustangensis.With simulated SNP and AFLP data sets, excess increases in bootstrap support were not always connected with the hybrid taxon (false positives), whereas the expected bootstrap signal failed to appear on several occasions (false negatives). Potential causes for both types of spurious results are discussed.With both empirical and simulated data sets, the taxon-jackknife output generated by hext provided additional signatures of hybrid taxa, including changes in tree topology across trees, consistent effects of exclusions of the hybrid and the parent taxa, and moderate (rather than excessive) increases in bootstrap support. hext significantly facilitates the taxon-jackknife approach to hybrid taxon detection, even though the simple test for excess bootstrap increase may not reliably identify hybrid taxa in all applications.
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Affiliation(s)
- Kevin Schneider
- Institute of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria ; Department of Systematic Botany and Geobotany, Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria
| | - Stephan Koblmüller
- Institute of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Kristina M Sefc
- Institute of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
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Alter SE, Brown B, Stiassny MLJ. Molecular phylogenetics reveals convergent evolution in lower Congo River spiny eels. BMC Evol Biol 2015; 15:224. [PMID: 26472465 PMCID: PMC4608218 DOI: 10.1186/s12862-015-0507-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/04/2015] [Indexed: 11/16/2022] Open
Abstract
Background The lower Congo River (LCR) is a region of exceptional species diversity and endemism in the Congo basin, including numerous species of spiny eels (genus Mastacembelus). Four of these exhibit distinctive phenotypes characterized by greatly reduced optic globes deeply embedded into the head (cryptophthalmia) and reduced (or absent) melanin pigmentation, among other characteristics. A strikingly similar cryptophthalmic phenotype is also found in members of a number of unrelated fish families, strongly suggesting the possibility of convergent evolution. However, little is known about the evolutionary processes that shaped diversification in LCR Mastacembelus, their biogeographic origins, or when colonization of the LCR occurred. Methods We sequenced mitochondrial and nuclear genes from Mastacembelus species collected in the lower Congo River, and compared them with other African species and Asian representatives as outgroups. We analyzed the sequence data using Maximum Likelihood and Bayesian phylogenetic inference. Results Bayesian and Maximum Likelihood phylogenetic analyses, and Bayesian coalescent methods for species tree reconstruction, reveal that endemic LCR spiny eels derive from two independent origins, clearly demonstrating convergent evolution of the cryptophthalmic phenotype. Mastacembelus crassus, M. aviceps, and M. simbi form a clade, allied to species found in southern, eastern and central Africa. Unexpectedly, M. brichardi and brachyrhinus fall within a clade otherwise endemic to Lake Tanganikya (LT) ca. 1500 km east of the LCR. Divergence dating suggests the ages of these two clades of LCR endemics differ markedly. The age of the crassus group is estimated at ~4 Myr while colonization of the LCR by the brichardi-brachyrhinus progenitor was considerably more recent, dated at ~0.5 Myr. Conclusions The phylogenetic framework of spiny eels presented here, the first to include LCR species, demonstrates that cryptophthalmia and associated traits evolved at least twice in Mastacembelus: once in M. brichardi and at least once in the M. crassus clade. Timing of diversification is broadly consistent with the onset of modern high-energy flow conditions in the LCR and with previous studies of endemic cichlids. The close genetic relationship between M. brichardi and M. brachyrhinus is particularly notable given the extreme difference in phenotype between these species, and additional work is needed to better understand the evolutionary history of diversification in this clade. The findings presented here demonstrate strong, multi-trait convergence in LCR spiny eels, suggesting that extreme selective pressures have shaped numerous phenotypic attributes of the endemic species of this region. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0507-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- S Elizabeth Alter
- Department of Biology, York College, City University of New York, 94-20 Guy R. Brewer Blvd, Jamaica, NY, 11415, USA. .,CUNY Graduate Center, 365 Fifth Avenue, New York, NY, 10016, USA. .,Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th St and Central Park West, New York, NY, 10024, USA.
| | - Bianca Brown
- Department of Biology, York College, City University of New York, 94-20 Guy R. Brewer Blvd, Jamaica, NY, 11415, USA
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, 79th St and Central Park West, New York, NY, 10024, USA
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Alter SE, Brown B, Stiassny MLJ. Molecular phylogenetics reveals convergent evolution in lower Congo River spiny eels. BMC Evol Biol 2015. [PMID: 26472465 DOI: 10.1186/s12862015-0507-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND The lower Congo River (LCR) is a region of exceptional species diversity and endemism in the Congo basin, including numerous species of spiny eels (genus Mastacembelus). Four of these exhibit distinctive phenotypes characterized by greatly reduced optic globes deeply embedded into the head (cryptophthalmia) and reduced (or absent) melanin pigmentation, among other characteristics. A strikingly similar cryptophthalmic phenotype is also found in members of a number of unrelated fish families, strongly suggesting the possibility of convergent evolution. However, little is known about the evolutionary processes that shaped diversification in LCR Mastacembelus, their biogeographic origins, or when colonization of the LCR occurred. METHODS We sequenced mitochondrial and nuclear genes from Mastacembelus species collected in the lower Congo River, and compared them with other African species and Asian representatives as outgroups. We analyzed the sequence data using Maximum Likelihood and Bayesian phylogenetic inference. RESULTS Bayesian and Maximum Likelihood phylogenetic analyses, and Bayesian coalescent methods for species tree reconstruction, reveal that endemic LCR spiny eels derive from two independent origins, clearly demonstrating convergent evolution of the cryptophthalmic phenotype. Mastacembelus crassus, M. aviceps, and M. simbi form a clade, allied to species found in southern, eastern and central Africa. Unexpectedly, M. brichardi and brachyrhinus fall within a clade otherwise endemic to Lake Tanganikya (LT) ca. 1500 km east of the LCR. Divergence dating suggests the ages of these two clades of LCR endemics differ markedly. The age of the crassus group is estimated at ~4 Myr while colonization of the LCR by the brichardi-brachyrhinus progenitor was considerably more recent, dated at ~0.5 Myr. CONCLUSIONS The phylogenetic framework of spiny eels presented here, the first to include LCR species, demonstrates that cryptophthalmia and associated traits evolved at least twice in Mastacembelus: once in M. brichardi and at least once in the M. crassus clade. Timing of diversification is broadly consistent with the onset of modern high-energy flow conditions in the LCR and with previous studies of endemic cichlids. The close genetic relationship between M. brichardi and M. brachyrhinus is particularly notable given the extreme difference in phenotype between these species, and additional work is needed to better understand the evolutionary history of diversification in this clade. The findings presented here demonstrate strong, multi-trait convergence in LCR spiny eels, suggesting that extreme selective pressures have shaped numerous phenotypic attributes of the endemic species of this region.
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Affiliation(s)
- S Elizabeth Alter
- Department of Biology, York College, City University of New York, 94-20 Guy R. Brewer Blvd, Jamaica, NY, 11415, USA.
- CUNY Graduate Center, 365 Fifth Avenue, New York, NY, 10016, USA.
- Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th St and Central Park West, New York, NY, 10024, USA.
| | - Bianca Brown
- Department of Biology, York College, City University of New York, 94-20 Guy R. Brewer Blvd, Jamaica, NY, 11415, USA
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, 79th St and Central Park West, New York, NY, 10024, USA
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Correction: Lake Tanganyika-A 'Melting Pot' of Ancient and Young Cichlid Lineages (Teleostei: Cichlidae)? PLoS One 2015; 10:e0132615. [PMID: 26177021 PMCID: PMC4503626 DOI: 10.1371/journal.pone.0132615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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