1
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Melo BF, Conde-Saldaña CC, Villa-Navarro FA, McMahan CD, Oliveira C. Phylogeographic patterns of Cyphocharax from trans-Andean rivers and northward expansion to lower Central America (Teleostei, Curimatidae). JOURNAL OF FISH BIOLOGY 2024; 105:314-325. [PMID: 38757464 DOI: 10.1111/jfb.15777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 05/18/2024]
Abstract
Phylogenetic analyses of mitochondrial and nuclear data of 31 specimens of Cyphocharax from trans-Andean rivers support the presence of one lineage of Cyphocharax aspilos in Lago Maracaibo and three cryptic lineages of Cyphocharax magdalenae: (1) Cauca-Magdalena and Ranchería, (2) León and Atrato, and (3) Chucunaque-Tuira, Santa María, and Chiriquí basins of Central America. Results suggest that the Serranía del Perijá facilitated Late Miocene cladogenetic events, whereas post-Isthmian C. magdalenae expansion was enabled by gene flow across the lower Magdalena valley and Central American lowlands. Time-calibrated phylogenetics indicate that the C. magdalenae colonized lower Central America in the Pliocene (3.7 MYA; Ma), the divergence Atrato-Magdalena occurred in Late Pliocene (3.0 Ma) and the split Ranchería-Magdalena during the Middle Pleistocene (1.3 Ma). Updated geographic distribution data support the hypothesis that the Cordillera de Talamanca functions as a barrier to northward expansion of C. magdalenae in Central America.
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Affiliation(s)
- Bruno F Melo
- Department of Ichthyology, American Museum of Natural History, New York, New York, USA
| | | | | | | | - Claudio Oliveira
- Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
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2
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Escobar Camacho D, Barragán KS, Guayasamin JM, Gavilanes G, Encalada AC. New records of native and introduced fish species in a river basin of Western Ecuador, the Chocó-Darien Ecoregion, using DNA barcoding. PLoS One 2024; 19:e0298970. [PMID: 38457426 PMCID: PMC10923491 DOI: 10.1371/journal.pone.0298970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024] Open
Abstract
DNA barcoding, based on mitochondrial markers, is widely applied in species identification and biodiversity studies. The aim of this study was to establish a barcoding reference database of fishes inhabiting the Cube River from Western Ecuador in the Chocó-Darien Global Ecoregion (CGE), a threatened ecoregion with high diversity and endemism, and evaluate the applicability of using barcoding for the identification of fish species. Barcode sequences were obtained from seven orders, 17 families, 23 genera and 26 species, which were validated through phylogenetic analysis, morphological measurements, and literature review. Our results showed that 43% of fish species in this region are endemic, confirmed the presence of known species in the area, and included the addition of three new records of native (Hoplias microlepis, Rhamdia guatemalensis and Sicydium salvini) and an introduced species (Xiphophorus maculatus) to Ecuador. In addition, eight species were barcoded for the first time. Species identification based on barcoding and morphology showed discrepancy with species lists from previous studies in the CGE, suggesting that the current baseline of western fishes of Ecuador is still incomplete. Because this study analyzed fishes from a relatively small basin (165 km2), more molecular-based studies focusing on fish are needed to achieve a robust sequence reference library of species inhabiting Western Ecuador. The new sequences of this study will be useful for future comparisons and biodiversity monitoring, supporting the application of barcoding tools for studying fish diversity in genetically unexplored regions and to develop well-informed conservation programs.
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Affiliation(s)
- Daniel Escobar Camacho
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Karla S. Barragán
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Juan M. Guayasamin
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Gabriela Gavilanes
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Andrea C. Encalada
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
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3
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Torgersen KT, Albert JS. A New Species of Sternopygus (Gymnotiformes: Sternopygidae) from the Atlantic Coast of the Guiana Shield. ICHTHYOLOGY & HERPETOLOGY 2022. [DOI: 10.1643/i2022013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kevin T. Torgersen
- University of Louisiana at Lafayette, Department of Biology, Lafayette, Louisiana 70504; (KTT) ; and (JSA)
| | - James S. Albert
- University of Louisiana at Lafayette, Department of Biology, Lafayette, Louisiana 70504; (KTT) ; and (JSA)
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4
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Stout C, Schonhuth S, Mayden R, Garrison NL, Armbruster JW. Phylogenomics and classification of Notropis and related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups. PeerJ 2022; 10:e14072. [PMID: 36248715 PMCID: PMC9558623 DOI: 10.7717/peerj.14072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/27/2022] [Indexed: 01/20/2023] Open
Abstract
North American minnows of the Shiner Clade, within the family Leuciscidae, represent one of the most taxonomically complex clades of the order Cypriniformes due to the large number of taxa coupled with conserved morphologies. Species within this clade were moved between genera and subgenera until the community decided to lump many of the unclassified taxa with similar morphologies into one genus, Notropis, which has held up to 325 species. Despite phylogentic studies that began to re-elevate some genera merged into Notropis, such as Cyprinella, Luxilus, Lythrurus, and Pteronotropis, the large genus Notropis remained as a taxonomic repository for many shiners of uncertain placement. Recent molecular advances in sequencing technologies have provided the opportunity to re-examine the Shiner Clade using phylogenomic markers. Using a fish probe kit, we sequenced 90 specimens in 87 species representing 16 genera included in the Shiner Clade, with a resulting dataset of 1,004 loci and 286,455 base pairs. Despite the large dataset, only 32,349 bp (11.29%) were phylogenetically informative. In our maximum likelihood tree, 78% of nodes are 100% bootstrap supported demonstrating the utility of the phylogenomic markers at lower taxonomic levels. Unsurprisingly, species within Notropis as well as Hudsonius, Luxilus, and Alburnops are not resolved as monophyletic groups. Cyprinella is monophyletic if Cyprinella callistia is excluded, and Pteronotropis is monophyletic if it includes Hudsonius cummingsae. Taxonomic changes we propose are: restriction of species included in Alburnops and Notropis, elevation of the subgenus Hydrophlox, expansion of species included in Miniellus, movement of Hudsonius cummingsae to Pteronotropis, and resurrection of the genera Coccotis and Paranotropis. We additionally had two specimens of three species, Notropis atherinoides, Ericymba amplamala, and Pimephales vigilax and found signficant differences between the localities (1,086, 1,424, and 845 nucleotides respectively).
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Affiliation(s)
- Carla Stout
- Department of Biological Sciences, California State Polytechnic University, Pomona, Pomona, CA, United States of America
| | - Susana Schonhuth
- Department of Biology, Saint Louis University, St. Louis, MO, United States of America
| | - Richard Mayden
- Department of Biology, Saint Louis University, St. Louis, MO, United States of America
| | - Nicole L. Garrison
- Department of Biology, West Liberty University, West Liberty, WV, United States of America
| | - Jonathan W. Armbruster
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
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5
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Chak STC, Harris SE, Hultgren KM, Duffy JE, Rubenstein DR. Demographic inference provides insights into the extirpation and ecological dominance of eusocial snapping shrimps. J Hered 2022; 113:552-562. [PMID: 35921239 DOI: 10.1093/jhered/esac035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 07/27/2022] [Indexed: 11/14/2022] Open
Abstract
Although eusocial animals often achieve ecological dominance in the ecosystems where they occur, many populations are unstable, resulting in local extinction. Both patterns may be linked to the characteristic demography of eusocial species-high reproductive skew and reproductive division of labor support stable effective population sizes that make eusocial groups more competitive in some species, but also lower effective population sizes that increase susceptibility to population collapse in others. Here, we examine the relationship between demography and social organization in Synalpheus snapping shrimps, a group in which eusociality has evolved recently and repeatedly. We show using coalescent demographic modelling that eusocial species have had lower but more stable effective population sizes across 100,000 generations. Our results are consistent with the idea that stable population sizes may enable competitive dominance in eusocial shrimps, but they also suggest that recent population declines are likely caused by eusocial shrimps' heightened sensitivity to environmental changes, perhaps as a result of their low effective population sizes and localized dispersal. Thus, although the unique life histories and demography of eusocial shrimps have likely contributed to their persistence and ecological dominance over evolutionary timescales, these social traits may also make them vulnerable to contemporary environmental change.
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Affiliation(s)
- Solomon T C Chak
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, USA.,Department of Biological Sciences, SUNY College at Old Westbury, Old Westbury, NY, USA
| | - Stephen E Harris
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Biology Department, SUNY Purchase College, Purchase, NY, USA
| | | | - J Emmett Duffy
- Tennenbaum Marine Observatories Network, Smithsonian Institution, Edgewater, MD, USA
| | - Dustin R Rubenstein
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
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6
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García‐Andrade AB, Beltrán‐Lopéz RG, Pérez‐Rodríguez R, Domínguez‐Domínguez O, Mejía‐Mojica H, Doadrio I. Evolutionary history of the Aztec shiner
Aztecula sallaei
(Günther, 1868) (Teleostei: Cyprinidae): An endemic and monotypic species of Mexico. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Ana Berenice García‐Andrade
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva Instituto de Ecología, A.C. Xalapa México
- Laboratorio de Biología Acuática Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia México
- Programa Institucional de Maestría en Ciencias Biológicas Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia México
| | - Rosa Gabriela Beltrán‐Lopéz
- Programa Institucional de Doctorado en Ciencias Biológicas Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia México
- Laboratorio de Ictiología Centro de Investigaciones Biológicas Universidad Autónoma del Estado de Morelos Morelos México
| | - Rodolfo Pérez‐Rodríguez
- Laboratorio de Biología Acuática Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia México
| | - Omar Domínguez‐Domínguez
- Laboratorio de Biología Acuática Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia México
| | - Humberto Mejía‐Mojica
- Laboratorio de Ictiología Centro de Investigaciones Biológicas Universidad Autónoma del Estado de Morelos Morelos México
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva Museo Nacional de Ciencias Naturales, CSIC Madrid España
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7
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Dussex N, Bergfeldt N, de Anca Prado V, Dehasque M, Díez-Del-Molino D, Ersmark E, Kanellidou F, Larsson P, Lemež Š, Lord E, Mármol-Sánchez E, Meleg IN, Måsviken J, Naidoo T, Studerus J, Vicente M, von Seth J, Götherström A, Dalén L, Heintzman PD. Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics. Proc Biol Sci 2021; 288:20211252. [PMID: 34428961 PMCID: PMC8385357 DOI: 10.1098/rspb.2021.1252] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Nora Bergfeldt
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Marianne Dehasque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Foteini Kanellidou
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Petter Larsson
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Špela Lemež
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Emilio Mármol-Sánchez
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ioana N Meleg
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,'Emil Racoviță' Institute of Speleology of the Romanian Academy, Calea 13 Septembrie, nr. 13, 050711, Sector 5, Bucharest, Romania.,Emil. G. Racoviță Institute, Babeș-Bolyai University, Clinicilor 5-7, 400006 Cluj-Napoca, Romania
| | - Johannes Måsviken
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Ancient DNA Unit, SciLifeLab, Stockholm and Uppsala, Sweden
| | - Jovanka Studerus
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Mário Vicente
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Peter D Heintzman
- The Arctic University Museum of Norway, The Arctic University of Norway, 9037 Tromsø, Norway
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8
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Mehraban H, Zarei F, Esmaeili HR. A prelude to the molecular systematics and diversity of combtooth blennies (Teleostei: Blenniidae) in the Persian Gulf and Oman Sea. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1895900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Hamidreza Mehraban
- Ichthyology and Molecular Systematics Research Laboratory, Zoology Section, Department of Biology, School of Science, Shiraz University, Shiraz, Iran
| | - Fatah Zarei
- Ichthyology and Molecular Systematics Research Laboratory, Zoology Section, Department of Biology, School of Science, Shiraz University, Shiraz, Iran
| | - Hamid Reza Esmaeili
- Ichthyology and Molecular Systematics Research Laboratory, Zoology Section, Department of Biology, School of Science, Shiraz University, Shiraz, Iran
- Center for Hydrobiology and Aquatic Biotechnology, Shiraz University, Shiraz, Iran
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9
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Agudelo-Zamora HD, Tavera J, Murillo YD, Ortega-Lara A. The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data. JOURNAL OF FISH BIOLOGY 2020; 97:1662-1675. [PMID: 32893347 DOI: 10.1111/jfb.14527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
Two new species of Characidium, C. tatama and C. dule, are described from the biogeographic Chocó region in western Colombia. Both new species are supported by both morphological and molecular data. C. tatama from the San Juan River in the Pacific and C. dule from the Atrato River in the Caribbean portion of Colombia are both distributed in the upper and lower portions of these basins. An extensive comparison with other trans- and cis-Andean species of Characidium was made, in addition to species delimitation, using COI sequences by distinct methods (GMYC, ABGD, bPTP).
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Affiliation(s)
- Henry D Agudelo-Zamora
- Grupo de Investigación en Peces Neotrópicales, Fundación para la Investigación y el Desarrollo Sostenible FUNINDES, Cali, Colombia
- Programa de Informática de la Biodiversidad, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
| | - José Tavera
- Grupo de Investigación Sistemática, Evolución y Biogeografía Animal, Departamento de Biología, Universidad del Valle, Cali, Colombia
| | - Yiskar D Murillo
- Grupo de Investigación Conocimiento, Manejo y Conservación de los Ecosistemas del Chocó Biogeográfico, Instituto de Investigaciones Ambientales del Pacífico "John Von Neumann", Quibdó, Colombia
| | - Armando Ortega-Lara
- Grupo de Investigación en Peces Neotrópicales, Fundación para la Investigación y el Desarrollo Sostenible FUNINDES, Cali, Colombia
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10
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Hughes LC, Ortí G, Saad H, Li C, White WT, Baldwin CC, Crandall KA, Arcila D, Betancur-R R. Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics. Mol Ecol Resour 2020; 21:816-833. [PMID: 33084200 DOI: 10.1111/1755-0998.13287] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 10/09/2020] [Indexed: 11/28/2022]
Abstract
Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.
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Affiliation(s)
- Lily C Hughes
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Guillermo Ortí
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Hadeel Saad
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Chenhong Li
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - William T White
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Keith A Crandall
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA
| | - Dahiana Arcila
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Sam Noble Oklahoma Museum of Natural History, Norman, OK, USA.,Department of Biology, University of Oklahoma, Norman, OK, USA
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11
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McLaughlin JF, Faircloth BC, Glenn TC, Winker K. Divergence, gene flow, and speciation in eight lineages of trans-Beringian birds. Mol Ecol 2020; 29:3526-3542. [PMID: 32745340 DOI: 10.1111/mec.15574] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 12/13/2022]
Abstract
Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans-Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks, shorebirds and passerines) at population, subspecies and species levels. Using ultraconserved elements (UCEs), we found that these lineages represent conditions from slightly differentiated populations to full biological species. Although allopatric speciation is considered the predominant mode of divergence in birds, all of our best divergence models included gene flow, supporting speciation with gene flow as the predominant mode in Beringia. In our eight lineages, three were best described by a split-migration model (divergence with gene flow), three best fit a secondary contact scenario (isolation followed by gene flow), and two showed support for both models. The lineages were not evenly distributed across a divergence space defined by gene flow (M) and differentiation (FST ), instead forming two discontinuous groups: one with relatively shallow divergence, no fixed single nucleotide polymorphisms (SNPs), and high rates of gene flow between populations; and the second with relatively deeply divergent lineages, multiple fixed SNPs, and low gene flow. Our results highlight the important role that gene flow plays in avian divergence in Beringia.
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Affiliation(s)
- Jessica F McLaughlin
- University of Alaska Museum, Fairbanks, AK, USA.,Sam Noble Oklahoma Museum of Natural History, Norman, OK, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Travis C Glenn
- Department of Environmental Health Science and Institute of Bioinformatics, University of Georgia, Athens, GA, USA
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12
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De la Ossa-Guerra LE, Santos MH, Artoni RF. Genetic Diversity of the Cichlid Andinoacara latifrons (Steindachner, 1878) as a Conservation Strategy in Different Colombian Basins. Front Genet 2020; 11:815. [PMID: 32793289 PMCID: PMC7393254 DOI: 10.3389/fgene.2020.00815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 07/07/2020] [Indexed: 11/25/2022] Open
Abstract
Cichlids constitute a diverse monophyletic group that have developed adaptive strategies to thrive in diverse environments. Andinoacara represents an example of diversification on the South American Andean uplift, providing a key model for understanding the evolution of biogeographic patterns. In this study, we analyzed the species Andinoacara latifrons using two mitochondrial markers (COI, cytb) and one nuclear marker (RAG1) in a populational level. Sequences were obtained through tissue collection and from the GenBank database. Populational analysis showed significant structuration among populations, also corroborated with population pairwise Fst results. Fu’s Fs and Tajima’s D results showed populations that seems to be under populational expansion. We identified 22 haplotypes using cytb. The population associations in the Cauca haplotype are related to the Momposina depression and the mixture of the Cauca-Magdalena river basins in the lower Cauca-Magdalena region. We constructed a new phylogenetic tree, which grouped mainly two A. latifrons lineages: (1) an upper Magdalena and Catatumbo clade and (2) an upper Cauca and upper Magdalena clade. Thus, A. latifrons represents a diverse entity that contributes to our understanding of the evolutionary history of northern South America. Our findings provide insight into devising public policies in determining refuges for the preservation of biodiversity in the lower Cauca and Magdalena regions in Colombia.
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Affiliation(s)
- Luz Elena De la Ossa-Guerra
- Laboratório de Genética e Evolução (LabGEv), Programa de Pós-Graduação em Biologia Evolutiva, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil.,Postgraduate Program in Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Paulo, Brazil
| | - Mateus Henrique Santos
- Laboratório de Genética e Evolução (LabGEv), Programa de Pós-Graduação em Biologia Evolutiva, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Roberto Ferreira Artoni
- Laboratório de Genética e Evolução (LabGEv), Programa de Pós-Graduação em Biologia Evolutiva, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil.,Postgraduate Program in Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Paulo, Brazil
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13
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Li Z, Li M, Xu S, Liu L, Chen Z, Zou K. Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations. Int J Mol Sci 2020; 21:E4685. [PMID: 32630142 PMCID: PMC7370159 DOI: 10.3390/ijms21134685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/31/2022] Open
Abstract
Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that ATP8 showed the highest evolutionary rate and COXI/COXII were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene.
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Affiliation(s)
- Zhenhai Li
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, China; (Z.L.); (L.L.)
| | - Min Li
- Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (M.L.); (S.X.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shannan Xu
- Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (M.L.); (S.X.)
| | - Li Liu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, China; (Z.L.); (L.L.)
| | - Zuozhi Chen
- Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (M.L.); (S.X.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Keshu Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, China; (Z.L.); (L.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agriculture University, Guangzhou 510642, China
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14
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Rangel-Medrano JD, Ortega-Lara A, Márquez EJ. Ancient genetic divergence in bumblebee catfish of the genus Pseudopimelodus (Pseudopimelodidae: Siluriformes) from northwestern South America. PeerJ 2020; 8:e9028. [PMID: 32537262 PMCID: PMC7265895 DOI: 10.7717/peerj.9028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/31/2020] [Indexed: 01/29/2023] Open
Abstract
Pseudopimelodus is a Neotropical genus of bumblebee catfish, composed of four valid species occurring in both trans- and cis-Andean rivers of South America. The orogeny of the Andes has led to diversification in the genus Pseudopimelodus in Colombia. This study analyzed partial sequences of mitochondrial cox1 and nuclear rag2 genes to test the hypothesis that the species, nominally recognized as P. schultzi and P. bufonius in Colombia, correspond to more than two different evolutionary lineages. Results indicate high levels of genetic divergence among individuals of nominal P. schultzi and P. bufonius, from trans- and cis-Andean basins in Colombia. In addition, five divergent lineages of Pseudopimelodus were confidently delimited by using a single-locus species-discovery approach and confirmed by species tree analyses. Additionally, molecular-clock dating showed that most diversification processes in Pseudopimelodus took place during the Miocene, when Andean tectonic evolution was occurring in northwestern South America. The present study provides, for the first time, phylogeographic insight into this Neotropical genus.
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Affiliation(s)
- José D Rangel-Medrano
- Facultad de Ciencias, Escuela de Biociencias, Laboratorio de Biología Molecular y Celular, Universidad Nacional de Colombia-Sede Medellín, Medellín, Colombia
| | - Armando Ortega-Lara
- Grupo de Investigación en Peces Neotropicales, Fundación para la Investigación y el Desarrollo Sostenible (FUNINDES), Cali, Colombia.,Programa de Doctorado en Ciencias-Biología, Facultad de Ciencias, Universidad del Valle, Cali, Colombia
| | - Edna J Márquez
- Facultad de Ciencias, Escuela de Biociencias, Laboratorio de Biología Molecular y Celular, Universidad Nacional de Colombia-Sede Medellín, Medellín, Colombia
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15
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Ibagón N, Maldonado-Ocampo JA, Cioffi MDB, Dergam JA. Chromosomal Diversity of Hoplias malabaricus (Characiformes, Erythrinidae) Along the Magdalena River (Colombia—Northern South America) and Its Significance for the Neotropical Region. Zebrafish 2020. [DOI: 10.1089/zeb.2019.1827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Nicole Ibagón
- Departamento de Biologia Geral, Universidad Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Programa de Ecología, Fundación Universitaria de Popayán, Popayán, Cauca, Colombia
| | - Javier A. Maldonado-Ocampo
- Laboratorio de Ictiologia, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | | | - Jorge A. Dergam
- Departamento de Biologia Animal, Universidad Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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16
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Gagnaire PA. Comparative genomics approach to evolutionary process connectivity. Evol Appl 2020; 13:1320-1334. [PMID: 32684961 PMCID: PMC7359831 DOI: 10.1111/eva.12978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 01/01/2023] Open
Abstract
The influence of species life history traits and historical demography on contemporary connectivity is still poorly understood. However, these factors partly determine the evolutionary responses of species to anthropogenic landscape alterations. Genetic connectivity and its evolutionary outcomes depend on a variety of spatially dependent evolutionary processes, such as population structure, local adaptation, genetic admixture, and speciation. Over the last years, population genomic studies have been interrogating these processes with increasing resolution, revealing a large diversity of species responses to spatially structured landscapes. In parallel, multispecies meta-analyses usually based on low-genome coverage data have provided fundamental insights into the ecological determinants of genetic connectivity, such as the influence of key life history traits on population structure. However, comparative studies still lack a thorough integration of macro- and micro-evolutionary scales to fully realize their potential. Here, I present how a comparative genomics framework may provide a deeper understanding of evolutionary process connectivity. This framework relies on coupling the inference of long-term demographic and selective history with an assessment of the contemporary consequences of genetic connectivity. Standardizing this approach across several species occupying the same landscape should help understand how spatial environmental heterogeneity has shaped the diversity of historical and contemporary connectivity patterns in different taxa with contrasted life history traits. I will argue that a reasonable amount of genome sequence data can be sufficient to resolve and connect complex macro- and micro-evolutionary histories. Ultimately, implementing this framework in varied taxonomic groups is expected to improve scientific guidelines for conservation and management policies.
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17
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Xue AT, Hickerson MJ. Comparative phylogeographic inference with genome‐wide data from aggregated population pairs. Evolution 2020; 74:808-830. [DOI: 10.1111/evo.13945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Alexander T. Xue
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyGraduate Center of City University of New York New York NY 10016
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyCity College of City University of New York New York NY 10031
- Human Genetics Institute of New Jersey and Department of GeneticsRutgers University Piscataway NJ 08854
- Simons Center for Quantitative BiologyCold Spring Harbor Laboratory Cold Spring Harbor NY 11724
| | - Michael J. Hickerson
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyGraduate Center of City University of New York New York NY 10016
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyCity College of City University of New York New York NY 10031
- Division of Invertebrate ZoologyAmerican Museum of Natural History New York NY 10024
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18
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Wang P, Chen B, Zheng J, Cheng W, Zhang H, Wang J, Su Y, Xu P, Mao Y. Fine-Scale Population Genetic Structure and Parapatric Cryptic Species of Kuruma Shrimp ( Marsupenaeus japonicus), Along the Northwestern Pacific Coast of China. Front Genet 2020; 11:118. [PMID: 32161618 PMCID: PMC7052491 DOI: 10.3389/fgene.2020.00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/31/2020] [Indexed: 11/13/2022] Open
Abstract
The kuruma shrimp (Marsupenaeus japonicus) includes two cryptic species, which are distributed mostly allopatrically but co-occur in the northern South China Sea (from Huilai to Beihai). To obtain a better understanding of the fine-scale genetic structure and parapatric diversification of these two varieties in the northwestern Pacific region, we used a genotyping-by-sequencing (GBS) and comparative transcriptomics approach to establish their phylogenetic relationships. Using the GBS technique, we genotyped 28891 SNPs in 160 individuals in the Northwest Pacific. The results supported two highly diverged evolutionary lineages of kuruma shrimp (var. I and II). The ND and XM populations showed complex genetic patterns, which might be affected by the complex environment of the Taiwan Strait. In addition, the migration rates and inbreeding coefficients of XM and BH were much lower than those of the other populations, which might be related to the land-sea changes and complex ocean currents in the Taiwan Strait and Qiongzhou Strait. Based on the synonymous substitution rates (ds) of 2,491 candidate orthologs, we estimated that the divergence time between the two varieties was 0.26~0.69 Mya. Choice and no-choice interbreeding experiments provided support for the biological species concept, by showing the existence of reproductive isolation or incompatibility. In view of these differences between the two Marsupenaeus species, we believe that it is essential and urgent to establish a genetic database for each and reevaluate their ecological suitable conditions in order to improve species-specific culturing techniques. Moreover, this research can serve as a case study for future research on speciation and hybridization.
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Affiliation(s)
- Panpan Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| | - Baohua Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| | - Jinbin Zheng
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wenzhi Cheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| | - Heqian Zhang
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Jun Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yongquan Su
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| | - Yong Mao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
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19
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Ochoa LE, Melo BF, García-Melo JE, Maldonado-Ocampo JA, Souza CS, Albornoz-Garzón JG, Conde-Saldaña CC, Villa-Navarro F, Ortega-Lara A, Oliveira C. Species delimitation reveals an underestimated diversity of Andean catfishes of the family Astroblepidae (Teleostei: Siluriformes). NEOTROPICAL ICHTHYOLOGY 2020. [DOI: 10.1590/1982-0224-2020-0048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT Catfishes of the family Astroblepidae form a group composed by 82 valid species of the genus Astroblepus inhabiting high-gradient streams and rivers throughout tropical portions of the Andean Cordillera. Little has been advanced in the systematics and biodiversity of astroblepids other than an unpublished thesis, a single regional multilocus study and isolated species descriptions. Here, we examined 208 specimens of Astroblepus that apparently belong to 16 valid species from several piedmont rivers from northern Colombia to southern Peru. Using three single-locus approaches for species delimitation in combination with a species tree analysis estimated from three mitochondrial genes, we identified a total of 25 well-delimited lineages including eight valid and 17 potential undescribed species distributed in two monophyletic groups: the Central Andes Clade, which contains 14 lineages from piedmont rivers of the Peruvian Amazon, and the Northern Andes Clade with 11 lineages from trans- and cis-Andean rivers of Colombia and Ecuador, including the Orinoco, Amazon, and Magdalena-Cauca basins and Pacific coastal drainages. Results of species delimitation methods highlight several taxonomical incongruences in recently described species denoting potential synonymies.
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Affiliation(s)
- Luz E. Ochoa
- Universidade de São Paulo, Brazil; Universidade Estadual Paulista, Brazil
| | | | | | | | | | - Juan G. Albornoz-Garzón
- Universidad del Tolima, Colombia; Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Colombia
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20
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Aguilar C, Miller MJ, Loaiza JR, González R, Krahe R, De León LF. Tempo and mode of allopatric divergence in the weakly electric fish Sternopygus dariensis in the Isthmus of Panama. Sci Rep 2019; 9:18828. [PMID: 31827183 PMCID: PMC6906317 DOI: 10.1038/s41598-019-55336-y] [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: 07/20/2018] [Accepted: 11/27/2019] [Indexed: 01/12/2023] Open
Abstract
Spatial isolation is one of the main drivers of allopatric speciation, but the extent to which spatially-segregated populations accumulate genetic differences relevant to speciation is not always clear. We used data from ultraconserved elements (UCEs) and whole mitochondrial genomes (i.e., mitogenomes) to explore genetic variation among allopatric populations of the weakly electric fish Sternopygus dariensis across the Isthmus of Panama. We found strong genetic divergence between eastern and western populations of S. dariensis. Over 77% of the UCE loci examined were differentially fixed between populations, and these loci appear to be distributed across the species' genome. Population divergence occurred within the last 1.1 million years, perhaps due to global glaciation oscillations during the Pleistocene. Our results are consistent with a pattern of genetic differentiation under strict geographic isolation, and suggest the presence of incipient allopatric species within S. dariensis. Genetic divergence in S. dariensis likely occurred in situ, long after the closure of the Isthmus of Panama. Our study highlights the contribution of spatial isolation and vicariance to promoting rapid diversification in Neotropical freshwater fishes. The study of spatially-segregated populations within the Isthmus of Panama could reveal how genetic differences accumulate as allopatric speciation proceeds.
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Affiliation(s)
- Celestino Aguilar
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Matthew J Miller
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Jose R Loaiza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá
- Programa Centroamericano de Maestría en Entomología, Universidad de Panamá, Panamá, República de Panamá
| | - Rigoberto González
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá
| | - Rüdiger Krahe
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Luis F De León
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá.
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá.
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.
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