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Mar-Silva AF, Diaz-Jaimes P, Domínguez-Mendoza C, Domínguez-Domínguez O, Valdiviezo-Rivera J, Espinoza-Herrera E. Genomic assessment reveals signal of adaptive selection in populations of the Spotted rose snapper Lutjanus guttatus from the Tropical Eastern Pacific. PeerJ 2023; 11:e15029. [PMID: 37009151 PMCID: PMC10062342 DOI: 10.7717/peerj.15029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/17/2023] [Indexed: 03/29/2023] Open
Abstract
Background
The lack of barriers in the marine environment has promoted the idea of panmixia in marine organisms. However, oceanographic conditions and habitat characteristics have recently been linked to genetic structure in marine species. The Tropical Eastern Pacific (TEP) is characterized by dynamic current systems and heterogeneous oceanographic conditions. The Gulf of Panama (part of the equatorial segment for the TEP) is influenced by a complex current system and heterogeneous environment, which has been shown to limit the gene flow for shoreline species. Next Generation Sequencing (NGS) has contributed to detect genetic differences in previously reported panmictic species by the assessment of loci associated with selection and to understand how selection acts affects marine populations. Lutjanus guttatus is a species distributed in the TEP for which previous studies using mitochondrial data recovered a panmictic pattern along its distributional range. In this study, we used SNP data of L. guttatus individuals sampled along its range to evaluate population genetic structure and investigate whether oceanographic factors influence the species’ genetic architecture. Finally, we assessed the role of adaptive selection by evaluating the contribution of outlier and neutral loci to genetic divergence.
Methods
The RADcap method was used to obtain 24 million paired reads for 123 individuals of L. guttatus covering nearly all its distributional area. Genetic variation was assessed using both spatial and non-spatial methods by comparing three different data sets: (i) a Combined Loci (CL dataset = 2003 SNPs); a search for putative loci under selection allowed the evaluation of (ii) Neutral Loci (NL dataset = 1858 SNPs) and (iii) Outlier Loci (OL dataset = 145 SNPs). We used the estimating effective migration surface (EEMS) approach to detect possible barriers to gene flow.
Results
Genetic differences were found in the OL dataset, showing two clusters (Northern and Southern), whereas NL showed no differences. This result may be related to the Selection-Migration balance model. The limit between the Northern and Southern groups was in the Gulf of Panama, which has been previously identified as a barrier to gene flow for other species, mainly due to its heterogeneous oceanographic conditions. The results suggest that selection plays an important role in generating genetic differences in Lutjanus guttatus. A migration corridor was detected that coincides with the Costa Rica Coastal Current that flows from Central America to the Gulf of California, allowing the homogenization of the northern population. In the Southern cluster, a migration corridor was observed with the OL from Panama to Colombia, which could be associated with the currents found in the Gulf of Panama. Genetic variation found in the OL of Lutjanus guttatus highlights the usefulness of NGS data in evaluating the role of selection in population differentiation.
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Affiliation(s)
- Adán F. Mar-Silva
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Pindaro Diaz-Jaimes
- Unidad de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Cristina Domínguez-Mendoza
- Unidad de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
- Instituto Nacional de Biodiversidad, Quito, Ecuador
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2
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Phylogeography and evolutionary history of the Panamic Clingfish Gobiesox adustus in the Tropical Eastern Pacific. Mol Phylogenet Evol 2022; 173:107496. [PMID: 35569809 DOI: 10.1016/j.ympev.2022.107496] [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: 10/29/2021] [Revised: 02/26/2022] [Accepted: 04/18/2022] [Indexed: 11/20/2022]
Abstract
The Panamic Clingfish Gobiesox adustus is widely distributed in the Tropical Eastern Pacific (TEP), from the central Gulf of California, Mexico to Ecuador, including the oceanic Revillagigedo Archipelago, and Isla del Coco. This cryptobenthic species is restricted to very shallow rocky-reef habitats. Here, we used one mitochondrial and three nuclear DNA markers from 155 individuals collected across the distribution range of the species in order to evaluate if geographically structured populations exist and to elucidate its evolutionary history. Phylogenetic analyses recovered a monophyletic group, with four well-supported, allopatric subgroups. Each subgroup corresponded to one of the following well-known biogeographic regions/provinces: 1) the Revillagigedo Archipelago, 2) the Cortez + Mexican provinces (Mexico), 3) the Panamic province (from El Salvador to Ecuador), and 4) Isla del Coco. A molecular-clock analysis showed a mean date for the divergence between clade I (the Revillagigedos and Cortez + Mexican provinces) and clade II (Panamic province and Isla del Coco) in the Pliocene, at ca. 5.33 Mya. Within clade I, the segregation between the Revillagigedos and Cortez + Mexican province populations was dated at ca. 1.18 Mya, during the Pleistocene. Within clade II, the segregation between samples of Isla del Coco and the Panamic province samples was dated at ca. 0.77 Mya, during the Pleistocene. The species tree, Bayesian species delimitation tests (BPP and STACEY), the ΦST, AMOVA, and the substantial genetic distances that exist between those four subgroups, indicate that they are independent evolutionary units. These cladogenetic events seem to be related to habitat discontinuities, and oceanographic and geological processes that produce barriers to gene flow for G. adustus, effects of which are enhanced by the intrinsic ecological characteristics of this species.
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Salvatteci R, Schneider RR, Galbraith E, Field D, Blanz T, Bauersachs T, Crosta X, Martinez P, Echevin V, Scholz F, Bertrand A. Smaller fish species in a warm and oxygen-poor Humboldt Current system. Science 2022; 375:101-104. [PMID: 34990239 DOI: 10.1126/science.abj0270] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Climate change is expected to result in smaller fish size, but the influence of fishing has made it difficult to substantiate the theorized link between size and ocean warming and deoxygenation. We reconstructed the fish community and oceanographic conditions of the most recent global warm period (last interglacial; 130 to 116 thousand years before present) by using sediments from the northern Humboldt Current system off the coast of Peru, a hotspot of small pelagic fish productivity. In contrast to the present-day anchovy-dominated state, the last interglacial was characterized by considerably smaller (mesopelagic and goby-like) fishes and very low anchovy abundance. These small fish species are more difficult to harvest and are less palatable than anchovies, indicating that our rapidly warming world poses a threat to the global fish supply.
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Affiliation(s)
- Renato Salvatteci
- Center for Ocean and Society, Christian-Albrechts-University, Kiel, Germany
| | - Ralph R Schneider
- Institute of Geosciences, Christian-Albrechts-University, Kiel, Germany
| | - Eric Galbraith
- Earth and Planetary Sciences, McGill University, Montreal, QC, Canada.,Institut de Ciència i Tecnologia Ambientals (ICTA-UAB), Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - David Field
- College of Natural Sciences, Hawaii Pacific University, Kaneohe, HI, USA
| | - Thomas Blanz
- Institute of Geosciences, Christian-Albrechts-University, Kiel, Germany
| | | | - Xavier Crosta
- Université de Bordeaux, CNRS, EPHE, UMR 5805 EPOC, Pessac, France
| | | | - Vincent Echevin
- Sorbonne Université, LOCEAN-IPSL, CNRS/IRD/MNHN, 4 place Jussieu, 75252 Paris, France
| | - Florian Scholz
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Arnaud Bertrand
- Institut de Recherche pour le Développement (IRD), MARBEC, University Montpellier, CNRS, Ifremer, IRD, Sète, France
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Love MS, Bizzarro JJ, Cornthwaite AM, Frable BW, Maslenikov KP. Checklist of marine and estuarine fishes from the AlaskaYukon Border, Beaufort Sea, to Cabo San Lucas, Mexico. Zootaxa 2021; 5053:1-285. [PMID: 34810850 DOI: 10.11646/zootaxa.5053.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Indexed: 11/04/2022]
Abstract
This paper is a checklist of the fishes that have been documented, through both published and unpublished sources, in marine and estuarine waters, and out 200 miles, from the United States-Canadian border on the Beaufort Sea to Cabo San Lucas, Mexico. A minimum of 241 families and 1,644 species are known within this range, including both native and nonnative species. For each of these species, we include maximum size, geographic and depth ranges, whether it is native or nonnative, as well as a brief mention of any taxonomic issues.
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Affiliation(s)
- Milton S Love
- Marine Science Institute, University of California, Santa Barbara, CA 93106.
| | - Joseph J Bizzarro
- Cooperative Institute for Marine Ecosystems and Climate, University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060. .
| | - A Maria Cornthwaite
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada .
| | - Benjamin W Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0244, USA. .
| | - Katherine P Maslenikov
- University of Washington Fish Collection, School of Aquatic and Fishery Sciences and Burke Museum of Natural History and Culture, 1122 NE Boat St., Seattle, WA 98105.
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5
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Torres-Hernández E, Betancourt-Resendes I, Angulo A, Robertson DR, Barraza E, Espinoza E, Díaz-Jaimes P, Domínguez-Domínguez O. A multi-locus approach to elucidating the evolutionary history of the clingfish Tomicodon petersii (Gobiesocidae) in the Tropical Eastern Pacific. Mol Phylogenet Evol 2021; 166:107316. [PMID: 34537324 DOI: 10.1016/j.ympev.2021.107316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Marine species that are widely distributed in the Tropical Eastern Pacific (TEP) has served as a model for studying biogeographic patterns resulting from the effects of intraregional habitat discontinuities and oceanographic processes on the diversification and evolution of cryptobenthic reef fishes. Tomicodon petersii, a clingfish (Gobiesocidae) endemic to the TEP, is found on very shallow rocky reefs from central Mexico to northern Peru, and in the Cocos and Galapagos islands. We evaluated the effect of likely biogeographic barriers in different parts of the TEP on the diversification process of this species. We used one mitochondrial and three nuclear DNA markers from 112 individuals collected across the distribution range of T. petersii. Our phylogenetic results showed the samples constituted a monophyletic group, with three well-supported, allopatric subgroups: in the Mexican province, the Panamic province (from El Salvador to Ecuador), and the Galapagos Islands. The split between the Mexican and more southerly clades was estimated to occur at the end of the Miocene ca. 5.74 Mya, and the subsequent cladogenetic event separating the Galapagos population from the Panamic population at the junction of the Pliocene and Pleistocene, ca. 2.85 Mya. The species tree, Bayesian species delimitation tests (BPP), STACEY, and substantial genetic distances separating these three populations indicate that these three independent evolutionary units likely include two unnamed species. The cladogenetic events that promoted the formation of those genetically differentiated groups are consistent with disruptive effects on gene flow of habitat discontinuities and oceanographic processes along the mainland shoreline in the TEP and of ocean-island isolation, in conjunction with the species intrinsic life-history characteristics.
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Affiliation(s)
- Eloísa Torres-Hernández
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, Mexico; Instituto Nacional de Biodiversidad (INABIO), Colección de Peces Calle Rumipamba 341, Av. De los Shyris, Parque "La Carolina", Quito, Ecuador.
| | - Isai Betancourt-Resendes
- CONACYT-Laboratorio de Zoología, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. De las Ciencias s/n, Juriquilla, C.P 76230, Delegación Santa Rosa Jáuregui, Santiago de Querétaro, Mexico.
| | - Arturo Angulo
- Museo de Zoología/ Centro de Investigación en Biodiversidad y Ecología Tropical (CIBET) y Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, San Pedro de Montes de Oca, 11501-2060 San José, Costa Rica.
| | - D Ross Robertson
- Naos Marine Laboratory, Smithsonian Tropical Research Institute, Balboa, Panama.
| | - Enrique Barraza
- Universidad Francisco Gavidia, Instituto de Ciencia, Tecnología e Inovación, Segundo Nivel, Calle El Progreso N°2748, San Salvador, El Salvador.
| | - Eduardo Espinoza
- Dirección del Parque Nacional Galápagos, Puerto Ayora, Islas Galápagos, Ecuador.
| | - Píndaro Díaz-Jaimes
- Unidad de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, Mexico.
| | - Omar Domínguez-Domínguez
- Instituto Nacional de Biodiversidad (INABIO), Colección de Peces Calle Rumipamba 341, Av. De los Shyris, Parque "La Carolina", Quito, Ecuador; Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" Planta Baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico.
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Beltrán-López RG, Pérez-Rodríguez R, Montañez-García OC, Artigas-Azas JM, Köck M, Mar-Silva AF, Domínguez-Domínguez O. Genetic differentiation in the genus Characodon: implications for conservation and taxonomy. PeerJ 2021; 9:e11492. [PMID: 34285828 PMCID: PMC8272924 DOI: 10.7717/peerj.11492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/28/2021] [Indexed: 11/20/2022] Open
Abstract
The subfamily Goodeinae is a group of fishes endemic to the Mexican highlands. Most of the species are restricted to small and isolated streams or springs. Within this subfamily, the genus Characodon is the earliest diverging lineage of which three species have been described: C. lateralis, C. audax, and C. garmani, with the latter, considered extinct. Characodon lateralis and C. audax are classed as endangered, and have been the subject of taxonomic controversy since their description: previous studies have recognized a genetic differentiation in two groups separated by the El Salto waterfall, but morphological analyses contradict these genetic results. We perform a phylogeographic study using the mitochondrial cytb gene and d-loop region to elucidate the evolutionary history of C. lateralis and C. audax. The results with both markers show the presence of two highly differentiated haplogroups; one distributed north and the other distributed south of the waterfall, with genetic distances of 1.7 and 13.1% with cytb and d-loop respectively, and divergence calculated to have occurred 1.41 Mya. Significant genetic structure was found within each haplogroup and suggests the existence of at least four Evolutionary Significant Units (ESUs) within the examined populations. The possible processes identified as contributing to the formation of differentiated genetic groups are isolation, low population size, recurrent bottlenecks, and the strong sexual selection exhibited by the genus.
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Affiliation(s)
- Rosa G Beltrán-López
- Laboratorio de Ictiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México.,Programa Institucional de Doctorado en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Rodolfo Pérez-Rodríguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Ofelia C Montañez-García
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | | | | | - Adán F Mar-Silva
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
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7
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Reguera-Rouzaud N, Díaz-Viloria N, Pérez-Enríquez R, Espino-Barr E, Rivera-Lucero MI, Munguía-Vega A. Drivers for genetic structure at different geographic scales for Pacific red snapper (Lutjanus peru) and yellow snapper (Lutjanus argentiventris) in the tropical eastern Pacific. JOURNAL OF FISH BIOLOGY 2021; 98:1267-1280. [PMID: 33349917 DOI: 10.1111/jfb.14656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/03/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
The tropical eastern Pacific (TEP) is a highly dynamic region and a model system to study how habitat discontinuities affect the distribution of shorefishes, particularly for species that display ontogenetic habitat shifts, including snappers (Lutjanidae). To evaluate the genetic structure of the Pacific red snapper (Lutjanus peru) and the yellow snapper (Lutjanus argentiventris) throughout their distribution range along the TEP, 13 and 11 microsatellite loci were analysed, respectively. The genetic diversity of L. peru (N = 446) and L. argentiventris (N = 170) was evaluated in 10 and 5 localities, respectively, showing slightly higher but non-significant values in the Gulf of California for both species. The genetic structure analysis identified the presence of significant genetic structure in both species, but the locations of the identified barriers for the gene flow differed between species. The principal driver for the genetic structure at large scales >2500 km was isolation by distance. At smaller scales (<250 km), the habitat discontinuity for juveniles and adults and the environmental differences throughout the distribution range represented potential barriers to gene flow between populations for both species.
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Affiliation(s)
- Nicole Reguera-Rouzaud
- Departamento de Plancton y Ecología Marina, Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas (IPN-CICIMAR), La Paz, Mexico
| | - Noé Díaz-Viloria
- Departamento de Plancton y Ecología Marina, Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas (IPN-CICIMAR), La Paz, Mexico
| | - Ricardo Pérez-Enríquez
- Departamento de Acuicultura, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, Mexico
| | - Elaine Espino-Barr
- Instituto Nacional de Pesca, CRIP-Manzanillo, Playa Ventana, Colima, Mexico
| | | | - Adrián Munguía-Vega
- Conservation Genetics Laboratory & Desert Laboratory on Tumamoc Hill, University of Arizona, Tucson, Arizona, USA
- @Lab Applied Genomics, La Paz, Mexico
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Palmerín‐Serrano PN, Tavera J, Espinoza E, Angulo A, Martínez‐Gómez JE, González‐Acosta AF, Domínguez‐Domínguez O. Evolutionary history of the reef fish
Anisotremus interruptus
(Perciformes: Haemulidae) throughout the Tropical Eastern Pacific. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Paola Nallely Palmerín‐Serrano
- Programa Institucional de Maestría en Ciencias Biológicas Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
- Laboratorio de Biología Acuática Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
| | - Jose Tavera
- Laboratorio de Ictiología Departamento de Biología Universidad del Valle Cali Colombia
| | - Eduardo Espinoza
- Investigación Marina Aplicada Parque Nacional Galápagos “Charles Darwin” Puerto Ayora Isla Santa Cruz Ecuador
| | - Arturo Angulo
- Museo de Zoología y Centro de Investigación en Ciencias del Mar y Limnología Universidad de Costa Rica San Pedro de Montes de Oca San José Costa Rica
- Laboratorio de Ictiología Departamento de Zoología e Botánica Universidad Estadual Paulista “Julio de MesquitaFilho” São José do Rio Preto São Paul Brazil
| | - Juan E. Martínez‐Gómez
- Instituto de Ecología A. C. (INECOL)Red de Interacciones Multitróficas Xalapa Veracruz México
| | - Adrián F. González‐Acosta
- Instituto Politécnico NacionalCentro Interdisciplinario de Ciencias Marinas (CICIMAR)Pesquerías y Biología Marina La Paz México
| | - Omar Domínguez‐Domínguez
- Laboratorio de Biología Acuática Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
- Laboratorio Nacional de Análisis y Síntesis Ecológica para la Conservación de Recursos Genéticos de México Escuela Nacional de Estudios SuperioresUniversidad Nacional Autónoma de México Morelia Michoacán México
- Instituto Nacional de BiodiversidadColección de Peces Quito Ecuador
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9
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D'Aloia CC, Andrés JA, Bogdanowicz SM, McCune AR, Harrison RG, Buston PM. Unraveling hierarchical genetic structure in a marine metapopulation: A comparison of three high-throughput genotyping approaches. Mol Ecol 2020; 29:2189-2203. [PMID: 32147850 DOI: 10.1111/mec.15405] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 02/05/2020] [Accepted: 03/03/2020] [Indexed: 01/04/2023]
Abstract
Marine metapopulations often exhibit subtle population structure that can be difficult to detect. Given recent advances in high-throughput sequencing, an emerging question is whether various genotyping approaches, in concert with improved sampling designs, will substantially improve our understanding of genetic structure in the sea. To address this question, we explored hierarchical patterns of structure in the coral reef fish Elacatinus lori using a high-resolution approach with respect to both genetic and geographic sampling. Previously, we identified three putative E. lori populations within Belize using traditional genetic markers and sparse geographic sampling: barrier reef and Turneffe Atoll; Glover's Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals at ~10 km intervals throughout these reefs (1,129 individuals from 35 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs; 89 microsatellites; and 57 nonrepetitive nuclear loci. At broad spatial scales, the markers were consistent with each other and with previous findings. At finer spatial scales, there was new evidence of genetic substructure, but our three marker sets differed slightly in their ability to detect these patterns. Specifically, we found subtle structure between the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most effectively. We also documented isolation by distance within the barrier reef. Sensitivity analyses revealed that the number of loci (and alleles) had a strong effect on the detection of structure for all three marker sets, particularly at small spatial scales. Taken together, these results illustrate empirically that high-throughput genotyping data can elucidate subtle genetic structure at previously-undetected scales in a dispersive marine fish.
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Affiliation(s)
- Cassidy C D'Aloia
- Department of Biological Sciences, University of New Brunswick, Saint John, NB, Canada
| | - Jose A Andrés
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Steven M Bogdanowicz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Richard G Harrison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Peter M Buston
- Department of Biology and Marine Program, Boston University, Boston, MA, USA
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10
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Hernández-Álvarez C, Bayona-Vásquez NJ, Domínguez-Domínguez O, Uribe-Alcocer M, Díaz-Jaimes P. Phylogeography of the Pacific Red Snapper (Lutjanus peru) and Spotted Rose Snapper (Lutjanus guttatus) in the Inshore Tropical Eastern Pacific. COPEIA 2020. [DOI: 10.1643/cg-18-157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Cristóbal Hernández-Álvarez
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Circuito exterior s/n, Ciudad Universitaria, México D.F. C.P. 04510; (PDJ)
| | - Natalia J. Bayona-Vásquez
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Circuito exterior s/n, Ciudad Universitaria, México D.F. C.P. 04510; (PDJ)
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Universidad Michoacana de San Nicolás de Hidalgo, Edificio R, Ciudad Universitaria, Morelia, Michoacán C.P. 58030
| | - Manuel Uribe-Alcocer
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Circuito exterior s/n, Ciudad Universitaria, México D.F. C.P. 04510; (PDJ)
| | - Píndaro Díaz-Jaimes
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Circuito exterior s/n, Ciudad Universitaria, México D.F. C.P. 04510; (PDJ)
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