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Torres-García RQ, Gaither MR, Robertson DR, Torres-Hernández E, Caselle JE, Durand JD, Angulo A, Espinoza-Herrera E, García-De León FJ, Valdiviezo-Rivera J, Domínguez-Domínguez O. Geographic genetic variation in the Coral Hawkfish, Cirrhitichthys oxycephalus (Cirrhitidae), in relation to biogeographic barriers across the Tropical Indo-Pacific. PeerJ 2024; 12:e18058. [PMID: 39346056 PMCID: PMC11438443 DOI: 10.7717/peerj.18058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 08/17/2024] [Indexed: 10/01/2024] Open
Abstract
The Tropical Indo-Pacific (TIP) includes about two thirds of the world's tropical oceans and harbors an enormous number of marine species. The distributions of those species within the region is affected by habitat discontinuities and oceanographic features. As well as many smaller ones, the TIP contains seven large recognized biogeographic barriers that separate the Red Sea and Indian Ocean, the Indian from the Pacific Ocean, the central and eastern Pacific, the Hawaiian archipelago, the Marquesas and Easter Islands. We examined the genetic structuring of populations of Cirrhitichthys oxycephalus, a small cryptic species of reef fish, across its geographic range, which spans the longitudinal limits of the TIP. We assessed geographic variation in the mitochondrial cytb gene and the nuclear RAG1 gene, using 166 samples collected in 46 localities from the western to eastern edges of the TIP. Sequences from cytb show three well-structured groups that are separated by large genetic distances (1.58-2.96%): two in the Tropical Eastern Pacific (TEP), one at Clipperton Atoll another occupying the rest of that region and the third that ranges across the remainder of the TIP, from the central Pacific to the Red Sea and South Africa. These results indicate that the ~4,000 km wide Eastern Pacific Barrier between the central and eastern Pacific is an efficient barrier separating the two main groups. Further, the ~950 km of open ocean that isolates Clipperton Atoll from the rest of the TEP is also an effective barrier. Contrary to many other cases, various major and minor barriers from the Central Indo-Pacific to the Red Sea are not effective against dispersal by C. oxycephalus, although this species has not colonized the Hawiian islands and Easter Island. The nuclear gene partially supports the genetic structure evident in cytb, although all haplotypes are geographically mixed.
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Affiliation(s)
- Rolando Quetzalcoatl Torres-García
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
- Programa Institucional de Maestría en Ciencias Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
| | - Michelle R Gaither
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, Florida, United States
| | | | - Eloisa Torres-Hernández
- Colección Nacional de Peces, Pabellón Nacional de la Biodiversidad, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Jennifer E Caselle
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, California, United States
| | | | - Arturo Angulo
- Escuela de Biología, 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 José, San José, Costa Rica
| | - Eduardo Espinoza-Herrera
- Investigación Marina Aplicada, Parque Nacional Galápagos, Puerto Ayora, Isla Santa Cruz, Ecuador
| | - Francisco J García-De León
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste S. C., La Paz, Baja California Sur, Mexico
| | | | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
- Colección de Peces, Instituto Nacional de Biodiversidad, Quito, Pichincha, Ecuador
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2
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Haye PA, Segovia NI. Shedding light on variation in reproductive success through studies of population genetic structure in a Southeast Pacific Coast mussel. Heredity (Edinb) 2023; 130:402-413. [PMID: 37024547 PMCID: PMC10238476 DOI: 10.1038/s41437-023-00615-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Phylogeography often focuses on the spatial dimension of genetic diversity, rarely including the temporal dynamics occurring interannually among local populations, which can provide insight into past variations in reproductive success. Currently, there is an intense aquaculture industry of Mytilus spp. on the Southeast Pacific Coast which depends entirely on the spat released by natural populations forming a relevant and sensitive social-ecological system. Temporal and spatial spat variability from natural mussel beds could be related to interannual reproductive dynamics with variable reproductive success and recruitment, which leave genetic signatures. Temporal and spatial genetic structure was evaluated in six natural beds in the Southeast Pacific (from 39°25'S to 43°07'S) on the most abundant and widespread Mytilus lineage detected, Mytilus cf. chilensis, in 4 consecutive years. Analyses included data from >180 individuals per year, with a total of 751 (mitochondrial COI) and 747 (nuclear H1) individuals, respectively. Overall, both markers showed high haplotype diversity and low spatial and temporal genetic differentiation. Likely, the high dispersal capacity of Mytilus cf. chilensis maintains population homogeneity and prevents diversity erosion. The slight differences in genetic variance of COI were better explained by differences among sites (space), and conversely, the H1 genetic variance was better explained by interannual (temporal) comparisons, which could explain temporal variability in spat availability. This study highlights the important insights achieved with the evaluation of both temporal and spatial population genetic structures in marine species with high reproductive output, which can condition the success and sustainability of the relevant social-ecological system.
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Affiliation(s)
- Pilar A Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago, Chile
| | - Nicolás I Segovia
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago, Chile.
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3
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Amaral Rocha ÉA, Silva RM, Rodrigues da Silva BK, Cruz CG, Fernandes FL. Fitness cost and reversion of resistance Leucoptera coffeella (Lepidoptera: Lyonetiidae) to chlorpyrifos. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113831. [PMID: 35809395 DOI: 10.1016/j.ecoenv.2022.113831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/15/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
A better understanding of fitness costs and insecticide resistance reversion has practical applications for improving resistance management approaches. The coffee leaf miner, Leucoptera coffeella, is one of the most important coffee pests worldwide. Chlorpyrifos is still used to control L. coffeella despite studies showing resistance in this pest. The current study investigated the fitness costs and reversion of resistance to chlorpyrifos in L. coffeella populations in coffee. The control failure of this insecticide was evaluated in 15 field populations. Selection of resistant and susceptible L. coffeella (G1-G10), with and without chlorpyrifos exposure, was evaluated. The following parameters were investigated: consumed leaf area, adult longevity, number of eggs per female, and egg viability. The present study showed control failures of chlorpyrifos and low (< 31-folds) to high levels (> 80-folds) of resistance in all field populations tested. The resistant population showed less fitness than the susceptible population. The fitness of the resistant population decreased significantly after 10 generations of chlorpyrifos selection. Specifically, the number of eggs per female, larvae hatched, and adult longevity were reduced by factors of 5, 2.3 and 3, respectively. Furthermore, the chlorpyrifos-resistant L. coffeella population consumed more than the susceptible population. Therefore, we concluded that non-exposing L. coffeella populations to chlorpyrifos insecticide leads to rapid reversion of resistance and susceptibility. In addition, resistant populations show reduced reproductive fitness and longevity, while consuming more, probably to meet greater metabolic demands.
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Affiliation(s)
- Érick Alcides Amaral Rocha
- Universidade Federal de Viçosa, Instituto de Ciências Agrárias, Campus Rio Paranaíba, MG230, Km08, Rio Paranaíba, Minas Gerais 38810-000, Brazil
| | - Ronald Machado Silva
- Universidade Federal de Viçosa, Instituto de Ciências Agrárias, Campus Rio Paranaíba, MG230, Km08, Rio Paranaíba, Minas Gerais 38810-000, Brazil
| | - Brenda Karina Rodrigues da Silva
- Universidade Federal de Viçosa, Instituto de Ciências Agrárias, Campus Rio Paranaíba, MG230, Km08, Rio Paranaíba, Minas Gerais 38810-000, Brazil
| | - Carlos Gustavo Cruz
- Universidade Federal de Uberlândia, Campus Glória, Uberlândia 38410-337, Brazil
| | - Flávio Lemes Fernandes
- Universidade Federal de Viçosa, Instituto de Ciências Agrárias, Campus Rio Paranaíba, MG230, Km08, Rio Paranaíba, Minas Gerais 38810-000, Brazil.
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Torres-Gonzalez E, Makova KD. Exploring the Effects of Mitonuclear Interactions on Mitochondrial DNA Gene Expression in Humans. Front Genet 2022; 13:797129. [PMID: 35846132 PMCID: PMC9277102 DOI: 10.3389/fgene.2022.797129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Most mitochondrial protein complexes include both nuclear and mitochondrial gene products, which coevolved to work together. This coevolution can be disrupted due to disparity in genetic ancestry between the nuclear and mitochondrial genomes in recently admixed populations. Such mitonuclear DNA discordance might result in phenotypic effects. Several nuclear-encoded proteins regulate expression of mitochondrial DNA (mtDNA) genes. We hypothesized that mitonuclear DNA discordance affects expression of genes encoded by mtDNA. To test this, we utilized the data from the GTEx project, which contains expression levels for ∼100 African Americans and >600 European Americans. The varying proportion of African and European ancestry in recently admixed African Americans provides a range of mitonuclear discordance values, which can be correlated with mtDNA gene expression levels (adjusted for age and ischemic time). In contrast, European Americans did not undergo recent admixture. We demonstrated that, for most mtDNA protein-coding genes, expression levels in energetically-demanding tissues were lower in African Americans than in European Americans. Furthermore, gene expression levels were lower in individuals with higher mitonuclear discordance, independent of population. Moreover, we found a negative correlation between mtDNA gene expression and mitonuclear discordance. In African Americans, the average value of African ancestry was higher for nuclear-encoded mitochondrial than non-mitochondrial genes, facilitating a match in ancestry with the mtDNA and more optimal interactions. These results represent an example of a phenotypic effect of mitonuclear discordance on human admixed populations, and have potential biomedical applications.
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Affiliation(s)
| | - Kateryna D. Makova
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
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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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Tahami MS, Dincă V, Lee KM, Vila R, Joshi M, Heikkilä M, Dapporto L, Schmid S, Huemer P, Mutanen M. Genomics Reveal Admixture and Unexpected Patterns of Diversity in a Parapatric Pair of Butterflies. Genes (Basel) 2021; 12:genes12122009. [PMID: 34946956 PMCID: PMC8700966 DOI: 10.3390/genes12122009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
We studied the evolutionary relationship of two widely distributed parapatric butterfly species, Melitaea athalia and Melitaea celadussa, using the ddRAD sequencing approach, as well as genital morphology and mtDNA data. M. athalia was retrieved as paraphyletic with respect to M. celadussa. Several cases of mito-nuclear discordance and morpho-genetic mismatch were found in the contact zone. A strongly diverged and marginally sympatric clade of M. athalia from the Balkans was revealed. An in-depth analysis of genomic structure detected high levels of admixture between M. athalia and M. celadussa at the contact zone, though not reaching the Balkan clade. The demographic modelling of populations supported the intermediate genetic make-up of European M. athalia populations with regards to M. celadussa and the Balkan clade. However, the dissimilarity matrix of genotype data (PCoA) suggested the Balkan lineage having a genetic component that is unrelated to the athalia-celadussa group. Although narrowly sympatric, almost no signs of gene flow were found between the main M. athalia group and the Balkan clade. We propose two possible scenarios on the historical evolution of our model taxa and the role of the last glacial maximum in shaping their current distribution. Finally, we discuss the complexities regarding the taxonomic delimitation of parapatric taxa.
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Affiliation(s)
- Mohadeseh Sadat Tahami
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
- Correspondence:
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC—Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, 37, 08003 Barcelona, Spain;
| | - Mukta Joshi
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
| | - Maria Heikkilä
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, 00014 Helsinki, Finland;
| | - Leonardo Dapporto
- Numerical and Experimental Zoology Laboratory (ZEN Lab), Dipartimento di Biologia, Dell’ Università di Firenze, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy;
| | - Sarah Schmid
- Departement de Biologie Computationnelle, Faculte de Biologie et Medecine, Universite de Lausanne, 1015 Lausanne, Switzerland;
| | - Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H., Naturwissenschaftliche Sammlungen, Krajnc-Str. 1, A-6060 Hall, Austria;
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
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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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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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9
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O'Toole B, Simmons NB, Hekkala E. Reconstructing the Genomic Diversity of a Widespread Sub-Saharan Bat (Pteropodidae: Eidolon helvum) Using Archival Museum Collections. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2020.22.2.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Brian O'Toole
- Department of Biological Sciences, Fordham University, 441 East Fordham Road, Bronx, NY 10458, USA
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
| | - Evon Hekkala
- Department of Biological Sciences, Fordham University, 441 East Fordham Road, Bronx, NY 10458, USA
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10
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Genomic and phenotypic consequences of two independent secondary contact zones between allopatric lineages of the anadromous ice goby Leucopsarion petersii. Heredity (Edinb) 2019; 124:223-235. [PMID: 31186532 DOI: 10.1038/s41437-019-0239-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/10/2019] [Accepted: 05/14/2019] [Indexed: 11/08/2022] Open
Abstract
Genetic and phenotypic analyses of independent secondary contact zones between certain pairs of divergent populations offer powerful opportunities to assess whether the consequences vary with different environmental backgrounds. Populations of the ice goby Leucopsarion petersii are distributed throughout the Japanese archipelago and comprise genetically and phenotypically divergent groups in the Japan Sea and the Pacific Ocean. In particular, populations in the Japan Sea have a larger body size and numbers of vertebrae than those in the Pacific Ocean. Herein, we performed integrated analyses of genotypes and phenotypes of two independent secondary contact zones and investigated their consequences. Population genetic analyses revealed asymmetric introgression of the mitochondrial genome of either lineage relative to little admixture of nuclear genomes in both secondary contact zones. On phenotype analyses, vertebral numbers were clearly explained by nuclear genomic ancestry in both secondary contact zones, whereas body size was not, suggesting that a little introgression of nuclear genes regulates body size. Actually, we observed biased introgression of a candidate gene, neuropeptide Y (NPY), which potentially controls body size in the ice goby. Moreover, the body size changes in the introgressed populations possibly affect the introgression patterns of mitochondrial genomes across these zones. Collectively, our results demonstrated that genomic and phenotypic consequences of secondary contact varied in marine variable environments.
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11
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Otwoma LM, Diemel V, Reuter H, Kochzius M, Meyer A. Genetic population structure of the convict surgeonfish Acanthurus triostegus: a phylogeographic reassessment across its range. JOURNAL OF FISH BIOLOGY 2018; 93:597-608. [PMID: 29956317 DOI: 10.1111/jfb.13686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
This study investigates the genetic population structure and connectivity of Acanthurus triostegus in five Indo-Pacific biogeographic regions (western and eastern Indian Ocean, western, central and eastern Pacific Ocean), using a mitochondrial DNA marker spanning the ATPase8 and ATPase6 gene regions. In order to assess the phylogeography and genetic population structure of A. triostegus across its range, 35 individuals were sampled from five localities in the western Indian Ocean and complemented with 227 sequences from two previous studies. Results from the overall analysis of molecular variance (AMOVA) without a priori grouping showed evidence of significant differentiation in the Indo-Pacific, with 25 (8.3%) out of 300 pairwise ΦST comparisons being significant. However, the hierarchical AMOVA grouping of Indian and Pacific Ocean populations failed to support the vicariance hypothesis, showing a lack of a genetic break between the two ocean basins. Instead, the correlation between pairwise ΦST values and geographic distance showed that dispersal of A. triostegus in the Indo-Pacific Ocean follows an isolation-by-distance model. Three haplogroups could be deduced from the haplotype network and phylogenetic tree, with haplogroup 1 and 2 dominating the Indian and the Pacific Ocean, respectively, while haplogroup 3 exclusively occurring in the Hawaiian Archipelago of the central Pacific Ocean.
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Affiliation(s)
- Levy M Otwoma
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Kenya Marine and Fisheries Research Institute (KMFRI), Mombasa, Kenya
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Valeska Diemel
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Hauke Reuter
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | | | - Achim Meyer
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
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12
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Ebbs ET, Loker ES, Brant SV. Phylogeography and genetics of the globally invasive snail Physa acuta Draparnaud 1805, and its potential to serve as an intermediate host to larval digenetic trematodes. BMC Evol Biol 2018; 18:103. [PMID: 29969987 PMCID: PMC6029401 DOI: 10.1186/s12862-018-1208-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 06/05/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Physa acuta is a globally invasive freshwater snail native to North America. Prior studies have led to conflicting views of how P. acuta populations are connected and genetic diversity is partitioned globally. This study aims to characterize phylogeographic and population genetic structure within the native range of P. acuta, elucidate its invasion history and assess global patterns of genetic diversity. Further, using meta-analytic methods, we test the 'Enemy-Release hypothesis' within the P. acuta - digenetic trematode system. The 'Enemy-Release hypothesis' refers to the loss of native parasites following establishment of their host within an invasive range. Population genetic data is combined with surveys of trematode infections to map range-wide trematode species richness associated with P. acuta, and to identify relevant host-population parameters important in modeling host-parasite invasion. RESULTS Phylogenetic analyses using mtDNA uncovered two major clades (A & B). Clade A occurs globally while clade B was only recovered from the Western USA. All invasive populations sampled grouped within Clade A, where multiple independent source populations were identified from across North America. Significant population genetic structure was found within the native range of P. acuta, with some evidence for contemporary geographic barriers between western and eastern populations. Mito-nuclear discordance was found suggesting historical isolation with secondary contact between the two mitochondrial clades. Trematode species richness was found to differ significantly between native and invasive populations, in concordance with the 'Enemy-Release hypothesis'. Further, our data suggests a positive relationship between nucleotide diversity of invasive populations and trematode prevalence and richness. CONCLUSIONS This study includes a wider geographic sampling of P. acuta within its native range that provides insight into phylogeographic and population genetic structure, range-wide genetic diversity and estimation of the invasion history. Meta-analysis of P. acuta - trematode surveys globally is consistent with the 'Enemy-Release hypothesis'. Additionally, results from this study suggest that host demographic parameters, namely genetic diversity as a proxy for population size, may play an essential role in how parasite communities assemble within invasive host populations. This knowledge can be used to begin to construct a framework to model host-parasite invasion dynamics over time.
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Affiliation(s)
- Erika T. Ebbs
- Department of Biology, Museum of Southwestern Biology Parasite Division, Center for Evolutionary and Theoretical Immunology, University of New Mexico, 167 Castetter MSCO3 2020, Albuquerque, NM 87131 USA
| | - Eric S. Loker
- Department of Biology, Museum of Southwestern Biology Parasite Division, Center for Evolutionary and Theoretical Immunology, University of New Mexico, 167 Castetter MSCO3 2020, Albuquerque, NM 87131 USA
| | - Sara V. Brant
- Department of Biology, Museum of Southwestern Biology Parasite Division, Center for Evolutionary and Theoretical Immunology, University of New Mexico, 167 Castetter MSCO3 2020, Albuquerque, NM 87131 USA
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13
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Genetic homogeneity of the invasive lionfish across the Northwestern Atlantic and the Gulf of Mexico based on Single Nucleotide Polymorphisms. Sci Rep 2018; 8:5062. [PMID: 29567984 PMCID: PMC5864727 DOI: 10.1038/s41598-018-23339-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 03/07/2018] [Indexed: 12/01/2022] Open
Abstract
Despite the devastating impact of the lionfish (Pterois volitans) invasion on NW Atlantic ecosystems, little genetic information about the invasion process is available. We applied Genotyping by Sequencing techniques to identify 1,220 single nucleotide polymorphic sites (SNPs) from 162 lionfish samples collected between 2013 and 2015 from two areas chronologically identified as the first and last invaded areas in US waters: the east coast of Florida and the Gulf of Mexico. We used population genomic analyses, including phylogenetic reconstruction, Bayesian clustering, genetic distances, Discriminant Analyses of Principal Components, and coalescence simulations for detection of outlier SNPs, to understand genetic trends relevant to the lionfish’s long-term persistence. We found no significant differences in genetic structure or diversity between the two areas (FSTp-values > 0.01, and t-test p-values > 0.05). In fact, our genomic analyses showed genetic homogeneity, with enough gene flow between the east coast of Florida and Gulf of Mexico to erase previous signals of genetic divergence detected between these areas, secondary spreading, and bottlenecks in the Gulf of Mexico. These findings suggest rapid genetic changes over space and time during the invasion, resulting in one panmictic population with no signs of divergence between areas due to local adaptation.
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14
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Burns M, Hedin M, Tsurusaki N. Population genomics and geographical parthenogenesis in Japanese harvestmen (Opiliones, Sclerosomatidae, Leiobunum). Ecol Evol 2018; 8:36-52. [PMID: 29321849 PMCID: PMC5756897 DOI: 10.1002/ece3.3605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 01/03/2023] Open
Abstract
Naturally occurring population variation in reproductive mode presents an opportunity for researchers to test hypotheses regarding the evolution of sex. Asexual reproduction frequently assumes a geographical pattern, in which parthenogenesis-dominated populations are more broadly dispersed than their sexual conspecifics. We evaluate the geographical distribution of genomic signatures associated with parthenogenesis using nuclear and mitochondrial DNA sequence data from two Japanese harvestman sister taxa, Leiobunum manubriatum and Leiobunum globosum. Asexual reproduction is putatively facultative in these species, and female-biased localities are common in habitat margins. Past karyotypic and current cytometric work indicates L. globosum is entirely tetraploid, while L. manubriatum may be either diploid or tetraploid. We estimated species phylogeny, genetic differentiation, diversity, and mitonuclear discordance in females collected across the species range in order to identify range expansion toward marginal habitat, potential for hybrid origin, and persistence of asexual lineages. Our results point to northward expansion of a tetraploid ancestor of L. manubriatum and L. globosum, coupled with support for greater male gene flow in southern L. manubriatum localities. Specimens from localities in the Tohoku and Hokkaido regions were indistinct, particularly those of L. globosum, potentially due to little mitochondrial differentiation or haplotypic variation. Although L. manubriatum overlaps with L. globosum across its entire range, L. globosum was reconstructed as monophyletic with strong support using mtDNA, and marginal support with nuclear loci. Ultimately, we find evidence for continued sexual reproduction in both species and describe opportunities to clarify the rate and mechanism of parthenogenesis.
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Affiliation(s)
- Mercedes Burns
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
- Department of Biological SciencesUniversity of MarylandBaltimore County, BaltimoreMDUSA
| | - Marshal Hedin
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
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15
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Svensson O, Gräns J, Celander MC, Havenhand J, Leder EH, Lindström K, Schöld S, van Oosterhout C, Kvarnemo C. Immigrant reproductive dysfunction facilitates ecological speciation. Evolution 2017; 71:2510-2521. [PMID: 28791680 DOI: 10.1111/evo.13323] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/01/2017] [Accepted: 08/05/2017] [Indexed: 01/20/2023]
Abstract
The distributions of species are not only determined by where they can survive - they must also be able to reproduce. Although immigrant inviability is a well-established concept, the fact that immigrants also need to be able to effectively reproduce in foreign environments has not been fully appreciated in the study of adaptive divergence and speciation. Fertilization and reproduction are sensitive life-history stages that could be detrimentally affected for immigrants in non-native habitats. We propose that "immigrant reproductive dysfunction" is a hitherto overlooked aspect of reproductive isolation caused by natural selection on immigrants. This idea is supported by results from experiments on an externally fertilizing fish (sand goby, Pomatoschistus minutus). Growth and condition of adults were not affected by non-native salinity whereas males spawning as immigrants had lower sperm motility and hatching success than residents. We interpret these results as evidence for local adaptation or acclimation of sperm, and possibly also components of paternal care. The resulting loss in fitness, which we call "immigrant reproductive dysfunction," has the potential to reduce gene flow between populations with locally adapted reproduction, and it may play a role in species distributions and speciation.
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Affiliation(s)
- Ola Svensson
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden.,Centre for Marine Evolutionary Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden.,Current Address: School of Natural Sciences, Technology and Environmental Studies, Södertörn University, SE-141 89 Huddinge, Sweden
| | - Johanna Gräns
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Malin C Celander
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden.,Centre for Marine Evolutionary Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Jonathan Havenhand
- Centre for Marine Evolutionary Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden.,Department of Marine Sciences, University of Gothenburg, Tjärnö, SE-452 96 Strömstad, Sweden
| | - Erica H Leder
- Centre for Marine Evolutionary Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden.,Department of Biology, University of Turku, FI-20014 Turun yliopisto, Finland.,Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, NO-0318, Oslo, Norway
| | - Kai Lindström
- Environmental and Marine Biology, Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland
| | - Sofie Schöld
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden.,Current Address: Swedish Meteorological and Hydrological Institute, Folkborgsvägen 17, SE-603 80 Norrköping, Sweden
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Charlotta Kvarnemo
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden.,Centre for Marine Evolutionary Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
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16
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Co-phylogeographic study of the flatworm Gyrodactylus gondae and its goby host Pomatoschistus minutus. Parasitol Int 2017; 66:119-125. [DOI: 10.1016/j.parint.2016.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 11/23/2022]
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17
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Jang SJ, Park E, Lee WK, Johnson SB, Vrijenhoek RC, Won YJ. Population subdivision of hydrothermal vent polychaete Alvinella pompejana across equatorial and Easter Microplate boundaries. BMC Evol Biol 2016; 16:235. [PMID: 27793079 PMCID: PMC5084463 DOI: 10.1186/s12862-016-0807-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/14/2016] [Indexed: 11/29/2022] Open
Abstract
Background The Equator and Easter Microplate regions of the eastern Pacific Ocean exhibit geomorphological and hydrological features that create barriers to dispersal for a number of animals associated with deep-sea hydrothermal vent habitats. This study examined effects of these boundaries on geographical subdivision of the vent polychaete Alvinella pompejana. DNA sequences from one mitochondrial and eleven nuclear genes were examined in samples collected from ten vent localities that comprise the species’ known range from 23°N latitude on the East Pacific Rise to 38°S latitude on the Pacific Antarctic Ridge. Results Multi-locus genotypes inferred from these sequences clustered the individual worms into three metapopulation segments — the northern East Pacific Rise (NEPR), southern East Pacific Rise (SEPR), and northeastern Pacific Antarctic Ridge (PAR) — separated by the Equator and Easter Microplate boundaries. Genetic diversity estimators were negatively correlated with tectonic spreading rates. Application of the isolation-with-migration (IMa2) model provided information about divergence times and demographic parameters. The PAR and NEPR metapopulation segments were estimated to have split roughly 4.20 million years ago (Mya) (2.42–33.42 Mya, 95 % highest posterior density, (HPD)), followed by splitting of the SEPR and NEPR segments about 0.79 Mya (0.07–6.67 Mya, 95 % HPD). Estimates of gene flow between the neighboring regions were mostly low (2 Nm < 1). Estimates of effective population size decreased with southern latitudes: NEPR > SEPR > PAR. Conclusions Highly effective dispersal capabilities allow A. pompejana to overcome the temporal instability and intermittent distribution of active hydrothermal vents in the eastern Pacific Ocean. Consequently, the species exhibits very high levels of genetic diversity compared with many co-distributed vent annelids and mollusks. Nonetheless, its levels of genetic diversity in partially isolated populations are inversely correlated with tectonic spreading rates. As for many other vent taxa, this pioneering colonizer is similarly affected by local rates of habitat turnover and by major dispersal filters associated with the Equator and the Easter Microplate region. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0807-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sook-Jin Jang
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, South Korea
| | - Eunji Park
- Division of Ecoscience, Ewha Womans University, Seoul, South Korea
| | - Won-Kyung Lee
- Division of Ecoscience, Ewha Womans University, Seoul, South Korea
| | - Shannon B Johnson
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95039-9644, USA
| | | | - Yong-Jin Won
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, South Korea. .,Division of Ecoscience, Ewha Womans University, Seoul, South Korea.
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18
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Khalili Samani N, Esa Y, Amin SMN, Fatin Mohd Ikhsan N. Phylogenetics and population genetics of Plotosus canius (Siluriformes: Plotosidae) from Malaysian coastal waters. PeerJ 2016; 4:e1930. [PMID: 27231645 PMCID: PMC4878373 DOI: 10.7717/peerj.1930] [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: 11/07/2015] [Accepted: 03/22/2016] [Indexed: 11/20/2022] Open
Abstract
Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental research on biological characteristics of P. canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P. canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395–0.771 and 0.033–0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (Ho) value of 0.2168, which was lower than the standard heterozygosity in marine populations (Ho = 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940, which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in an equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P. canius, and should be necessary highlighted for appropriate management and conservation of species. Further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci.
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Affiliation(s)
- Nima Khalili Samani
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia , Serdang, Selangor , Malaysia
| | - Yuzine Esa
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia , Serdang, Selangor , Malaysia
| | - S M Nurul Amin
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia , Serdang, Selangor , Malaysia
| | - Natrah Fatin Mohd Ikhsan
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia , Serdang, Selangor , Malaysia
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19
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Nayfa MG, Zenger KR. Unravelling the effects of gene flow and selection in highly connected populations of the silver-lip pearl oyster (Pinctada maxima). Mar Genomics 2016; 28:99-106. [PMID: 26934995 DOI: 10.1016/j.margen.2016.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 11/19/2022]
Abstract
Many marine organisms often display weak levels of population genetic structuring as a result of both environmental characteristics (e.g., ocean currents) and life history traits (e.g., widely dispersed planktonic larval stages) maintaining high levels of gene flow. This can lead to the assumption that these organisms can be managed as a single stock based on high levels of population connectivity. However, this neglects to account for other micro-evolutionary forces such as selection, which also shape these populations. This study utilizes 1130 genome-wide SNP loci to unravel the effects of gene flow and selection shaping three highly connected populations of the silver-lip pearl oyster (Pinctada maxima) in the ecologically and economically important Indo-Pacific region (Aru, Bali, and West Papua). Twenty-two loci under directional selection were identified amongst the populations, providing further supporting evidence of strong local adaptation (i.e., G×E effects) among populations in this region. Global Fst values for directional outliers (0.348) were up to eight times greater than for neutral markers (0.043). Pairwise Fst comparisons between Aru and Bali revealed the largest directional differences (0.488), while Bali and West Papua had the least (0.062). Unrooted neighbour-joining (NJ) distance trees and genetic diversity indices of directional outliers revealed that individuals from Bali and West Papua had reduced allelic variation (MAFavg=0.144, Ho=0.238 and MAFavg=0.232, Ho=0.369, respectively) compared to Aru (MAFavg=0.292, Ho=0.412). This indicates that directional selection is most likely acting upon genetic variation within the Bali and West Papua populations. NJ distance trees, discriminant analysis of principal components, and Fst analyses of directional outliers revealed two divergent groups ("Bali/West Papua"; "Aru") that had previously gone unrecognized. This study not only illustrates that relatively strong local adaptive forces are occurring despite high gene flow, but identifies the populations that are most likely experiencing selection. Additionally, this study highlights the need to understand all micro-evolutionary forces acting on populations when resolving stock structure.
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Affiliation(s)
- Maria G Nayfa
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Marine and Environmental Sciences, James Cook University, Townsville 4811, QLD, Australia.
| | - Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Marine and Environmental Sciences, James Cook University, Townsville 4811, QLD, Australia.
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20
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Genome-wide SNP loci reveal novel insights into koala (Phascolarctos cinereus) population variability across its range. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0784-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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Glynn F, Houghton JDR, Provan J. Population genetic analyses reveal distinct geographical blooms of the jellyfishRhizostoma octopus(Scyphozoa). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12614] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fergal Glynn
- School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road BT9 7BL Belfast UK
- Institute for Global Food Security; Queen's University Belfast; Belfast UK
| | - Jonathan D. R. Houghton
- School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road BT9 7BL Belfast UK
- Institute for Global Food Security; Queen's University Belfast; Belfast UK
- Queen's Marine Laboratory; 12-13 The Strand BT22 1PF Portaferry UK
| | - Jim Provan
- School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road BT9 7BL Belfast UK
- Institute for Global Food Security; Queen's University Belfast; Belfast UK
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22
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Evidence for high dispersal ability and mito-nuclear discordance in the small brown planthopper, Laodelphax striatellus. Sci Rep 2015; 5:8045. [PMID: 25622966 PMCID: PMC4309506 DOI: 10.1038/srep08045] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 12/30/2014] [Indexed: 01/22/2023] Open
Abstract
Understanding dispersal ability in pest species is critical for both theoretical aspects of
evolutionary and population biology and from a practical standpoint, such as implementing effective
forecasting systems. The small brown planthopper (SBPH), Laodelphax striatellus
(Fallén), is an economically important pest, but few data exist on its dispersal ability.
Here, we used mitochondrial and nuclear markers to elucidate the population genetic structure of
SBPH and of the parasitic bacterium Wolbachia throughout temperate and subtropical China. Our
results showed that the SBPH populations in China lack significant differences in genetic structure,
suggesting extensive gene flow. Multilocus sequence typing revealed that Wolbachia infection
was systematic and due to the same strain (wStri) within and across populations. However, the
mtDNA haplogroups had a nonrandom distribution across the sampling localities, which correlated to
latitudinal and climatic gradients. We explain this mito-nuclear discordance as a result of
historical population recolonization or mitochondria adaptation to climate.
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23
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Worldwide phylogeography of the invasive ctenophore Mnemiopsis leidyi (Ctenophora) based on nuclear and mitochondrial DNA data. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0770-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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24
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Karlsen BO, Emblem Å, Jørgensen TE, Klingan KA, Nordeide JT, Moum T, Johansen SD. Mitogenome sequence variation in migratory and stationary ecotypes of North-east Atlantic cod. Mar Genomics 2014; 15:103-8. [DOI: 10.1016/j.margen.2014.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/11/2013] [Accepted: 01/06/2014] [Indexed: 11/25/2022]
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25
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Cordero D, Peña JB, Saavedra C. Phylogeographic analysis of introns and mitochondrial DNA in the clam Ruditapes decussatus uncovers the effects of Pleistocene glaciations and endogenous barriers to gene flow. Mol Phylogenet Evol 2013; 71:274-87. [PMID: 24269315 DOI: 10.1016/j.ympev.2013.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 10/30/2013] [Accepted: 11/06/2013] [Indexed: 12/22/2022]
Abstract
Studies on the phylogeography of species inhabiting the Mediterranean and the nearby coasts of the NE Atlantic Ocean (MEDAT) have found subdivision and/or phylogeographic structure in one or more of the Atlantic, western Mediterranean and eastern Mediterranean basins. This structure has been explained as the result of past population fragmentation caused by Pleistocene sea level changes and current patterns of marine circulation. However, the increasing use of nuclear markers has revealed that these two factors alone are not enough to explain the phylogeographic patterns, and an additional role has been suggested for endogenous barriers to gene flow or natural selection. In this article we examined the role of these factors in Ruditapes decussatus, a commercial clam species native to MEDAT. A genetic analysis of 11 populations was carried out by examining 6 introns with a PCR-RFLP technique. We found subdivision in three regions: Atlantic (ATL), western Mediterranean plus Tunisia (WMED), and Aegean and Adriatic seas (AEGAD). Two introns (Ech and Tbp) showed alleles that were restricted to AEGAD. Sequencing a subsample of individuals for these introns indicated that AEGAD-specific alleles were separate clades, thus revealing a phylogeographic brake at the WMED-AEGAD boundary. Sequencing of the mitochondrial COI locus confirmed this phylogeographic break. Dating of the AEGAD mitochondrial haplotypes and nuclear alleles with a Bayesian MCMC method revealed that they shared common ancestors in the Pleistocene. These results can be explained in the framework of Pleistocene sea level drops and patterns of gene flow in MEDAT. An additional observation was a lack of differentiation at COI between the ATL and WMED, in sharp contrast with 4 introns that showed clear genetic subdivision. Neutrality tests did not support the hypothesis of a selective sweep acting on mtDNA to explain the contrasting levels of differentiation between mitochondrial and nuclear markers across the ATL-WMED transition, and we argue that the difference between markers is best explained by the existence of an endogenous genetic barrier, rather than by a physical barrier to larval migration alone.
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Affiliation(s)
- David Cordero
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, 12595 Ribera de Cabanes (Castellón), Spain
| | - Juan B Peña
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, 12595 Ribera de Cabanes (Castellón), Spain
| | - Carlos Saavedra
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, 12595 Ribera de Cabanes (Castellón), Spain.
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Durand JD, Guinand B, Dodson JJ, Lecomte F. Pelagic life and depth: coastal physical features in West Africa shape the genetic structure of the Bonga Shad, Ethmalosa fimbriata. PLoS One 2013; 8:e77483. [PMID: 24130890 PMCID: PMC3793960 DOI: 10.1371/journal.pone.0077483] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 09/02/2013] [Indexed: 11/19/2022] Open
Abstract
The bonga shad, Ethmalosa fimbriata, is a West African pelagic species still abundant in most habitats of its distribution range and thought to be only recently affected by anthropogenic pressure (habitat destruction or fishing pressure). Its presence in a wide range of coastal habitats characterised by different hydrodynamic processes, represents a case study useful for evaluating the importance of physical structure of the west African shoreline on the genetic structure of a small pelagic species. To investigate this question, the genetic diversity of E. fimbriata was assessed at both regional and species range scales, using mitochondrial (mt) and nuclear DNA markers. Whereas only three panmictic units were identified with mtDNA at the large spatial scale, nuclear genetic markers (EPIC: exon-primed intron-crossing) indicated a more complex genetic pattern at the regional scale. In the northern-most section of shad’s distribution range, up to 4 distinct units were identified. Bayesian inference as well as spatial autocorrelation methods provided evidence that gene flow is impeded by the presence of deep-water areas near the coastline (restricting the width of the coastal shelf), such as the Cap Timiris and the Kayar canyons in Mauritania and Senegal, respectively. The added discriminatory power provided by the use of EPIC markers proved to be essential to detect the influence of more subtle, contemporary processes (e.g. gene flow, barriers, etc.) acting within the glacial refuges identified previously by mtDNA.
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Affiliation(s)
- Jean-Dominique Durand
- Institut de recherche pour le développement, Laboratoire Ecologie des Systèmes Marins Côtiers UMR 5119, Université Montpellier II, Montpellier, France
- * E-mail:
| | - Bruno Guinand
- Institut des Sciences de l’Evolution de Montpellier UMR 5554, Université Montpellier II, Montpellier, France
| | | | - Frédéric Lecomte
- Direction de la faune aquatique, Direction de l’expertise sur la faune et ses habitats, Ministère du Développement Durable, de l’Environnement, de la Faune et des Parcs du Québec, Québec, Canada
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27
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Di Giuseppe G, Barbieri M, Vallesi A, Luporini P, Dini F. Phylogeographical pattern ofEuplotes nobilii, a protist ciliate with a bipolar biogeographical distribution. Mol Ecol 2013; 22:4029-37. [DOI: 10.1111/mec.12363] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/19/2013] [Accepted: 04/25/2013] [Indexed: 11/26/2022]
Affiliation(s)
| | | | - Adriana Vallesi
- Laboratory of Eukaryotic Microbiology and Animal Biology; Department of Environmental Sciences; University of Camerino; 62032 Camerino MC Italy
| | - Pierangelo Luporini
- Laboratory of Eukaryotic Microbiology and Animal Biology; Department of Environmental Sciences; University of Camerino; 62032 Camerino MC Italy
| | - Fernando Dini
- Department of Biology; University of Pisa; 56126 Pisa Italy
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28
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Livi S, de Innocentiis S, Longobardi A, Cataudella S, Tancioni L, Rampacci M, Marino G. Genetic structure of Barbus spp. populations in the Marches Region of central Italy and its relevance to conservation actions. JOURNAL OF FISH BIOLOGY 2013; 82:806-826. [PMID: 23464545 DOI: 10.1111/jfb.12021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 11/08/2012] [Indexed: 06/01/2023]
Abstract
A genetic survey of Barbus spp. populations in the Marches Region (Adriatic River basins), central Italy, was carried out using mitochondrial and nuclear markers (partial D-loop, cyt b sequences and microsatellite loci) in order to ascertain their systematic position and to address their genetic structure which is key to conservation action planning. Analyses were conducted on sequences obtained from 91 individuals collected from eight sampling sites in five different rivers, from two specimens provided by the Ichthyological Centre of Rome and mitochondrial sequences of Barbus spp. retrieved from GenBank. Presumptive classification based on external morphological characters was not confirmed by genetic analysis, by means of which all specimens collected in the Marches Region were ascribed to Barbus plebejus. Genetic diversity values (h and π) of sampling groups were all different from 0 except the one sample collected from the upper reaches of the River Tenna, above a hydroelectric dam. Population connectivity and colonization patterns of the studied area were inferred from an analysis of molecular variance distribution and evolutionary relationships among haplotypes. The results point to different levels of isolation among sampling groups due to ecological and anthropogenic factors and the effect of an artificial barrier on genetic variability and conservation status of the population. Finally, this study confirms the uncertainty associated with systematic classification of Barbus spp. based on morphological characters due to the phenotypic plasticity of the species.
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Affiliation(s)
- S Livi
- ISPRA Higher Institute for Environmental Protection and Research, Via Vitaliano Brancati, 48-00144 Rome, Italy.
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29
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Puckridge M, Last PR, White WT, Andreakis N. Phylogeography of the Indo-West Pacific maskrays (Dasyatidae, Neotrygon): a complex example of chondrichthyan radiation in the Cenozoic. Ecol Evol 2012; 3:217-32. [PMID: 23467194 PMCID: PMC3586632 DOI: 10.1002/ece3.448] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 11/14/2012] [Accepted: 11/15/2012] [Indexed: 12/03/2022] Open
Abstract
Maskrays of the genus Neotrygon (Dasyatidae) have dispersed widely in the Indo-West Pacific being represented largely by an assemblage of narrow-ranging coastal endemics. Phylogenetic reconstruction methods reproduced nearly identical and statistically robust topologies supporting the monophyly of the genus Neotrygon within the family Dasyatidae, the genus Taeniura being consistently basal to Neotrygon, and Dasyatis being polyphyletic to the genera Taeniurops and Pteroplatytrygon. The Neotrygon kuhlii complex, once considered to be an assemblage of color variants of the same biological species, is the most derived and widely dispersed subgroup of the genus. Mitochondrial (COI, 16S) and nuclear (RAG1) phylogenies used in synergy with molecular dating identified paleoclimatic fluctuations responsible for periods of vicariance and dispersal promoting population fragmentation and speciation in Neotrygon. Signatures of population differentiation exist in N. ningalooensis and N. annotata, yet a large-scale geological event, such as the collision between the Australian and Eurasian Plates, coupled with subsequent sea-level falls, appears to have separated a once homogeneous population of the ancestral form of N. kuhlii into southern Indian Ocean and northern Pacific taxa some 4–16 million years ago. Repeated climatic oscillations, and the subsequent establishment of land and shallow sea connections within and between Australia and parts of the Indo-Malay Archipelago, have both promoted speciation and established zones of secondary contact within the Indian and Pacific Ocean basins.
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Affiliation(s)
- Melody Puckridge
- Institute for Marine and Antarctic Studies, University of Tasmania Private Bag 129, Hobart, TAS, 7001, Australia ; Wealth from Oceans Flagship, CSIRO Marine and Atmospheric Research Castray Esplanade, Hobart, TAS, 7000, Australia
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30
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Van de Putte AP, Janko K, Kasparova E, Maes GE, Rock J, Koubbi P, Volckaert FA, Choleva L, Fraser KP, Smykla J, Van Houdt JK, Marshall C. Comparative phylogeography of three trematomid fishes reveals contrasting genetic structure patterns in benthic and pelagic species. Mar Genomics 2012. [DOI: 10.1016/j.margen.2012.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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31
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Zhan A, Darling JA, Bock DG, Lacoursière-Roussel A, MacIsaac HJ, Cristescu ME. Complex genetic patterns in closely related colonizing invasive species. Ecol Evol 2012; 2:1331-46. [PMID: 22957143 PMCID: PMC3434944 DOI: 10.1002/ece3.258] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 03/16/2012] [Accepted: 03/16/2012] [Indexed: 11/30/2022] Open
Abstract
Anthropogenic activities frequently result in both rapidly changing environments and translocation of species from their native ranges (i.e., biological invasions). Empirical studies suggest that many factors associated with these changes can lead to complex genetic patterns, particularly among invasive populations. However, genetic complexities and factors responsible for them remain uncharacterized in many cases. Here, we explore these issues in the vase tunicate Ciona intestinalis (Ascidiacea: Enterogona: Cionidae), a model species complex, of which spA and spB are rapidly spreading worldwide. We intensively sampled 26 sites (N = 873) from both coasts of North America, and performed phylogenetic and population genetics analyses based on one mitochondrial fragment (cytochrome c oxidase subunit 3–NADH dehydrogenase subunit I, COX3-ND1) and eight nuclear microsatellites. Our analyses revealed extremely complex genetic patterns in both species on both coasts. We detected a contrasting pattern based on the mitochondrial marker: two major genetic groups in C. intestinalis spA on the west coast versus no significant geographic structure in C. intestinalis spB on the east coast. For both species, geo-graphically distant populations often showed high microsatellite-based genetic affinities whereas neighboring ones often did not. In addition, mitochondrial and nuclear markers provided largely inconsistent genetic patterns. Multiple factors, including random genetic drift associated with demographic changes, rapid selection due to strong local adaptation, and varying propensity for human-mediated propagule dispersal could be responsible for the observed genetic complexities.
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Affiliation(s)
- Aibin Zhan
- Great Lakes Institute for Environmental Research, University of Windsor401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
| | - John A Darling
- National Exposure Research Laboratory, US Environmental Protection Agency109 T. W. Alexander Drive, Durham, North Carolina 27711, USA
| | - Dan G Bock
- Great Lakes Institute for Environmental Research, University of Windsor401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
| | | | - Hugh J MacIsaac
- Great Lakes Institute for Environmental Research, University of Windsor401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
| | - Melania E Cristescu
- Great Lakes Institute for Environmental Research, University of Windsor401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
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Diversity of tuco-tucos (Ctenomys, Rodentia) in the Northeastern wetlands from Argentina: mitochondrial phylogeny and chromosomal evolution. Genetica 2012; 140:125-36. [DOI: 10.1007/s10709-012-9664-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 06/22/2012] [Indexed: 10/28/2022]
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33
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Population genetic structure of Cichla pleiozona (Perciformes: Cichlidae) in the Upper Madera basin (Bolivian Amazon): Sex-biased dispersal? Mol Phylogenet Evol 2010; 57:1334-40. [DOI: 10.1016/j.ympev.2010.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2010] [Accepted: 08/26/2010] [Indexed: 11/22/2022]
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34
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Guillot G. Splendor and misery of indirect measures of migration and gene flow. Heredity (Edinb) 2010; 106:11-2. [PMID: 20461102 DOI: 10.1038/hdy.2010.55] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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35
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LARMUSEAU MAARTENHD, VANCAMPENHOUT KIM, RAEYMAEKERS JOOSTAM, VAN HOUDT JEROENKJ, VOLCKAERT FILIPAM. Differential modes of selection on the rhodopsin gene in coastal Baltic and North Sea populations of the sand goby, Pomatoschistus minutus. Mol Ecol 2010; 19:2256-68. [DOI: 10.1111/j.1365-294x.2010.04643.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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