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Meta-Transcriptomic Analysis Reveals Novel RNA Viruses in Hippocampus erectus. Viruses 2023; 15:v15030772. [PMID: 36992480 PMCID: PMC10053862 DOI: 10.3390/v15030772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/22/2023] Open
Abstract
Lined seahorse, Hippocampus erectus, is an important aquatic animal due to its medicinal and ornamental purposes. However, our understanding of the viral spectrum in H. erectus is still limited. Here, we studied the viruses in H. erectus using meta-transcriptomic sequencing. A total of 213,770,166 reads were generated and assembled de novo into 539 virus-associated contigs. Three novel RNA viruses from the Astroviridae, Paramyxoviridae, and Picornaviridae families were finally identified. In addition, we identified a strain of nervous necrosis virus from H. erectus. In particular, the unhealthy group showed a higher viral diversity and abundance than the normal group. These results revealed the diversity and cross-species transmission of viruses in H. erectus and highlighted the threat of viral infections to H. erectus.
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2
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Population structure of threatened caribou in western Canada inferred from genome-wide SNP data. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01475-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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3
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Freret-Meurer NV, Fernández TC, Vaccani AC. Influence of the Atlantic Ocean thermal anomaly on the Longsnout seahorse Hippocampus reidi in a Brazilian estuary. JOURNAL OF FISH BIOLOGY 2022; 101:960-971. [PMID: 35781814 DOI: 10.1111/jfb.15156] [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: 12/08/2021] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
One of the consequences of climate change is an increase in the temperature of the oceans, which is considered to be one of the greatest impacts on biodiversity. Fish may respond to this impact in several ways, including shifts in their patterns of occurrence. The present study investigated the variation in the structure of a H. reidi population between 2015 and 2017 in the northern Guaíba Island area, highlighting a possible relationship to thermal anomaly associated with the El Niño phenomenon. The seahorse population monitoring was performed monthly, recording sex ratio, abundance, juvenile and adult proportion, depth of occurrence, total length and the holdfast which the seahorse were found attached. The influence of the El Niño event on the study population was evaluated by the correlation of the thermal anomaly data reported for the Tropical South Atlantic Index. Seahorse density on northern Guaíba island was positively and significantly correlated with water temperature, but the sex ratio and number of juveniles were not. The diversity of holdfasts used increased over the study period and was inversely proportional to the thermal anomaly. These results suggest that the thermal anomalies caused by the El Niño in the South Atlantic might trigger migration behaviour in the study species, providing a large aggregation during that period in Guaíba island.
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Affiliation(s)
- Natalie V Freret-Meurer
- Laboratório de Comportamento Animal e Conservação, Universidade Santa Úrsula, Rio de Janeiro, Brazil
- Projeto Cavalos-Marinhos/RJ, Rio de Janeiro, RJ, Brazil
| | - Tatiane C Fernández
- Laboratório de Comportamento Animal e Conservação, Universidade Santa Úrsula, Rio de Janeiro, Brazil
- Projeto Cavalos-Marinhos/RJ, Rio de Janeiro, RJ, Brazil
- Graduate Program in Ecology and Evolution, Roberto Alcantara Gomes Institute of Biology, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amanda C Vaccani
- Laboratório de Comportamento Animal e Conservação, Universidade Santa Úrsula, Rio de Janeiro, Brazil
- Projeto Cavalos-Marinhos/RJ, Rio de Janeiro, RJ, Brazil
- Graduate Program in Ecology and Evolution, Roberto Alcantara Gomes Institute of Biology, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
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4
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Diversity of Seahorse Species (Hippocampus spp.) in the International Aquarium Trade. DIVERSITY 2021. [DOI: 10.3390/d13050187] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Seahorses (Hippocampus spp.) are threatened as a result of habitat degradation and overfishing. They have commercial value as traditional medicine, curio objects, and pets in the aquarium industry. There are 48 valid species, 27 of which are represented in the international aquarium trade. Most species in the aquarium industry are relatively large and were described early in the history of seahorse taxonomy. In 2002, seahorses became the first marine fishes for which the international trade became regulated by CITES (Convention for the International Trade in Endangered Species of Wild Fauna and Flora), with implementation in 2004. Since then, aquaculture has been developed to improve the sustainability of the seahorse trade. This review provides analyses of the roles of wild-caught and cultured individuals in the international aquarium trade of various Hippocampus species for the period 1997–2018. For all species, trade numbers declined after 2011. The proportion of cultured seahorses in the aquarium trade increased rapidly after their listing in CITES, although the industry is still struggling to produce large numbers of young in a cost-effective way, and its economic viability is technically challenging in terms of diet and disease. Whether seahorse aquaculture can benefit wild populations will largely depend on its capacity to provide an alternative livelihood for subsistence fishers in the source countries. For most species, CITES trade records of live animals in the aquarium industry started a few years earlier than those of dead bodies in the traditional medicine trade, despite the latter being 15 times higher in number. The use of DNA analysis in the species identification of seahorses has predominantly been applied to animals in the traditional medicine market, but not to the aquarium trade. Genetic tools have already been used in the description of new species and will also help to discover new species and in various other kinds of applications.
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5
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Flanagan SP, Rose E, Jones AG. The population genomics of repeated freshwater colonizations by Gulf pipefish. Mol Ecol 2021; 30:1672-1687. [PMID: 33580570 DOI: 10.1111/mec.15841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/30/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022]
Abstract
How organisms adapt to the novel challenges imposed by the colonization of a new habitat has long been a central question in evolutionary biology. When multiple populations of the same species independently adapt to similar environmental challenges, the question becomes whether the populations have arrived at their adaptations through the same genetic mechanisms. In recent years, genetic techniques have been used to tackle these questions by investigating the genome-level changes underlying local adaptation. Here, we present a genomic analysis of colonization of freshwater habitats by a primarily marine fish, the Gulf pipefish (Syngnathus scovelli). We sample pipefish from four geographically distinct freshwater locations and use double-digest restriction site associated DNA sequencing to compare them to 12 previously studied saltwater populations. The two most geographically distant and isolated freshwater populations are the most genetically distinct, although demographic analysis suggests that these populations are experiencing ongoing migration with their saltwater neighbours. Additionally, outlier regions were found genome-wide, showing parallelism across ecotype pairs. We conclude that these multiple freshwater colonizations involve similar genomic regions, despite the large geographical distances and different underlying mechanisms. These similar patterns are probably facilitated by the interacting effects of intrinsic barriers, gene flow among populations and ecological selection in the Gulf pipefish.
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Affiliation(s)
- Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Emily Rose
- Department of Biology, Valdosta State University, Valdosta, GA, USA
| | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
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6
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Comprehensive genus-wide screening of seahorse microsatellite loci identifies priority species for conservation assessment. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01198-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Klanten OS, Gaither MR, Greaves S, Mills K, O’Keeffe K, Turnbull J, McKinnon R, Booth DJ. Genomic and morphological evidence of distinct populations in the endemic common (weedy) seadragon Phyllopteryx taeniolatus (Syngnathidae) along the east coast of Australia. PLoS One 2020; 15:e0243446. [PMID: 33362197 PMCID: PMC7757807 DOI: 10.1371/journal.pone.0243446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/22/2020] [Indexed: 11/30/2022] Open
Abstract
The common or weedy seadragon, Phyllopteryx taeniolatus, is an iconic and endemic fish found across temperate reefs of southern Australia. Despite its charismatic nature, few studies have been published, and the extent of population sub-structuring remains poorly resolved. Here we used 7462 single nucleotide polymorphisms (SNPs) to identify the extent of population structure in the weedy seadragon along the temperate southeast coast of Australia. We identified four populations, with strong genetic structure (FST = 0.562) between them. Both Discriminant Analysis of Principle Components (DAPC) and Bayesian clustering analyses support four distinct genetic clusters (north to south: central New South Wales, southern NSW, Victoria and Tasmania). In addition to these genetic differences, geographical variation in external morphology was recorded, with individuals from New South Wales shaped differently for a few measurements to those from the Mornington Peninsula (Victoria). We posit that these genetic and morphological differences suggest that the Victorian population of P. taeniolatus was historically isolated by the Bassian Isthmus during the last glacial maximum and should now be considered at least a distinct population. We also recorded high levels of genetic structure among the other locations. Based on the genomic and to a degree morphological evidence presented in this study, we recommend that the Victorian population be managed separately from the eastern populations (New South Wales and Tasmania).
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Affiliation(s)
- O. Selma Klanten
- Fish Ecology Lab, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
- * E-mail:
| | - Michelle R. Gaither
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, United States of America
| | - Samuel Greaves
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, United States of America
| | - Kade Mills
- Victorian National Parks Association, Carlton Melbourne, VIC, Australia
| | | | - John Turnbull
- Underwater Research Group (URG), Sydney, NSW, Australia
- Centre for Marine Biodiversity and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Rob McKinnon
- New South Wales National Parks and Wildlife Service, Merimbula, NSW, Australia
| | - David J. Booth
- Fish Ecology Lab, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
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8
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Aichelman HE, Barshis DJ. Adaptive divergence, neutral panmixia, and algal symbiont population structure in the temperate coral Astrangia poculata along the Mid-Atlantic United States. PeerJ 2020; 8:e10201. [PMID: 33240603 PMCID: PMC7680023 DOI: 10.7717/peerj.10201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/27/2020] [Indexed: 12/11/2022] Open
Abstract
Astrangia poculata is a temperate scleractinian coral that exists in facultative symbiosis with the dinoflagellate alga Breviolum psygmophilum across a range spanning the Gulf of Mexico to Cape Cod, Massachusetts. Our previous work on metabolic thermal performance of Virginia (VA) and Rhode Island (RI) populations of A. poculata revealed physiological signatures of cold (RI) and warm (VA) adaptation of these populations to their respective local thermal environments. Here, we used whole-transcriptome sequencing (mRNA-Seq) to evaluate genetic differences and identify potential loci involved in the adaptive signature of VA and RI populations. Sequencing data from 40 A. poculata individuals, including 10 colonies from each population and symbiotic state (VA-white, VA-brown, RI-white, and RI-brown), yielded a total of 1,808 host-associated and 59 algal symbiont-associated single nucleotide polymorphisms (SNPs) post filtration. Fst outlier analysis identified 66 putative high outlier SNPs in the coral host and 4 in the algal symbiont. Differentiation of VA and RI populations in the coral host was driven by putatively adaptive loci, not neutral divergence (Fst = 0.16, p = 0.001 and Fst = 0.002, p = 0.269 for outlier and neutral SNPs respectively). In contrast, we found evidence of neutral population differentiation in B. psygmophilum (Fst = 0.093, p = 0.001). Several putatively adaptive host loci occur on genes previously associated with the coral stress response. In the symbiont, three of four putatively adaptive loci are associated with photosystem proteins. The opposing pattern of neutral differentiation in B. psygmophilum, but not the A. poculata host, reflects the contrasting dynamics of coral host and algal symbiont population connectivity, dispersal, and gene by environment interactions.
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Affiliation(s)
- Hannah E Aichelman
- Department of Biology, Boston University, Boston, MA, USA.,Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | - Daniel J Barshis
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
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9
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Isolation and characterization of 100 SNP markers in lined seahorse (Hippocampus erectus) using RAD sequencing. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01163-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Bagley JC, Heming NM, Gutiérrez EE, Devisetty UK, Mock KE, Eckert AJ, Strauss SH. Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen ( Populus tremuloides). Ecol Evol 2020; 10:4609-4629. [PMID: 32551047 PMCID: PMC7297775 DOI: 10.1002/ece3.6214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 01/01/2023] Open
Abstract
Populus tremuloides is the widest-ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome-wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics of P. tremuloides, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal-Cascades (cluster 1), east-slope Cascades-Sierra Nevadas-Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of the P. tremuloides range, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the "stable-edge hypothesis" that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited "trailing-edge" dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the "inland dispersal hypothesis" predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific-coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable-edge, refugial locations, and postglacial expansion within P. tremuloides. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific-coastal genetic lineage of quaking aspen.
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Affiliation(s)
- Justin C. Bagley
- Plant Evolutionary Genomics LaboratoryDepartment of BiologyVirginia Commonwealth UniversityRichmondVAUSA
- Departamento de ZoologiaInstituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
| | - Neander M. Heming
- Departamento de ZoologiaInstituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
| | - Eliécer E. Gutiérrez
- Departamento de ZoologiaInstituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
- Programa de Pos‐Graduação em Biodiversidade AnimalCentro de Ciências Naturais e ExatasUniversidade Federal de Santa MariaSanta MariaBrazil
| | | | - Karen E. Mock
- Department of Wildland Resources and Ecology CenterUtah State UniversityLoganUTUSA
| | - Andrew J. Eckert
- Plant Evolutionary Genomics LaboratoryDepartment of BiologyVirginia Commonwealth UniversityRichmondVAUSA
| | - Steven H. Strauss
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
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11
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Morphological and molecular evidence for first records and range extension of the Japanese seahorse, Hippocampus mohnikei (Bleeker 1853) in a bay-estuarine system of Goa, central west coast of India. PLoS One 2020; 15:e0220420. [PMID: 32208467 PMCID: PMC7092974 DOI: 10.1371/journal.pone.0220420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 03/03/2020] [Indexed: 11/25/2022] Open
Abstract
Accurate information of taxonomy and geographic range of seahorse species (genus Hippocampus) is the first step in preparing threat assessments and designing effective conservation measures. Here, we report first records and a range extension of the Japanese seahorse, Hippocampus mohnikei (Bleeker, 1853) from the Mandovi estuarine ecosystem of Goa, central west coast of India (CWCI) based on morphological and molecular analyses. The morphometric and meristic traits, particularly short snout (29–35% head length), double cheek spine, low coronet, long tail (51.2–57.9% of standard length), 11 trunk rings, 37–39 tail rings, 15–16 dorsal and 12–14 fin rays observed in four collected specimens matched with the reported key diagnostic morphological criteria of vouchered specimens of H. mohnikei. The seahorse mitochondrial cytochrome oxidase subunit I (COI) and cytochrome b (Cyt b) genes were partially sequenced for conclusive genetic identification of the species under study. Molecular analysis showed that all four individuals clustered together suggesting a monophyletic lineage. Using the maximum similarity with GenBank database, maximum likelihood network and subsequent morphological analysis, the identity of the collected seahorse species was reconfirmed as H. mohnikei. With this new report, the geographic range of H. mohnikei extended significantly to the west from its previously known range. This new sighting of H. mohnikei could indicate a long-distance dispersal facilitated by the prevailing oceanic circulation in the Indo-Pacific region or increased habitat suitability in bay-estuarine systems of Goa, CWCI. Comparison of the pair-wise genetic distances (Kimura 2-parameter) based on COI and Cyt b sequences revealed that the specimens examined in this study are genetically closer to H. mohnikei populations from Vietnam and Thailand than they are to those in Japan and China. To test the hypothesis whether H. mohnikei are vagrants or previously unreported established population, long-term inter-annual sampling and analyses are warranted.
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12
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Louro B, De Moro G, Garcia C, Cox CJ, Veríssimo A, Sabatino SJ, Santos AM, Canário AVM. A haplotype-resolved draft genome of the European sardine (Sardina pilchardus). Gigascience 2019; 8:5494541. [PMID: 31112613 PMCID: PMC6528745 DOI: 10.1093/gigascience/giz059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/11/2019] [Accepted: 04/30/2019] [Indexed: 11/14/2022] Open
Abstract
Background The European sardine (Sardina pilchardus Walbaum, 1792) is culturally and economically important throughout its distribution. Monitoring studies of sardine populations report an alarming decrease in stocks due to overfishing and environmental change, which has resulted in historically low captures along the Iberian Atlantic coast. Important biological and ecological features such as population diversity, structure, and migratory patterns can be addressed with the development and use of genomics resources. Findings The genome of a single female individual was sequenced using Illumina HiSeq X Ten 10x Genomics linked reads, generating 113.8 gigabase pairs of data. Three draft genomes were assembled: 2 haploid genomes with a total size of 935 megabase pairs (N50 103 kilobase pairs) each, and a consensus genome of total size 950 megabase pairs (N50 97 kilobase pairs). The genome completeness assessment captured 84% of Actinopterygii Benchmarking Universal Single-Copy Orthologs. To obtain a more complete analysis, the transcriptomes of 11 tissues were sequenced to aid the functional annotation of the genome, resulting in 40,777 genes predicted. Variant calling on nearly half of the haplotype genome resulted in the identification of >2.3 million phased single-nucleotide polymorphisms with heterozygous loci. Conclusions A draft genome was obtained, despite a high level of sequence repeats and heterozygosity, which are expected genome characteristics of a wild sardine. The reference sardine genome and respective variant data will be a cornerstone resource of ongoing population genomics studies to be integrated into future sardine stock assessment modelling to better manage this valuable resource.
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Affiliation(s)
- Bruno Louro
- CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Gianluca De Moro
- CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Carlos Garcia
- CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Cymon J Cox
- CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Ana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Stephen J Sabatino
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - António M Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Adelino V M Canário
- CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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13
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Dupuis JR, Ruiz‐Arce R, Barr NB, Thomas DB, Geib SM. Range-wide population genomics of the Mexican fruit fly: Toward development of pathway analysis tools. Evol Appl 2019; 12:1641-1660. [PMID: 31462920 PMCID: PMC6708432 DOI: 10.1111/eva.12824] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 11/30/2022] Open
Abstract
Recurrently invading pests provide unique challenges for pest management, but also present opportunities to utilize genomics to understand invasion dynamics and inform regulatory management through pathway analysis. In the southern United States, the Mexican fruit fly Anastrepha ludens is such a pest, and its incursions into Texas and California represent major threats to the agricultural systems of those regions. We developed a draft genome assembly for A. ludens, conducted range-wide population genomics using restriction site-associated DNA sequencing, and then developed and demonstrated a panel of highly differentiated diagnostic SNPs for source determination of intercepted flies in this system. Using 2,081 genomewide SNPs, we identified four populations across the range of A. ludens, corresponding to western Mexico, eastern Mexico/Texas, Guatemala/Belize/Honduras, and Costa Rica/Panama, with some intergradation present between clusters, particularly in Central America. From this population genomics framework, we developed a diagnostic panel of 28 highly differentiated SNPs that were able to recreate the genomewide population structure in this species. We demonstrated this panel on a set of test specimens, including specimens intercepted as part of regular trapping surveillance in Texas and California, and we were able to predict populations of origin for these specimens. This methodology presents a highly applied use of genomic techniques and can be implemented in any group of recurrently invading pests.
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Affiliation(s)
- Julian R. Dupuis
- U.S. Department of Agriculture‐Agricultural Research ServiceDaniel K. Inouye U.S. Pacific Basin Agricultural Research CenterHiloHawaii
- Department of Plant and Environmental Protection SciencesUniversity of Hawai’i at MānoaHonoluluHawaii
| | - Raul Ruiz‐Arce
- U.S. Department of Agriculture‐Animal and Plant Health Inspection Service, Plant Protection & Quarantine, Science and TechnologyMission LaboratoryEdinburgTexas
| | - Norman B. Barr
- U.S. Department of Agriculture‐Animal and Plant Health Inspection Service, Plant Protection & Quarantine, Science and TechnologyMission LaboratoryEdinburgTexas
| | - Donald B. Thomas
- U.S. Department of Agriculture‐Agricultural Research ServiceCattle Fever Tick Research LaboratoryEdinburgTexas
| | - Scott M. Geib
- U.S. Department of Agriculture‐Agricultural Research ServiceDaniel K. Inouye U.S. Pacific Basin Agricultural Research CenterHiloHawaii
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14
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Miller AD, Hoffmann AA, Tan MH, Young M, Ahrens C, Cocomazzo M, Rattray A, Ierodiaconou DA, Treml E, Sherman CDH. Local and regional scale habitat heterogeneity contribute to genetic adaptation in a commercially important marine mollusc (
Haliotis rubra
) from southeastern Australia. Mol Ecol 2019; 28:3053-3072. [DOI: 10.1111/mec.15128] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/17/2019] [Accepted: 05/01/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Adam D. Miller
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
- Deakin Genomics Centre Deakin University Geelong Victoria Australia
| | - Ary A. Hoffmann
- School of BioSciences Bio21 Institute, The University of Melbourne Parkville Victoria Australia
| | - Mun Hua Tan
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
- Deakin Genomics Centre Deakin University Geelong Victoria Australia
| | - Mary Young
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Collin Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University Penrith New South Wales Australia
| | - Michael Cocomazzo
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Alex Rattray
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Daniel A. Ierodiaconou
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Eric Treml
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Craig D. H. Sherman
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
- Deakin Genomics Centre Deakin University Geelong Victoria Australia
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15
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Masonjones H, Rose E, Elson J, Roberts B, Curtis-Quick J. High density, early maturing, and morphometrically unique Hippocampus erectus population makes a Bahamian pond a priority site for conservation. ENDANGER SPECIES RES 2019. [DOI: 10.3354/esr00949] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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O'Connell KA, Santo VD, Maldonado J, Molina E, Fujita MK. A Tale of Two Skates: Comparative Phylogeography of North American Skate Species with Implications for Conservation. COPEIA 2019. [DOI: 10.1643/cg-18-114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Kyle A. O'Connell
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Valentina Di Santo
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138
| | - Jose Maldonado
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Erika Molina
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Matthew K. Fujita
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
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17
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Qin G, Johnson C, Zhang Y, Zhang H, Yin J, Miller G, Turingan RG, Guisbert E, Lin Q. Temperature-induced physiological stress and reproductive characteristics of the migratory seahorse Hippocampus erectus during a thermal stress simulation. Biol Open 2018; 7:bio.032888. [PMID: 29764809 PMCID: PMC6031341 DOI: 10.1242/bio.032888] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Inshore-offshore migration occurs frequently in seahorse species, either because of prey opportunities or because they are driven by reproduction, and variations in water temperature may dramatically change migratory seahorse behavior and physiology. The present study investigated the behavioral and physiological responses of the lined seahorse Hippocampus erectus under thermal stress and evaluated the potential effects of different temperatures on its reproduction. The results showed that the thermal tolerance of the seahorses was time dependent. Acute thermal stress (30°C, 2-10 h) increased the basal metabolic rate (breathing rate) and the expression of stress response genes (Hsp genes) significantly and further stimulated seahorse appetite. Chronic thermal treatment (30°C, 4 weeks) led to a persistently higher basal metabolic rate, higher stress response gene expression and higher mortality rates, indicating that the seahorses could not acclimate to chronic thermal stress and might experience massive mortality rates due to excessively high basal metabolic rates and stress damage. Additionally, no significant negative effects on gonad development or reproductive endocrine regulation genes were observed in response to chronic thermal stress, suggesting that seahorse reproductive behavior could adapt to higher-temperature conditions during migration and within seahorse breeding grounds. In conclusion, this simulation experiment indicates that temperature variations during inshore-offshore migration have no effect on reproduction, but promote significantly high basal metabolic rates and stress responses. Therefore, we suggest that the observed high tolerance of seahorse reproduction is in line with the inshore-offshore reproductive migration pattern of lined seahorses.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.164 Xingangxi Rd, Haizhu District, Guangzhou 510301, China.,University of Chinese Academy of Sciences, 19A Yuquan Rd, Shijingshan District, Beijing 100049, China
| | - Cara Johnson
- Department of Biological Science, Florida Institute of Technology, 150 W. University Blvd, Melbourne, FL 32901, USA
| | - Yuan Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.164 Xingangxi Rd, Haizhu District, Guangzhou 510301, China.,University of Chinese Academy of Sciences, 19A Yuquan Rd, Shijingshan District, Beijing 100049, China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.164 Xingangxi Rd, Haizhu District, Guangzhou 510301, China
| | - Jianping Yin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.164 Xingangxi Rd, Haizhu District, Guangzhou 510301, China
| | - Glen Miller
- Department of Biological Science, Florida Institute of Technology, 150 W. University Blvd, Melbourne, FL 32901, USA
| | - Ralph G Turingan
- Department of Biological Science, Florida Institute of Technology, 150 W. University Blvd, Melbourne, FL 32901, USA
| | - Eric Guisbert
- Department of Biological Science, Florida Institute of Technology, 150 W. University Blvd, Melbourne, FL 32901, USA
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.164 Xingangxi Rd, Haizhu District, Guangzhou 510301, China .,University of Chinese Academy of Sciences, 19A Yuquan Rd, Shijingshan District, Beijing 100049, China
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18
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Fontanella FM, Garner Y, Starnes J, Whitaker M. Evidence for panmixia despite barriers to gene flow in the hooked mussel, Ischadium recurvum (Mytilidae; Brachidontinae) along the North American coastline. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:75-81. [PMID: 29580117 DOI: 10.1080/24701394.2018.1455191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The discovery of phylogeographic patterns within broadly distributed marine species can be particularly challenging because absolute physical barriers to dispersal can be inconspicuous. Genetic boundaries often lie where ocean currents meet, forming sharp physical and ecological gradients, which may act as barriers to successful migrants. In eastern North America, coastal species often show phylogeographic differentiation associated with two recognized genetic barriers: the Gulf/Atlantic and the Virginia/Carolina discontinuities. We examined 185 specimens of the intertidal hooked mussel Ischadium recurvum collected from 15 locations along the eastern coastline of North America to examine phylogeographic, migration and historical demographic patterns associated climate change associated with Pleistocene glacial patterns. Hypothesis testing using Bayes factors in Migrate-n rejected the presence of phylogeographic breaks consistent with either maritime discontinuity and favoured a panmictic population model. The migration rate from the Gulf to the Atlantic was approximately three times higher than the migration from the Atlantic to the Gulf whereas the Carolina-Virginia migration rates were nearly equal. The summary statistics (Tajima's D, Fu's Fs) were significant and the demographic analyses (mismatch distributions, Bayesian skyline plot) were consistent with patterns of population expansion following glacial retreat during the Pleistocene epoch.
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Affiliation(s)
- Frank M Fontanella
- a Department of Biology , University of West Georgia , Carrollton , GA , USA
| | - Yvette Garner
- a Department of Biology , University of West Georgia , Carrollton , GA , USA
| | - Jasmine Starnes
- a Department of Biology , University of West Georgia , Carrollton , GA , USA
| | - Megan Whitaker
- a Department of Biology , University of West Georgia , Carrollton , GA , USA
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19
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Stobie CS, Oosthuizen CJ, Cunningham MJ, Bloomer P. Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing. Ecol Evol 2018; 8:2326-2342. [PMID: 29468047 PMCID: PMC5817159 DOI: 10.1002/ece3.3821] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 12/17/2017] [Indexed: 12/12/2022] Open
Abstract
The KwaZulu‐Natal yellowfish (Labeobarbus natalensis) is an abundant cyprinid, endemic to KwaZulu‐Natal Province, South Africa. In this study, we developed a single‐nucleotide polymorphism (SNP) dataset from double‐digest restriction site‐associated DNA (ddRAD) sequencing of samples across the distribution. We addressed several hidden challenges, primarily focusing on proper filtering of RAD data and selecting optimal parameters for data processing in polyploid lineages. We used the resulting high‐quality SNP dataset to investigate the population genetic structure of L. natalensis. A small number of mitochondrial markers present in these data had disproportionate influence on the recovered genetic structure. The presence of singleton SNPs also confounded genetic structure. We found a well‐supported division into northern and southern lineages, with further subdivision into five populations, one of which reflects north–south admixture. Approximate Bayesian Computation scenario testing supported a scenario where an ancestral population diverged into northern and southern lineages, which then diverged to yield the current five populations. All river systems showed similar levels of genetic diversity, which appears unrelated to drainage system size. Nucleotide diversity was highest in the smallest river system, the Mbokodweni, which, together with adjacent small coastal systems, should be considered as a key catchment for conservation.
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Affiliation(s)
- Cora Sabriel Stobie
- Molecular Ecology and Evolution Programme Department of Genetics University of Pretoria Pretoria South Africa
| | - Carel J Oosthuizen
- Molecular Ecology and Evolution Programme Department of Genetics University of Pretoria Pretoria South Africa
| | - Michael J Cunningham
- Molecular Ecology and Evolution Programme Department of Genetics University of Pretoria Pretoria South Africa
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme Department of Genetics University of Pretoria Pretoria South Africa
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20
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Population genomics and comparisons of selective signatures in two invasions of melon fly, Bactrocera cucurbitae (Diptera: Tephritidae). Biol Invasions 2017. [DOI: 10.1007/s10530-017-1621-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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Ni G, Kern E, Dong YW, Li Q, Park JK. More than meets the eye: The barrier effect of the Yangtze River outflow. Mol Ecol 2017; 26:4591-4602. [DOI: 10.1111/mec.14235] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 06/15/2017] [Accepted: 06/16/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Gang Ni
- Division of EcoScience; Ewha Womans University; Seodaemun-gu Seoul Korea
| | - Elizabeth Kern
- Division of EcoScience; Ewha Womans University; Seodaemun-gu Seoul Korea
| | - Yun-Wei Dong
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen Fujian Province China
- Marine Biodiversity and Global Change Laboratory; College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian Province China
| | - Qi Li
- The Key Laboratory of Mariculture; Ministry of Education; Ocean University of China; Qingdao China
| | - Joong-Ki Park
- Division of EcoScience; Ewha Womans University; Seodaemun-gu Seoul Korea
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22
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Benestan L, Moore JS, Sutherland BJG, Le Luyer J, Maaroufi H, Rougeux C, Normandeau E, Rycroft N, Atema J, Harris LN, Tallman RF, Greenwood SJ, Clark FK, Bernatchez L. Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems. Mol Ecol 2017; 26:6767-6783. [DOI: 10.1111/mec.14217] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/23/2017] [Accepted: 03/29/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Laura Benestan
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Jean-Sébastien Moore
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Ben J. G. Sutherland
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Jérémy Le Luyer
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Halim Maaroufi
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Clément Rougeux
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Eric Normandeau
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | | | - Jelle Atema
- Department of Biology; Boston University; Boston MA USA
| | - Les N. Harris
- Fisheries and Oceans Canada; Freshwater Institute; Winnipeg MB Canada
| | - Ross F. Tallman
- Fisheries and Oceans Canada; Freshwater Institute; Winnipeg MB Canada
| | - Spencer J. Greenwood
- Department of Biomedical Sciences & AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown PE Canada
| | - Fraser K. Clark
- Department of Biomedical Sciences & AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown PE Canada
| | - Louis Bernatchez
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
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23
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Affiliation(s)
- Josephine R. Paris
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Jamie R. Stevens
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Julian M. Catchen
- Department of Animal Biology University of Illinois at Urbana–Champaign Urbana IL 61801 USA
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24
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Shryock DF, Havrilla CA, DeFalco LA, Esque TC, Custer NA, Wood TE. Landscape genetic approaches to guide native plant restoration in the Mojave Desert. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2017; 27:429-445. [PMID: 28135767 DOI: 10.1002/eap.1447] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 09/02/2016] [Accepted: 09/15/2016] [Indexed: 05/12/2023]
Abstract
Restoring dryland ecosystems is a global challenge due to synergistic drivers of disturbance coupled with unpredictable environmental conditions. Dryland plant species have evolved complex life-history strategies to cope with fluctuating resources and climatic extremes. Although rarely quantified, local adaptation is likely widespread among these species and potentially influences restoration outcomes. The common practice of reintroducing propagules to restore dryland ecosystems, often across large spatial scales, compels evaluation of adaptive divergence within these species. Such evaluations are critical to understanding the consequences of large-scale manipulation of gene flow and to predicting success of restoration efforts. However, genetic information for species of interest can be difficult and expensive to obtain through traditional common garden experiments. Recent advances in landscape genetics offer marker-based approaches for identifying environmental drivers of adaptive genetic variability in non-model species, but tools are still needed to link these approaches with practical aspects of ecological restoration. Here, we combine spatially explicit landscape genetics models with flexible visualization tools to demonstrate how cost-effective evaluations of adaptive genetic divergence can facilitate implementation of different seed sourcing strategies in ecological restoration. We apply these methods to Amplified Fragment Length Polymorphism (AFLP) markers genotyped in two Mojave Desert shrub species of high restoration importance: the long-lived, wind-pollinated gymnosperm Ephedra nevadensis, and the short-lived, insect-pollinated angiosperm Sphaeralcea ambigua. Mean annual temperature was identified as an important driver of adaptive genetic divergence for both species. Ephedra showed stronger adaptive divergence with respect to precipitation variability, while temperature variability and precipitation averages explained a larger fraction of adaptive divergence in Sphaeralcea. We describe multivariate statistical approaches for interpolating spatial patterns of adaptive divergence while accounting for potential bias due to neutral genetic structure. Through a spatial bootstrapping procedure, we also visualize patterns in the magnitude of model uncertainty. Finally, we introduce an interactive, distance-based mapping approach that explicitly links marker-based models of adaptive divergence with local or admixture seed sourcing strategies, promoting effective native plant restoration.
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Affiliation(s)
- Daniel F Shryock
- U.S. Geological Survey, Western Ecological Research Center, 160 North Stephanie Street, Henderson, Nevada, 89074, USA
| | | | - Lesley A DeFalco
- U.S. Geological Survey, Western Ecological Research Center, 160 North Stephanie Street, Henderson, Nevada, 89074, USA
| | - Todd C Esque
- U.S. Geological Survey, Western Ecological Research Center, 160 North Stephanie Street, Henderson, Nevada, 89074, USA
| | - Nathan A Custer
- U.S. Geological Survey, Western Ecological Research Center, 160 North Stephanie Street, Henderson, Nevada, 89074, USA
| | - Troy E Wood
- U.S. Geological Survey, Colorado Plateau Research Station, Southwest Biological Science Center, PO Box 5614, Flagstaff, Arizona, 86011, USA
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25
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Luo W, Wang X, Qu H, Qin G, Zhang H, Lin Q. Genomic structure and expression pattern of MHC IIα and IIβ genes reveal an unusual immune trait in lined seahorse Hippocampus erectus. FISH & SHELLFISH IMMUNOLOGY 2016; 58:521-529. [PMID: 27697560 DOI: 10.1016/j.fsi.2016.09.057] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/26/2016] [Accepted: 09/30/2016] [Indexed: 06/06/2023]
Abstract
The major histocompatibility complex (MHC) genes are crucial in the adaptive immune system, and the gene duplication of MHC in animals can generally result in immune flexibility. In this study, we found that the lined seahorse (Hippocampus erectus) has only one gene copy number (GCN) of MHC IIα and IIβ, which is different from that in other teleosts. Together with the lack of spleen and gut-associated lymphatic tissue (GALT), the seahorse may be referred to as having a partial but natural "immunodeficiency". Highly variable amino acid residues were found in the IIα and IIβ domains, especially in the α1 and β1 domains with 9.62% and 8.43% allelic variation, respectively. Site models revealed seven and ten positively selected positions in the α1 and β1 domains, respectively. Real-time PCR experiments showed high expression levels of the MHC II genes in intestine (In), gill (Gi) and trunk kidney (TK) and medium in muscle (Mu) and brood pouch (BP), and the expression levels were significantly up-regulated after bacterial infection. Specially, relative higher expression level of both MHC IIα and IIβ was found in Mu and BP when compared with other fish species, in which MHC II is expressed negligibly in Mu. These results indicate that apart from TK, Gi and In, MU and BP play an important role in the immune response against pathogens in the seahorse. In conclusion, high allelic variation and strong positive selection in PBR and relative higher expression in MU and BP are speculated to partly compensate for the immunodeficiency.
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Affiliation(s)
- Wei Luo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyue Qu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
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26
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Everett MV, Park LK, Berntson EA, Elz AE, Whitmire CE, Keller AA, Clarke ME. Large-Scale Genotyping-by-Sequencing Indicates High Levels of Gene Flow in the Deep-Sea Octocoral Swiftia simplex (Nutting 1909) on the West Coast of the United States. PLoS One 2016; 11:e0165279. [PMID: 27798660 PMCID: PMC5087884 DOI: 10.1371/journal.pone.0165279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 10/10/2016] [Indexed: 11/26/2022] Open
Abstract
Deep-sea corals are a critical component of habitat in the deep-sea, existing as regional hotspots for biodiversity, and are associated with increased assemblages of fish, including commercially important species. Because sampling these species is so difficult, little is known about the connectivity and life history of deep-sea octocoral populations. This study evaluates the genetic connectivity among 23 individuals of the deep-sea octocoral Swiftia simplex collected from Eastern Pacific waters along the west coast of the United States. We utilized high-throughput restriction-site associated DNA (RAD)-tag sequencing to develop the first molecular genetic resource for the deep-sea octocoral, Swiftia simplex. Using this technique we discovered thousands of putative genome-wide SNPs in this species, and after quality control, successfully genotyped 1,145 SNPs across individuals sampled from California to Washington. These SNPs were used to assess putative population structure across the region. A STRUCTURE analysis as well as a principal coordinates analysis both failed to detect any population differentiation across all geographic areas in these collections. Additionally, after assigning individuals to putative population groups geographically, no significant FST values could be detected (FST for the full data set 0.0056), and no significant isolation by distance could be detected (p = 0.999). Taken together, these results indicate a high degree of connectivity and potential panmixia in S. simplex along this portion of the continental shelf.
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Affiliation(s)
- Meredith V Everett
- National Research Council, under contract to Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
| | - Linda K Park
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
| | - Ewann A Berntson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
| | - Anna E Elz
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
| | - Curt E Whitmire
- Fishery Resource Analysis and Monitoring Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
| | - Aimee A Keller
- Fishery Resource Analysis and Monitoring Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
| | - M Elizabeth Clarke
- Office of the Science Director, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
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27
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Jenny MJ, Payton SL, Baltzegar DA, Lozier JD. Phylogenetic Analysis of Molluscan Metallothioneins: Evolutionary Insight from Crassostrea virginica. J Mol Evol 2016; 83:110-125. [DOI: 10.1007/s00239-016-9758-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 09/21/2016] [Indexed: 11/29/2022]
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28
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Verdu CF, Guichoux E, Quevauvillers S, De Thier O, Laizet Y, Delcamp A, Gévaudant F, Monty A, Porté AJ, Lejeune P, Lassois L, Mariette S. Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L. Ecol Evol 2016; 6:7323-7333. [PMID: 28725400 PMCID: PMC5513258 DOI: 10.1002/ece3.2466] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 12/20/2022] Open
Abstract
The RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative paralogous RAD loci as a function of both the depth of coverage and the mismatch threshold allowed between loci. Putative paralogy was detected in a very variable number of loci, from 1% to more than 20%, with the depth of coverage having a major influence on the result. Putative paralogy artificially increased the observed degree of polymorphism and resulting estimates of diversity. The choice of the depth of coverage also affected diversity estimation and SNP validation: A low threshold decreased the chances of detecting minor alleles while a high threshold increased allelic dropout. SNP validation was better for the low threshold (4×) than for the high threshold (18×) we tested. Using the strategy developed here, we were able to validate more than 80% of the SNPs tested by means of individual genotyping, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications.
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Affiliation(s)
- Cindy F Verdu
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | | | - Samuel Quevauvillers
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | - Olivier De Thier
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | | | | | | | - Arnaud Monty
- Biodiversity and Landscape Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | | | - Philippe Lejeune
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | - Ludivine Lassois
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium.,Biodiversity and Landscape Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
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29
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Flanagan SP, Rose E, Jones AG. Population genomics reveals multiple drivers of population differentiation in a sex‐role‐reversed pipefish. Mol Ecol 2016; 25:5043-5072. [DOI: 10.1111/mec.13794] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 07/08/2016] [Accepted: 07/14/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Sarah P. Flanagan
- Biology Department Texas A&M University College Station TX 77843 USA
| | - Emily Rose
- Biology Department Texas A&M University College Station TX 77843 USA
| | - Adam G. Jones
- Biology Department Texas A&M University College Station TX 77843 USA
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30
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Rose E, Masonjones HD, Jones AG. A DNA-Based Assessment of the Phylogenetic Position of a Morphologically Distinct, Anchialine-Lake-Restricted Seahorse. J Hered 2016; 107:553-8. [PMID: 27481774 DOI: 10.1093/jhered/esw048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 07/28/2016] [Indexed: 11/13/2022] Open
Abstract
Isolated populations provide special opportunities to study local adaptation and incipient speciation. In some cases, however, morphological evolution can obscure the taxonomic status of recently founded populations. Here, we use molecular markers to show that an anchialine-lake-restricted population of seahorses, originally identified as Hippocampus reidi, appears on the basis of DNA data to be Hippocampus erectus We collected seahorses from Sweetings Pond, on Eleuthera Island, Bahamas, during the summer of 2014. We measured morphological traits and sequenced 2 genes, cytochrome b and ribosomal protein S7, from 19 seahorses in our sample. On the basis of morphology, Sweetings Pond seahorses could not be assigned definitively to either of the 2 species of seahorse, H. reidi and H. erectus, that occur in marine waters surrounding the Bahamas. However, our DNA-based phylogenetic analysis showed that the Sweetings Pond fish were firmly nested within the H. erectus clade with a Bayesian posterior probability greater than 0.99. Thus, Sweetings Pond seahorses most recently shared a common ancestor with H. erectus populations from the Western Atlantic. Interestingly, the seahorses from Sweetings Pond differ morphologically from other marine populations of H. erectus in having a more even torso to tail length ratio. The substantial habitat differences between Sweetings Pond and the surrounding coastal habitat make Sweetings Pond seahorses particularly interesting from the perspectives of conservation, local adaptation, and incipient speciation.
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Affiliation(s)
- Emily Rose
- From the Biology Department, Texas A&M University, 3258 TAMU College Station, TX 77843 (Rose and Jones) and Biology Department, University of Tampa, Tampa, FL (Masonjones).
| | - Heather D Masonjones
- From the Biology Department, Texas A&M University, 3258 TAMU College Station, TX 77843 (Rose and Jones) and Biology Department, University of Tampa, Tampa, FL (Masonjones)
| | - Adam G Jones
- From the Biology Department, Texas A&M University, 3258 TAMU College Station, TX 77843 (Rose and Jones) and Biology Department, University of Tampa, Tampa, FL (Masonjones)
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Miller AD, van Rooyen A, Rašić G, Ierodiaconou DA, Gorfine HK, Day R, Wong C, Hoffmann AA, Weeks AR. Contrasting patterns of population connectivity between regions in a commercially important mollusc Haliotis rubra: integrating population genetics, genomics and marine LiDAR data. Mol Ecol 2016; 25:3845-64. [PMID: 27322873 DOI: 10.1111/mec.13734] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 05/10/2016] [Accepted: 06/08/2016] [Indexed: 01/13/2023]
Abstract
Estimating contemporary genetic structure and population connectivity in marine species is challenging, often compromised by genetic markers that lack adequate sensitivity, and unstructured sampling regimes. We show how these limitations can be overcome via the integration of modern genotyping methods and sampling designs guided by LiDAR and SONAR data sets. Here we explore patterns of gene flow and local genetic structure in a commercially harvested abalone species (Haliotis rubra) from southeastern Australia, where the viability of fishing stocks is believed to be dictated by recruitment from local sources. Using a panel of microsatellite and genomewide SNP markers, we compare allele frequencies across a replicated hierarchical sampling area guided by bathymetric LiDAR imagery. Results indicate high levels of gene flow and no significant genetic structure within or between benthic reef habitats across 1400 km of coastline. These findings differ to those reported for other regions of the fishery indicating that larval supply is likely to be spatially variable, with implications for management and long-term recovery from stock depletion. The study highlights the utility of suitably designed genetic markers and spatially informed sampling strategies for gaining insights into recruitment patterns in benthic marine species, assisting in conservation planning and sustainable management of fisheries.
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Affiliation(s)
- A D Miller
- Deakin University, Geelong, Australia, School of Life and Environmental Sciences, Centre for Integrative Ecology, Warrnambool, Vic., 3280, Australia.,School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - A van Rooyen
- Cesar, 293 Royal Parade, Parkville, Vic., 3052, Australia
| | - G Rašić
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - D A Ierodiaconou
- Deakin University, Geelong, Australia, School of Life and Environmental Sciences, Centre for Integrative Ecology, Warrnambool, Vic., 3280, Australia
| | - H K Gorfine
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia.,Department of Economic Development, Jobs, Transport, and Resources, Queenscliff, Vic., 3225, Australia
| | - R Day
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - C Wong
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - A A Hoffmann
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - A R Weeks
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia.,Cesar, 293 Royal Parade, Parkville, Vic., 3052, Australia
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32
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Qu H, Luo W, Lin Q. Development of SNP markers in lined seahorse (Hippocampus erectus) based on transcriptome sequencing. CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-015-0510-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago. Sci Rep 2015; 5:18211. [PMID: 26656261 PMCID: PMC4674749 DOI: 10.1038/srep18211] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 11/12/2015] [Indexed: 01/16/2023] Open
Abstract
Following a global coral bleaching event in 1998, Acropora corals surrounding most of Okinawa island (OI) were devastated, although they are now gradually recovering. In contrast, the Kerama Islands (KIs) only 30 km west of OI, have continuously hosted a great variety of healthy corals. Taking advantage of the decoded Acropora digitifera genome and using genome-wide SNP analyses, we clarified Acropora population structure in the southern Ryukyu Archipelago (sRA). Despite small genetic distances, we identified distinct clusters corresponding to specific island groups, suggesting infrequent long-distance dispersal within the sRA. Although the KIs were believed to supply coral larvae to OI, admixture analyses showed that such dispersal is much more limited than previously realized, indicating independent recovery of OI coral populations and the necessity of local conservation efforts for each region. We detected strong historical migration from the Yaeyama Islands (YIs) to OI, and suggest that the YIs are the original source of OI corals. In addition, migration edges to the KIs suggest that they are a historical sink population in the sRA, resulting in high diversity. This population genomics study provides the highest resolution data to date regarding coral population structure and history.
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Past and present drivers of population structure in a small coastal fish, the European long snouted seahorse Hippocampus guttulatus. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0728-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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