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Long KM, Rivera-Colón AG, Bennett KFP, Catchen JM, Braun MJ, Brawn JD. Ongoing introgression of a secondary sexual plumage trait in a stable avian hybrid zone. Evolution 2024; 78:1539-1553. [PMID: 38753474 DOI: 10.1093/evolut/qpae076] [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: 04/03/2023] [Accepted: 05/14/2024] [Indexed: 05/18/2024]
Abstract
Hybrid zones are dynamic systems where natural selection, sexual selection, and other evolutionary forces can act on reshuffled combinations of distinct genomes. The movement of hybrid zones, individual traits, or both are of particular interest for understanding the interplay between selective processes. In a hybrid zone involving two lek-breeding birds, secondary sexual plumage traits of Manacus vitellinus, including bright yellow collar and olive belly color, have introgressed ~50 km asymmetrically across the genomic center of the zone into populations more genetically similar to Manacus candei. Males with yellow collars are preferred by females and are more aggressive than parental M. candei, suggesting that sexual selection was responsible for the introgression of male traits. We assessed the spatial and temporal dynamics of this hybrid zone using historical (1989-1994) and contemporary (2017-2020) transect samples to survey both morphological and genetic variation. Genome-wide single nucleotide polymorphism data and several male phenotypic traits show that the genomic center of the zone has remained spatially stable, whereas the olive belly color of male M. vitellinus has continued to introgress over this time period. Our data suggest that sexual selection can continue to shape phenotypes dynamically, independent of a stable genomic transition between species.
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Affiliation(s)
- Kira M Long
- Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, United States
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Kevin F P Bennett
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, United States
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Julian M Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Michael J Braun
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, United States
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Jeffrey D Brawn
- Department of Natural Resources & Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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2
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Hogg CJ. Translating genomic advances into biodiversity conservation. Nat Rev Genet 2024; 25:362-373. [PMID: 38012268 DOI: 10.1038/s41576-023-00671-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 11/29/2023]
Abstract
A key action of the new Global Biodiversity Framework is the maintenance of genetic diversity in all species to safeguard their adaptive potential. To achieve this goal, a translational mindset, which aims to convert results of basic research into direct practical benefits, needs to be applied to biodiversity conservation. Despite much discussion on the value of genomics to conservation, a disconnect between those generating genomic resources and those applying it to biodiversity management remains. As global efforts to generate reference genomes for non-model species increase, investment into practical biodiversity applications is critically important. Applications such as understanding population and multispecies diversity and longitudinal monitoring need support alongside education for policymakers on integrating the data into evidence-based decisions. Without such investment, the opportunity to revolutionize global biodiversity conservation using genomics will not be fully realized.
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Affiliation(s)
- Carolyn J Hogg
- School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
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3
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Garcia-Erill G, Hanghøj K, Heller R, Wiuf C, Albrechtsen A. Estimating admixture pedigrees of recent hybrids without a contiguous reference genome. Mol Ecol Resour 2023; 23:1604-1619. [PMID: 37400991 DOI: 10.1111/1755-0998.13830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
The genome of recently admixed individuals or hybrids has characteristic genetic patterns that can be used to learn about their recent admixture history. One of these are patterns of interancestry heterozygosity, which can be inferred from SNP data from either called genotypes or genotype likelihoods, without the need for information on genomic location. This makes them applicable to a wide range of data that are often used in evolutionary and conservation genomic studies, such as low-depth sequencing mapped to scaffolds and reduced representation sequencing. Here we implement maximum likelihood estimation of interancestry heterozygosity patterns using two complementary models. We furthermore develop apoh (Admixture Pedigrees of Hybrids), a software that uses estimates of paired ancestry proportions to detect recently admixed individuals or hybrids, and to suggest possible admixture pedigrees. It furthermore calculates several hybrid indices that make it easier to identify and rank possible admixture pedigrees that could give rise to the estimated patterns. We implemented apoh both as a command line tool and as a Graphical User Interface that allows the user to automatically and interactively explore, rank and visualize compatible recent admixture pedigrees, and calculate the different summary indices. We validate the performance of the method using admixed family trios from the 1000 Genomes Project. In addition, we show its applicability on identifying recent hybrids from RAD-seq data of Grant's gazelle (Nanger granti and Nanger petersii) and whole genome low-depth data of waterbuck (Kobus ellipsiprymnus) which shows complex admixture of up to four populations.
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Affiliation(s)
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Wiuf
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
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Zbinden ZD, Douglas MR, Chafin TK, Douglas ME. A community genomics approach to natural hybridization. Proc Biol Sci 2023; 290:20230768. [PMID: 37192670 PMCID: PMC10188237 DOI: 10.1098/rspb.2023.0768] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/26/2023] [Indexed: 05/18/2023] Open
Abstract
Hybridization is a complicated, oft-misunderstood process. Once deemed unnatural and uncommon, hybridization is now recognized as ubiquitous among species. But hybridization rates within and among communities are poorly understood despite the relevance to ecology, evolution and conservation. To clarify, we examined hybridization across 75 freshwater fish communities within the Ozarks of the North American Interior Highlands (USA) by single nucleotide polymorphism (SNP) genotyping 33 species (N = 2865 individuals; double-digest restriction site-associated DNA sequencing (ddRAD)). We found evidence of hybridization (70 putative hybrids; 2.4% of individuals) among 18 species-pairs involving 73% (24/33) of study species, with the majority being concentrated within one family (Leuciscidae/minnows; 15 species; 66 hybrids). Interspecific genetic exchange-or introgression-was evident from 24 backcrossed individuals (10/18 species-pairs). Hybrids occurred within 42 of 75 communities (56%). Four selected environmental variables (species richness, protected area extent, precipitation (May and annually)) exhibited 73-78% accuracy in predicting hybrid occurrence via random forest classification. Our community-level assessment identified hybridization as spatially widespread and environmentally dependent (albeit predominantly within one diverse, omnipresent family). Our approach provides a more holistic survey of natural hybridization by testing a wide range of species-pairs, thus contrasting with more conventional evaluations.
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Affiliation(s)
- Zachery D. Zbinden
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Marlis R. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Tyler K. Chafin
- Biomathematics and Statistics Scotland, Edinburgh, Scotland, UK
| | - Michael E. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
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5
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Evans SA, Whigham DF, Hartvig I, McCormick MK. Hybridization in the Fringed Orchids: An Analysis of Species Boundaries in the Face of Gene Flow. DIVERSITY 2023. [DOI: 10.3390/d15030384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Natural hybridization between closely related species in sympatry is an evolutionary process that is common in orchids. Once seen as a threat to parent species, interspecific genetic change is increasingly viewed as a source of novel variation in some ecological contexts. Terrestrial fringed orchids in the genus Platanthera contain several clades with high genetic compatibility among species and many putative hybrids. We used biallelic SNPs generated with 3RAD sequencing to study the hybrid complex formed from the parent species P. blephariglottis, P. ciliaris, and P. cristata with high resolution. The genetic structure and phylogenetic relationship of the hybrid complex revealed site-dependent gene flow between species. We documented extensive hybridization and cryptic hybrids in sympatric sites. Interspecific genetic exchange is particularly common between P. blephariglottis and P. ciliaris, with cryptic hybrids among putative P. ciliaris samples being more common than parental assignments in sympatric sites. Hybridization across the triad species complex can reticulate lineages and introduce adaptive alleles. Conversely, it can reduce diversification rates and introduce maladaptive alleles. Investigation into whether anthropogenic forces are eroding species boundaries, particularly the permeable P. blephariglottis and P. ciliaris boundary, is appropriate for conservation efforts.
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González-Castro M, Cardoso YP, Hughes LC, Ortí G. Hybridization is strongly constrained by salinity during secondary contact between silverside fishes (Odontesthes, Atheriniformes). Heredity (Edinb) 2022; 129:233-243. [PMID: 35821279 PMCID: PMC9519950 DOI: 10.1038/s41437-022-00555-9] [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: 07/08/2021] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 11/08/2022] Open
Abstract
This study investigates a contact zone between two silverside fish species (marine Odontesthes argentinensis and freshwater O. bonariensis) in the estuarine Mar Chiquita lagoon along the Atlantic coast in Argentina (MChL), in which intermediate morphs had been reported. It has been suggested that admixture and introgression occur in MChL between these two species, but direct genetic evidence is lacking. Leveraging samples collected over several years (n = 676), we document the spatial distribution of both species and intermediate morphs within this habitat and collect landmark-based morphometric and multilocus genetic data (9876 loci for n = 110 individuals) to test the hypothesis of hybridization. Our analysis unambiguously characterizes intermediate morphs as F1 or F2 hybrids. We show that the low frequency of hybrid individuals in MChL may be explained by uneven abundance of parental species, which in turn are strongly affected by water salinity, limiting the size of the contact zone. Although hybrids seem to be fertile, their fitness may be reduced by external and intrinsic factors that may limit their success and suggest that this is an unstable hybrid zone. Genetic distinctiveness of both parental species is strongly supported by genome-wide data, explaining a known pattern of mitonuclear discordance as a consequence of hybridization followed by mitochondrial introgression. A clear signature of population genetic structure was detected in O. argentinensis, distinguishing MChL residents from marine populations of this species, that also was supported by distinctive morphometric features among these groups. Previous hypotheses of speciation in these fishes are discussed in the light of the new findings.
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Affiliation(s)
- Mariano González-Castro
- Grupo de Biotaxonomía Morfológica y molecular de peces, IIMyC-CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Yamila P Cardoso
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
- Laboratorio de Sistemática y Biología Evolutiva, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina.
- Department of Biological Sciences, George Washington University, Washington, DC, USA.
| | - Lily C Hughes
- Department of Biological Sciences, George Washington University, Washington, DC, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Guillermo Ortí
- Department of Biological Sciences, George Washington University, Washington, DC, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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7
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Poelstra JW, Montero BK, Lüdemann J, Yang Z, Rakotondranary SJ, Hohenlohe P, Stetter N, Ganzhorn JU, Yoder AD. RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results. Proc Biol Sci 2022; 289:20220596. [PMID: 35946151 PMCID: PMC9364002 DOI: 10.1098/rspb.2022.0596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Microsatellites have been a workhorse of evolutionary genetic studies for decades and are still commonly in use for estimating signatures of genetic diversity at the population and species level across a multitude of taxa. Yet, the very high mutation rate of these loci is a double-edged sword, conferring great sensitivity at shallow levels of analysis (e.g. paternity analysis) but yielding considerable uncertainty for deeper evolutionary comparisons. For the present study, we used reduced representation genome-wide data (restriction site-associated DNA sequencing (RADseq)) to test for patterns of interspecific hybridization previously characterized using microsatellite data in a contact zone between two closely related mouse lemur species in Madagascar (Microcebus murinus and Microcebus griseorufus). We revisit this system by examining populations in, near, and far from the contact zone, including many of the same individuals that had previously been identified as hybrids with microsatellite data. Surprisingly, we find no evidence for admixed nuclear ancestry. Instead, re-analyses of microsatellite data and simulations suggest that previously inferred hybrids were false positives and that the program NewHybrids can be particularly sensitive to erroneously inferring hybrid ancestry. Combined with results from coalescent-based analyses and evidence for local syntopic co-occurrence, we conclude that the two mouse lemur species are in fact completely reproductively isolated, thus providing a new understanding of the evolutionary rate whereby reproductive isolation can be achieved in a primate.
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Affiliation(s)
- Jelmer W. Poelstra
- Department of Biology, Duke University, Durham, NC 27708, USA,Molecular and Cellular Imaging Center, Ohio State University, Wooster, OH 44691, USA
| | - B. Karina Montero
- Institute of Zoology, Department of Animal Ecology and Conservation, Universität Hamburg, Hamburg, 20146, Germany
| | - Jan Lüdemann
- Institute of Zoology, Department of Animal Ecology and Conservation, Universität Hamburg, Hamburg, 20146, Germany
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - S. Jacques Rakotondranary
- Institute of Zoology, Department of Animal Ecology and Conservation, Universität Hamburg, Hamburg, 20146, Germany,Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, PO Box 906, Antananarivo 101, Madagascar
| | - Paul Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Nadine Stetter
- Institute of Zoology, Department of Animal Ecology and Conservation, Universität Hamburg, Hamburg, 20146, Germany,Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Jörg U. Ganzhorn
- Institute of Zoology, Department of Animal Ecology and Conservation, Universität Hamburg, Hamburg, 20146, Germany
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
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8
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Chang SL, Ward HGM, Elliott LD, Russello MA. Genotyping-in-Thousands by sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon. Sci Rep 2022; 12:3441. [PMID: 35236892 PMCID: PMC8891347 DOI: 10.1038/s41598-022-07309-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/17/2022] [Indexed: 11/09/2022] Open
Abstract
Stocking programs have been widely implemented to re-establish extirpated fish species to their historical ranges; when employed in species with complex life histories, such management activities should include careful consideration of resulting hybridization dynamics with resident stocks and corresponding outcomes on recovery initiatives. Genetic monitoring can be instrumental for quantifying the extent of introgression over time, however conventional markers typically have limited power for the identification of advanced hybrid classes, especially at the intra-specific level. Here, we demonstrate a workflow for developing, evaluating and deploying a Genotyping-in-Thousands by Sequencing (GT-seq) SNP panel with the power to detect advanced hybrid classes to assess the extent and trajectory of intra-specific hybridization, using the sockeye salmon (Oncorhynchus nerka) stocking program in Skaha Lake, British Columbia as a case study. Previous analyses detected significant levels of hybridization between the anadromous (sockeye) and freshwater resident (kokanee) forms of O. nerka, but were restricted to assigning individuals to pure-stock or “hybrid”. Simulation analyses indicated our GT-seq panel had high accuracy, efficiency and power (> 94.5%) of assignment to pure-stock sockeye salmon/kokanee, F1, F2, and B2 backcross-sockeye/kokanee. Re-analysis of 2016/2017 spawners previously analyzed using TaqMan® assays and otolith microchemistry revealed shifts in assignment of some hybrids to adjacent pure-stock or B2 backcross classes, while new assignment of 2019 spawners revealed hybrids comprised 31% of the population, ~ 74% of which were B2 backcross or F2. Overall, the GT-seq panel development workflow presented here could be applied to virtually any system where genetic stock identification and intra-specific hybridization are important management parameters.
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Affiliation(s)
- Sarah L Chang
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Hillary G M Ward
- Lands and Natural Resource Operations and Rural Development, British Columbia Ministry of Forests, Penticton, BC, Canada
| | - Lucas D Elliott
- Department of Biology, University of British Columbia, Kelowna, BC, Canada.,UiT The Arctic University of Norway, Tromsø, Norway
| | - Michael A Russello
- Department of Biology, University of British Columbia, Kelowna, BC, Canada.
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Zheng W, Yan LJ, Burgess KS, Luo YH, Zou JY, Qin HT, Wang JH, Gao LM. Natural hybridization among three Rhododendron species (Ericaceae) revealed by morphological and genomic evidence. BMC PLANT BIOLOGY 2021; 21:529. [PMID: 34763662 PMCID: PMC8582147 DOI: 10.1186/s12870-021-03312-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 11/02/2021] [Indexed: 06/08/2023]
Abstract
BACKGROUND Natural hybridization can influence the adaptive response to selection and accelerate species diversification. Understanding the composition and structure of hybrid zones may elucidate patterns of hybridization processes that are important to the formation and maintenance of species, especially for taxa that have experienced rapidly adaptive radiation. Here, we used morphological traits, ddRAD-seq and plastid DNA sequence data to investigate the structure of a Rhododendron hybrid zone and uncover the hybridization patterns among three sympatric and closely related species. RESULTS Our results show that the hybrid zone is complex, where bi-directional hybridization takes place among the three sympatric parental species: R. spinuliferum, R. scabrifolium, and R. spiciferum. Hybrids between R. spinuliferum and R. spiciferum (R. ×duclouxii) comprise multiple hybrid classes and a high proportion of F1 generation hybrids, while a novel hybrid taxon between R. spinuliferum and R. scabrifolium dominated the F2 generation, but no backcross individuals were detected. The hybrid zone showed basically coincident patterns of population structure between genomic and morphological data. CONCLUSIONS Natural hybridization exists among the three Rhododendron species in the hybrid zone, although patterns of hybrid formation vary between hybrid taxa, which may result in different evolutionary outcomes. This study represents a unique opportunity to dissect the ecological and evolutionary mechanisms associated with adaptive radiation of Rhododendron species in a biodiversity hotspot.
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Affiliation(s)
- Wei Zheng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Li-Jun Yan
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
- College of Vocational and Technical Education, Yunnan Normal University, 650092, Kunming, Yunnan, China
| | - Kevin S Burgess
- Department of Biology, Columbus State University, University System of Georgia, 31907-5645, Columbus, GA, USA
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Jia-Yun Zou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Han-Tao Qin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Ji-Hua Wang
- The Flower Research Institute, Yunnan Academy of Agricultural Sciences, 650205, Kunming, China.
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China.
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, 674100, Lijiang, Yunnan, China.
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10
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Faust E, Jansson E, André C, Halvorsen KT, Dahle G, Knutsen H, Quintela M, Glover KA. Not that clean: Aquaculture-mediated translocation of cleaner fish has led to hybridization on the northern edge of the species' range. Evol Appl 2021; 14:1572-1587. [PMID: 34178105 PMCID: PMC8210792 DOI: 10.1111/eva.13220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/11/2022] Open
Abstract
Translocation and introduction of non-native organisms can have major impacts on local populations and ecosystems. Nevertheless, translocations are common practices in agri- and aquaculture. Each year, millions of wild-caught wrasses are transported large distances to be used as cleaner fish for parasite control in marine salmon farms. Recently, it was documented that translocated cleaner fish are able to escape and reproduce with local wild populations. This is especially a challenge in Norway, which is the world's largest salmon producer. Here, a panel of 84 informative SNPs was developed to identify the presence of nonlocal corkwing wrasse (Symphodus melops) escapees and admixed individuals in wild populations in western Norway. Applying this panel to ~2000 individuals, escapees and hybrids were found to constitute up to 20% of the local population at the northern edge of the species' distribution. The introduction of southern genetic material at the northern edge of the species distribution range has altered the local genetic composition and could obstruct local adaptation and further range expansion. Surprisingly, in other parts of the species distribution where salmon farming is also common, few escapees and hybrids were found. Why hybridization seems to be common only in the far north is discussed in the context of demographic and transport history. However, the current lack of reporting of escapes makes it difficult to evaluate possible causes for why some aquaculture-dense areas have more escapees and hybrids than others. The results obtained in this study, and the observed high genomic divergence between the main export and import regions, puts the sustainability of mass translocation of nonlocal wild wrasse into question and suggests that the current management regime needs re-evaluation.
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Affiliation(s)
- Ellika Faust
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | | | - Carl André
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | | | - Geir Dahle
- Institute of Marine ResearchBergenNorway
| | - Halvor Knutsen
- Institute of Marine ResearchHisNorway
- Centre of Coastal ResearchUniversity of AgderKristiansandNorway
| | | | - Kevin A. Glover
- Institute of Marine ResearchBergenNorway
- Institute of BiologyUniversity of BergenBergenNorway
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11
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Genetic interactions among native and introduced stocks of Oncorhynchus mykiss in the upper Willamette River, Oregon. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01322-1] [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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12
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Carlon DB, Robertson DR, Barron RL, Choat JH, Anderson DJ, Schwartz SA, Sánchez-Ortiz CA. The origin of the parrotfish species Scarus compressus in the Tropical Eastern Pacific: region-wide hybridization between ancient species pairs. BMC Ecol Evol 2021; 21:7. [PMID: 33514314 PMCID: PMC7853319 DOI: 10.1186/s12862-020-01731-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/07/2020] [Indexed: 12/04/2022] Open
Abstract
Background In the Tropical Eastern Pacific (TEP), four species of parrotfishes with complex phylogeographic histories co-occur in sympatry on rocky reefs from Baja California to Ecuador: Scarus compressus, S. ghobban, S. perrico, and S. rubroviolaceus. The most divergent, S. perrico, separated from a Central Indo-Pacific ancestor in the late Miocene (6.6 Ma). We tested the hypothesis that S. compressus was the result of ongoing hybridization among the other three species by sequencing four nuclear markers and a mitochondrial locus in samples spanning 2/3 of the latitudinal extent of the TEP. Results A Structure model indicated that K = 3 fit the nuclear data and that S. compressus individuals had admixed genomes. Our data could correctly detect and assign pure adults and F1 hybrids with > 0.90 probability, and correct assignment of F2s was also high in some cases. NewHybrids models revealed that 89.8% (n = 59) of the S. compressus samples were F1 hybrids between either S. perrico × S. ghobban or S. perrico × S. rubroviolaceus. Similarly, the most recently diverged S. ghobban and S. rubroviolaceus were hybridizing in small numbers, with half of the admixed individuals assigned to F1 hybrids and the remainder likely > F1 hybrids. We observed strong mito-nuclear discordance in all hybrid pairs. Migrate models favored gene flow between S. perrico and S. ghobban, but not other species pairs. Conclusions Mating between divergent species is giving rise to a region-wide, multispecies hybrid complex, characterized by a high frequency of parental and F1 genotypes but a low frequency of > F1 hybrids. Trimodal structure, and evidence for fertility of both male and female F1 hybrids, suggest that fitness declines sharply in later generation hybrids. In contrast, the hybrid population of the two more recently diverged species had similar frequencies of F1 and > F1 hybrids, suggesting accelerating post-mating incompatibility with time. Mitochondrial genotypes in hybrids suggest that indiscriminate mating by male S. perrico is driving pre-zygotic breakdown, which may reflect isolation of this endemic species for millions of years resulting in weak selection for conspecific mate recognition. Despite overlapping habitat use and high rates of hybridization, species boundaries are maintained by a combination of pre- and post-mating processes in this complex.
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Affiliation(s)
- David B Carlon
- Schiller Coastal Studies Centre and Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME, 04011, USA.
| | | | - Robert L Barron
- Schiller Coastal Studies Centre and Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME, 04011, USA
| | - John Howard Choat
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - David J Anderson
- Schiller Coastal Studies Centre and Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME, 04011, USA
| | - Sonja A Schwartz
- Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, 94720, USA
| | - Carlos A Sánchez-Ortiz
- Departamento de Biología Marina, Universidad Autónoma de Baja California Sur, CP 23081, La Paz, Baja California Sur, México
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13
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Yang T, Miller M, Forgacs D, Derr J, Stothard P. Development of SNP-Based Genomic Tools for the Canadian Bison Industry: Parentage Verification and Subspecies Composition. Front Genet 2020; 11:585999. [PMID: 33329724 PMCID: PMC7714993 DOI: 10.3389/fgene.2020.585999] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/28/2020] [Indexed: 11/30/2022] Open
Abstract
Genomic technologies have been increasingly applied in livestock production due to their utility in production management and animal genetic improvement. The current project aimed to develop genomic resources for the Canadian bison industry, specifically a parentage verification tool and a subspecies composition tool. Both products stand to help with building and maintaining purebred and crossbred bison populations, and in turn bison conservation and production. The development of this genomic toolkit proceeded in two stages. In the single-nucleotide polymorphism (SNP) discovery and selection stage, raw sequence information from 41 bison samples was analyzed, and approximately 52.5 million candidate biallelic SNPs were discovered from 21 samples with high sequence quality. A set of 19,954 SNPs (2,928 for parentage verification and 17,026 for subspecies composition) were then selected for inclusion on an Axiom myDesign custom array. In the refinement and validation stage, 480 bison were genotyped using the custom SNP panel, and the resulting genotypes were analyzed to further filter SNPs and assess tool performance. In various tests using real and simulated genotypes, the two genomic tools showed excellent performance for their respective tasks. Final SNP sets consisting of 191 SNPs for parentage and 17,018 SNPs for subspecies composition are described. As the first SNP-based genomic toolkit designed for the Canadian bison industry, our results may provide a new opportunity in improving the competitiveness and profitability of the industry in a sustainable manner.
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Affiliation(s)
- Tianfu Yang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | | | - David Forgacs
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - James Derr
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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14
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Martin BT, Douglas MR, Chafin TK, Placyk JS, Birkhead RD, Phillips CA, Douglas ME. Contrasting signatures of introgression in North American box turtle (
Terrapene
spp.) contact zones. Mol Ecol 2020; 29:4186-4202. [DOI: 10.1111/mec.15622] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Bradley T. Martin
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
| | - Marlis R. Douglas
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
| | - Tyler K. Chafin
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
| | - John S. Placyk
- Department of Biology University of Texas Tyler TX USA
- Science Division Trinity Valley Community College Athens TX USA
| | | | - Christopher A. Phillips
- Illinois Natural History Survey Prairie Research Institute University of Illinois Champaign IL USA
| | - Michael E. Douglas
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
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15
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Barreto SB, Knowles LL, Affonso PRADM, Batalha-Filho H. Riverscape properties contribute to the origin and structure of a hybrid zone in a Neotropical freshwater fish. J Evol Biol 2020; 33:1530-1542. [PMID: 32862491 DOI: 10.1111/jeb.13689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 11/28/2022]
Abstract
Understanding the structure of hybrid zones provides valuable insights about species boundaries and speciation, such as the evolution of barriers to gene flow and the strength of selection. In river networks, studying evolutionary processes in hybrid zones can be especially challenging, given the influence of past and current river properties along with biological species-specific traits. Here, we suggest that a natural hybrid zone between two divergent lineages of the sexually dimorphic Neotropical fish Nematocharax venustus was probably established by secondary contact as a result of a river capture event between the Contas and Pardo river basins. This putative river capture is supported by hydrogeological evidence of elbows of capture, wind gaps and geological faults. The morphological (colour pattern) and genetic (mtDNA and RADseq) variation reveal a clinal transition between parental lineages along the main river, with predominance of F2 hybrids at the centre of the hybrid zone, absence of early generation backcrosses and different levels of hybridization in the tributaries. We highlight that different sources of information are crucial for understanding how the riverscape spatial history influences the connectivity between and within river systems and, consequently, the dynamics of gene flow between freshwater lineages/species.
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Affiliation(s)
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
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16
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Genomic evidence of recent hybridization between sea turtles at Abrolhos Archipelago and its association to low reproductive output. Sci Rep 2020; 10:12847. [PMID: 32733067 PMCID: PMC7393485 DOI: 10.1038/s41598-020-69613-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 07/15/2020] [Indexed: 11/24/2022] Open
Abstract
Hybridization between sea turtle species occurs with particularly high frequency at two adjacent nesting areas in northeastern Brazil. To understand the outcomes of hybridization and their consequences for sea turtle conservation, we need to evaluate the extent of hybridization occurrence and possible deleterious effects in the hybrid progeny. Thus, we investigated the hypothesis of the existence of a new hybrid spot offshore of Brazil’s northeastern coast. The Abrolhos Archipelago is surrounded by the largest and richest coral reefs in the South Atlantic and is known to be a nesting site for loggerhead turtles (Carettacaretta). In this study, we performed a multidisciplinary investigation into levels of hybridization in sea turtles and their reproductive output in the Abrolhos beaches. Genetic data from mitochondrial DNA (mtDNA) and six autosomal markers showed that there are first-generation hybrid females nesting in Abrolhos, resulting from crossings between hawksbill males (Eretmochelysimbricata) and loggerhead females, and backcrossed hatchlings from both parental species. The type and extent of hybridization were characterized using genomic data obtained with the 3RAD method, which confirmed backcrossing between F1 hybrids and loggerhead turtles. The reproductive output data of Abrolhos nests suggests a disadvantage of hybrids when compared to loggerheads. For the first time, we have shown the association between hybridization and low reproductive success, which may represent a threat to sea turtle conservation.
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17
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Arantes LS, Vilaça ST, Mazzoni CJ, Santos FR. New Genetic Insights About Hybridization and Population Structure of Hawksbill and Loggerhead Turtles From Brazil. J Hered 2020; 111:444-456. [DOI: 10.1093/jhered/esaa024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/23/2020] [Indexed: 12/11/2022] Open
Abstract
Abstract
An extremely high incidence of hybridization among sea turtles is found along the Brazilian coast. This atypical phenomenon and its impact on sea turtle conservation can be elucidated through research focused on the evolutionary history of sea turtles. We assessed high-quality multilocus haplotypes of 143 samples of the 5 species of sea turtles that occur along the Brazilian coast to investigate the hybridization process and the population structure of hawksbill (Eretmochelys imbricata) and loggerhead turtles (Caretta caretta). The multilocus data were initially used to characterize interspecific hybrids. Introgression (F2 hybrids) was only confirmed in hatchlings of F1 hybrid females (hawksbill × loggerhead), indicating that introgression was either previously overestimated and F2 hybrids may not survive to adulthood, or the first-generation hybrid females nesting in Brazil were born as recent as few decades ago. Phylogenetic analyses using nuclear markers recovered the mtDNA-based Indo-Pacific and Atlantic lineages for hawksbill turtles, demonstrating a deep genetic divergence dating from the early Pliocene. In addition, loggerhead turtles that share a common feeding area and belong to distinct Indo-Pacific and Atlantic mtDNA clades present no clear genetic differentiation at the nuclear level. Finally, our results indicate that hawksbill and loggerhead rookeries along the Brazilian coast are likely connected by male-mediated gene flow.
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Affiliation(s)
- Larissa S Arantes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Avenida Antônio Carlos, Belo Horizonte - MG, Brazil
| | - Sibelle T Vilaça
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 6–8, Berlin, Germany (Vilaça and Mazzoni)
- Evolutionary Genetics Department, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, Berlin, Germany
| | - Camila J Mazzoni
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 6–8, Berlin, Germany (Vilaça and Mazzoni)
- Evolutionary Genetics Department, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, Berlin, Germany
| | - Fabrício R Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Avenida Antônio Carlos, Belo Horizonte - MG, Brazil
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18
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Lehnert SJ, Baillie SM, MacMillan J, Paterson IG, Buhariwalla CF, Bradbury IR, Bentzen P. Multiple decades of stocking has resulted in limited hatchery introgression in wild brook trout ( Salvelinus fontinalis) populations of Nova Scotia. Evol Appl 2020; 13:1069-1089. [PMID: 32431753 PMCID: PMC7232767 DOI: 10.1111/eva.12923] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 12/06/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
Many populations of freshwater fishes are threatened with losses, and increasingly, the release of hatchery individuals is one strategy being implemented to support wild populations. However, stocking of hatchery individuals may pose long-term threats to wild populations, particularly if genetic interactions occur between wild and hatchery individuals. One highly prized sport fish that has been heavily stocked throughout its range is the brook trout (Salvelinus fontinalis). In Nova Scotia, Canada, hatchery brook trout have been stocked since the early 1900s, and despite continued stocking efforts, populations have suffered declines in recent decades. Before this study, the genetic structure of brook trout populations in the province was unknown; however, given the potential negative consequences associated with hatchery stocking, it is possible that hatchery programs have adversely affected the genetic integrity of wild populations. To assess the influence of hatchery supplementation on wild populations, we genotyped wild brook trout from 12 river systems and hatchery brook trout from two major hatcheries using 100 microsatellite loci. Genetic analyses of wild trout revealed extensive population genetic structure among and within river systems and significant isolation-by-distance. Hatchery stocks were genetically distinct from wild populations, and most populations showed limited to no evidence of hatchery introgression (<5% hatchery ancestry). Only a single location had a substantial number of hatchery-derived trout and was located in the only river where a local strain is used for supplementation. The amount of hatchery stocking within a watershed did not influence the level of hatchery introgression. Neutral genetic structure of wild populations was influenced by geography with some influence of climate and stocking indices. Overall, our study suggests that long-term stocking has not significantly affected the genetic integrity of wild trout populations, highlighting the variable outcomes of stocking and the need to evaluate the consequences on a case-by-case basis.
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Affiliation(s)
- Sarah J. Lehnert
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Shauna M. Baillie
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
| | - John MacMillan
- Inland Fisheries DivisionNova Scotia Department of Fisheries and AquaculturePictouNSCanada
| | - Ian G. Paterson
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
| | - Colin F. Buhariwalla
- Inland Fisheries DivisionNova Scotia Department of Fisheries and AquaculturePictouNSCanada
| | - Ian R. Bradbury
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
| | - Paul Bentzen
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
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19
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Caniglia R, Galaverni M, Velli E, Mattucci F, Canu A, Apollonio M, Mucci N, Scandura M, Fabbri E. A standardized approach to empirically define reliable assignment thresholds and appropriate management categories in deeply introgressed populations. Sci Rep 2020; 10:2862. [PMID: 32071323 PMCID: PMC7028925 DOI: 10.1038/s41598-020-59521-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/28/2020] [Indexed: 11/09/2022] Open
Abstract
Anthropogenic hybridization is recognized as a major threat to the long-term survival of natural populations. While identifying F1 hybrids might be simple, the detection of older admixed individuals is far from trivial and it is still debated whether they should be targets of management. Examples of anthropogenic hybridization have been described between wolves and domestic dogs, with numerous cases detected in the Italian wolf population. After selecting appropriate wild and domestic reference populations, we used empirical and simulated 39-autosomal microsatellite genotypes, Bayesian assignment and performance analyses to develop a workflow to detect different levels of wolf x dog admixture. Membership proportions to the wild cluster (qiw) and performance indexes identified two q-thresholds which allowed to efficiently classify the analysed genotypes into three assignment classes: pure (with no or negligible domestic ancestry), older admixed (with a marginal domestic ancestry) and recent admixed (with a clearly detectable domestic ancestry) animals. Based on their potential to spread domestic variants, such classes were used to define three corresponding management categories: operational pure, introgressed and operational hybrid individuals. Our multiple-criteria approach can help wildlife managers and decision makers in more efficiently targeting the available resources for the long-term conservation of species threatened by anthropogenic hybridization.
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Affiliation(s)
- Romolo Caniglia
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy.
| | | | - Edoardo Velli
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Federica Mattucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Antonio Canu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Marco Apollonio
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Massimo Scandura
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Elena Fabbri
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
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20
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Ebersbach J, Posso-Terranova A, Bogdanowicz S, Gómez-Díaz M, García-González MX, Bolívar-García W, Andrés J. Complex patterns of differentiation and gene flow underly the divergence of aposematic phenotypes in Oophaga poison frogs. Mol Ecol 2020; 29:1944-1956. [PMID: 31971303 DOI: 10.1111/mec.15360] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/11/2019] [Accepted: 01/04/2020] [Indexed: 12/16/2022]
Abstract
Hybridization and introgression can have complex consequences for both species evolution and conservation. Here, we investigated the origin and characteristics of a putative hybrid zone between two South American poison dart frog species, Oophaga anchicayensis and the critically endangered Oophaga lehmanni, which are heavily sought after on the illegal pet market. Using a combination of phenotypic (49 traits) and genomic (ddRADseq) data, we found that the putative hybrids are morphologically distinct from their parental species and confirmed genomic signatures of admixture in these populations. Several lines of evidence (hybrid indices, interspecific hybrid heterozygosity, genomic clines, comparisons with simulated hybrids and demographic modelling) support the conclusion that these populations are not comprised of early-generation hybrids and thus, they probably did not arise as a result of illegal translocations associated with wildlife trafficking. Instead, they probably represent an independent lineage which has persisted through isolation and has only relatively recently re-established gene flow with both parental species. Furthermore, we detected signals of differential introgression from parental species into these hybrid populations which suggest relaxed stabilizing selection on these aposematic colour morphs, potentially via context-dependent female choice. These populations thus provide a fascinating window into the role of hybridization, isolation and female choice in the diversification of South American poison dart frogs. In addition, our results underline the importance of landscape conservation measures to protect, not only known localities of nominal species, but also the phenotypic and genomic variation harbored by admixed lineages which represent crucial repositories for the impressive diversity in this system.
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Affiliation(s)
- Jana Ebersbach
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Andrés Posso-Terranova
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia sede Palmira, Palmira, Colombia
| | - Steven Bogdanowicz
- Department of Ecology and Evolution, Cornell University, Ithaca, NY, USA
| | - Mónica Gómez-Díaz
- Research Group in Animal Ecology, Department of Biology, Universidad del Valle, Cali, Colombia
| | | | - Wilmar Bolívar-García
- Research Group in Animal Ecology, Department of Biology, Universidad del Valle, Cali, Colombia
| | - José Andrés
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Department of Ecology and Evolution, Cornell University, Ithaca, NY, USA
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21
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Chafin TK, Douglas MR, Martin BT, Douglas ME. Hybridization drives genetic erosion in sympatric desert fishes of western North America. Heredity (Edinb) 2019; 123:759-773. [PMID: 31431737 PMCID: PMC6834602 DOI: 10.1038/s41437-019-0259-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 01/26/2023] Open
Abstract
Many species have evolved or currently coexist in sympatry due to differential adaptation in a heterogeneous environment. However, anthropogenic habitat modifications can either disrupt reproductive barriers or obscure environmental conditions which underlie fitness gradients. In this study, we evaluated the potential for an anthropogenically-mediated shift in reproductive boundaries that separate two historically sympatric fish species (Gila cypha and G. robusta) endemic to the Colorado River Basin using ddRAD sequencing of 368 individuals. We first examined the integrity of reproductive isolation while in sympatry and allopatry, then characterized hybrid ancestries using genealogical assignment tests. We tested for localized erosion of reproductive isolation by comparing site-wise genomic clines against global patterns and identified a breakdown in the drainage-wide pattern of selection against interspecific heterozygotes. This, in turn, allowed for the formation of a hybrid swarm in one tributary, and asymmetric introgression where species co-occur. We also detected a weak but significant relationship between genetic purity and degree of consumptive water removal, suggesting a role for anthropogenic habitat modifications in undermining species boundaries or expanding historically limited introgression. In addition, results from basin-wide genomic clines suggested that hybrids and parental forms are adaptively nonequivalent. If so, then a failure to manage for hybridization will exacerbate the long-term extinction risk in parental populations. These results reinforce the role of anthropogenic habitat modification in promoting interspecific introgression in sympatric species by relaxing divergent selection. This, in turn, underscores a broader role for hybridization in decreasing global biodiversity within rapidly deteriorating environments.
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Affiliation(s)
- Tyler K Chafin
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Marlis R Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Bradley T Martin
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Michael E Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
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22
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Žužul I, Šegvić-Bubić T, Talijančić I, Džoić T, Lepen Pleić I, Beg Paklar G, Ivatek-Šahdan S, Katavić I, Grubišić L. Spatial connectivity pattern of expanding gilthead seabream populations and its interactions with aquaculture sites: a combined population genetic and physical modelling approach. Sci Rep 2019; 9:14718. [PMID: 31604982 PMCID: PMC6788985 DOI: 10.1038/s41598-019-51256-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/28/2019] [Indexed: 11/24/2022] Open
Abstract
In gilthead seabream the number of domesticated individuals increased annually, and escape events occur regularly in the Adriatic Sea. Still there is a lack of population genetic characteristics and evidence of the extent and geographic scale of interbreeding resulting from fish-farm escapees. We screened 1586 individuals using a panel of 21 neutral microsatellite loci in several consecutive years and here report on the medium-scale detection of hybrid and farmed seabream in the natural environment. Wild adults showed a lack of genetic structure within basin and sampling years and reduced connectivity with wild offspring collection, suggesting their temporal residency within the Adriatic. On the contrary, by linking the results of multiannual genetic analyses with the results of coupled hydrodynamic and individual based models (IBM-Ichthyop), we observed a strong connection of wild seabream associated with tuna-aquaculture sites and offspring from the nursery grounds, indicating that the surroundings of tuna sea-cage farms can function as a spawning grounds. The study results present the genetic baseline of wild and farmed strains from the eastern Adriatic Sea, as a first step toward development of a mitigation strategy for fish escapees aimed at controlling further erosion of genetic integrity.
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Affiliation(s)
- Iva Žužul
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
| | - Tanja Šegvić-Bubić
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia.
| | - Igor Talijančić
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
| | - Tomislav Džoić
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
| | - Ivana Lepen Pleić
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
| | - Gordana Beg Paklar
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
| | | | - Ivan Katavić
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
| | - Leon Grubišić
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
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23
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Lachmuth S, Molofsky J, Milbrath L, Suda J, Keller SR. Associations between genomic ancestry, genome size and capitula morphology in the invasive meadow knapweed hybrid complex ( Centaurea × moncktonii) in eastern North America. AOB PLANTS 2019; 11:plz055. [PMID: 31632628 PMCID: PMC6790064 DOI: 10.1093/aobpla/plz055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
Plant invasions are prime opportunities for studying hybridization and the nature of species boundaries, but hybrids also complicate the taxonomic treatment and management of introduced taxa. In this study, we use population genomics to estimate the extent of genomic admixture and test for its association with morphology and genome size in a hybrid complex of knapweeds invasive to North America: meadow knapweed (Centaurea × moncktonii) and its parental species (C. jacea and C. nigra). We sampled 20 populations from New York and Vermont, USA, and used genotyping by sequencing to identify single nucleotide polymorphisms in order to estimate genome-wide ancestry and classify individuals into hybrid genotype classes. We then tested for association between degree of genomic introgression and variation in a subset of traits diagnostic for the parental taxa, namely capitula morphology and monoploid genome size. Genomic clustering revealed two clearly defined lineages, as well as many admixed individuals forming a continuous gradation of introgression. Individual assignments to hybrid genotype classes revealed many advanced generation intercrosses and backcrosses, suggesting introgression has been extensive and unimpeded by strong reproductive barriers between taxa. Variation in capitula traits between the two unadmixed, presumed parental, lineages exhibited continuous, and in some cases transgressive, segregation among introgressed hybrids. Genome size was also divergent between lineages, although advanced generation hybrids had smaller genomes relative to additive expectations. Our study demonstrates deep introgression between the porous genomes of a hybrid invasive species complex. In addition to strong associations among genomic ancestry, genome size and morphology, hybrids expressed more extreme phenotypic values for capitula traits and genome size, indicating transgressive segregation, as well as a bias towards smaller genomes, possibly due to genomic downsizing. Future studies will apply these results to experimentally test how introgression, transgressive segregation and genome size reduction interact to confer invasiveness.
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Affiliation(s)
- Susanne Lachmuth
- University of Vermont, Department of Plant Biology, Burlington, VT, USA
- Martin Luther University Halle Wittenberg, Institute of Biology, Geobotany & Botanical Garden, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jane Molofsky
- University of Vermont, Department of Plant Biology, Burlington, VT, USA
| | - Lindsey Milbrath
- United Sates Department of Agriculture, Agricultural Research Service (USDA-ARS), Ithaca, NY, USA
| | - Jan Suda
- Charles University Prague, Department of Botany, Prague, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Stephen R Keller
- University of Vermont, Department of Plant Biology, Burlington, VT, USA
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24
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Sylvester EVA, Wringe BF, Duffy SJ, Hamilton LC, Fleming IA, Castellani M, Bentzen P, Bradbury IR. Estimating the relative fitness of escaped farmed salmon offspring in the wild and modelling the consequences of invasion for wild populations. Evol Appl 2019; 12:705-717. [PMID: 30976304 PMCID: PMC6439497 DOI: 10.1111/eva.12746] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 12/25/2022] Open
Abstract
Throughout their native range, wild Atlantic salmon populations are threatened by hybridization and introgression with escapees from net-pen salmon aquaculture. Although domestic-wild hybrid offspring have shown reduced fitness in laboratory and field experiments, consequential impacts on population abundance and genetic integrity remain difficult to predict in the field, in part because the strength of selection against domestic offspring is often unknown and context-dependent. Here, we follow a single large escape event of farmed Atlantic salmon in southern Newfoundland and monitor changes in the in-river proportions of hybrids and feral individuals over time using genetically based hybrid identification. Over a three-year period following the escape, the overall proportion of wild parr increased consistently (total wild proportion of 71.6%, 75.1% and 87.5% each year, respectively), with subsequent declines in feral (genetically pure farmed individuals originating from escaped, farmed adults) and hybrid parr. We quantify the strength of selection against parr of aquaculture ancestry and explore the genetic and demographic consequences for populations in the region. Within-cohort changes in the relative proportions of feral and F1 parr suggest reduced relative survival compared to wild individuals over the first (0.15 and 0.81 for feral and F1, respectively) and second years of life (0.26, 0.83). These relative survivorship estimates were used to inform an individual-based salmon eco-genetic model to project changes in adult abundance and overall allele frequency across three invasion scenarios ranging from short-term to long-term invasion and three relative survival scenarios. Modelling results indicate that total population abundance and time to recovery were greatly affected by relative survivorship and predict significant declines in wild population abundance under continued large escape events and calculated survivorship. Overall, this work demonstrates the importance of estimating the strength of selection against domestic offspring in the wild to predict the long-term impact of farmed salmon escape events on wild populations.
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Affiliation(s)
- Emma V. A. Sylvester
- Science Branch, Fisheries and Oceans CanadaSt. John’sNewfoundland and LabradorCanada
| | - Brendan F. Wringe
- Science Branch, Department of Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Steven J. Duffy
- Science Branch, Fisheries and Oceans CanadaSt. John’sNewfoundland and LabradorCanada
| | - Lorraine C. Hamilton
- Aquatic Biotechnology Laboratory, Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Ian A. Fleming
- Memorial University of NewfoundlandDepartment of Ocean SciencesSt. John’sNewfoundland and LabradorCanada
| | - Marco Castellani
- Department of Mechanical EngineeringUniversity of BirminghamBirminghamUK
| | - Paul Bentzen
- Marine Gene Probe Laboratory, Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Ian R. Bradbury
- Science Branch, Fisheries and Oceans CanadaSt. John’sNewfoundland and LabradorCanada
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Knief U, Bossu CM, Saino N, Hansson B, Poelstra J, Vijay N, Weissensteiner M, Wolf JBW. Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone. Nat Ecol Evol 2019; 3:570-576. [PMID: 30911146 PMCID: PMC6445362 DOI: 10.1038/s41559-019-0847-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/18/2019] [Indexed: 12/22/2022]
Abstract
The evolution of genetic barriers opposing inter-specific gene flow is key to the origin of new species. Drawing from information of over 400 admixed genomes sourced from replicate transects across the European hybrid zone between all-black carrion crows and grey-coated hooded crows, we decipher the interplay between phenotypic divergence and selection at the molecular level. Over 68% of plumage variation was explained by epistasis between the gene NDP and a ~2.8 Mb region on chromosome 18 with suppressed recombination. Both pigmentation loci showed evidence for divergent selection resisting introgression. This study reveals how few, large-effect loci can govern prezygotic isolation and shield phenotypic divergence from gene flow.
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Affiliation(s)
- Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany
| | - Christen M Bossu
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Institute of the Environment and Sustainability, Center for Tropical Research, University of California, Los Angeles, CA, USA
| | - Nicola Saino
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - Jelmer Poelstra
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Biology Department, Duke University, Durham, NC, USA
| | - Nagarjun Vijay
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Matthias Weissensteiner
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany.,Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany. .,Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.
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Development of a Novel Mule Deer Genomic Assembly and Species-Diagnostic SNP Panel for Assessing Introgression in Mule Deer, White-Tailed Deer, and Their Interspecific Hybrids. G3-GENES GENOMES GENETICS 2019; 9:911-919. [PMID: 30670611 PMCID: PMC6404596 DOI: 10.1534/g3.118.200838] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mule deer (Odocoileus hemionus) are endemic to a wide variety of habitats in western North America, many of which are shared in sympatry with their closely related sister-species white-tailed deer (Odocoileus virginianus), whom they hybridize with in wild populations. Although mule deer meet many ideal conditions for a molecular ecological research species, such as high abundance, ecological importance, and broad dispersal and gene flow, conservation genetic studies have been limited by a relative lack of existing genomic resources and inherent difficulties caused by introgression with white-tailed deer. Many molecular tools currently available for the study of cervids were designed using reference assemblies of divergent model species, specifically cattle (Bos taurus). Bovidae and Cervidae diverged approximately 28 million years ago, therefore, we sought to ameliorate the available resources by contributing the first mule deer whole genome sequence draft assembly with an average genome-wide read depth of 25X, using the white-tailed genome assembly (Ovir.te_1.0) as a reference. Comparing the two assemblies, we identified ∼33 million single nucleotide polymorphisms (SNPs) and insertion/deletion variants. We then verified fixed SNP differences between the two species and developed a 40-loci SNP assay capable of identifying pure mule deer, white-tailed deer, and interspecific hybrids. Assignment capacity of the panel, which was tested on simulated datasets, is reliable up to and including the third backcross hybrid generation. Identification of post-F1 hybrids will be necessary for hybrid zone population studies going forward, and the new mule deer assembly will be a valuable resource for genetic and comparative genomics studies.
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Lehnert SJ, DiBacco C, Jeffery NW, Blakeslee AMH, Isaksson J, Roman J, Wringe BF, Stanley RRE, Matheson K, McKenzie CH, Hamilton LC, Bradbury IR. Temporal dynamics of genetic clines of invasive European green crab ( Carcinus maenas) in eastern North America. Evol Appl 2018; 11:1656-1670. [PMID: 30344634 PMCID: PMC6183463 DOI: 10.1111/eva.12657] [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] [Received: 09/28/2017] [Revised: 05/28/2018] [Accepted: 06/03/2018] [Indexed: 12/12/2022] Open
Abstract
Two genetically distinct lineages of European green crabs (Carcinus maenas) were independently introduced to eastern North America, the first in the early 19th century and the second in the late 20th century. These lineages first came into secondary contact in southeastern Nova Scotia, Canada (NS), where they hybridized, producing latitudinal genetic clines. Previous studies have documented a persistent southward shift in the clines of different marker types, consistent with existing dispersal and recruitment pathways. We evaluated current clinal structure by quantifying the distribution of lineages and fine-scale hybridization patterns across the eastern North American range (25 locations, ~39 to 49°N) using informative single nucleotide polymorphisms (SNPs; n = 96). In addition, temporal changes in the genetic clines were evaluated using mitochondrial DNA and microsatellite loci (n = 9-11) over a 15-year period (2000-2015). Clinal structure was consistent with prior work demonstrating the existence of both northern and southern lineages with a hybrid zone occurring between southern New Brunswick (NB) and southern NS. Extensive later generation hybrids were detected in this region and in southeastern Newfoundland. Temporal genetic analysis confirmed the southward progression of clines over time; however, the rate of this progression was slower than predicted by forecasting models, and current clines for all marker types deviated significantly from these predictions. Our results suggest that neutral and selective processes contribute to cline dynamics, and ultimately, highlight how selection, hybridization, and dispersal can collectively influence invasion success.
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Affiliation(s)
- Sarah J. Lehnert
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundlandCanada
| | - Claudio DiBacco
- Bedford Institute of OceanographyFisheries and Oceans CanadaDartmouthNova ScotiaCanada
| | - Nicholas W. Jeffery
- Bedford Institute of OceanographyFisheries and Oceans CanadaDartmouthNova ScotiaCanada
| | | | - Jonatan Isaksson
- Gund Institute for EnvironmentUniversity of VermontBurlingtonVermont
| | - Joe Roman
- Gund Institute for EnvironmentUniversity of VermontBurlingtonVermont
| | - Brendan F. Wringe
- Bedford Institute of OceanographyFisheries and Oceans CanadaDartmouthNova ScotiaCanada
| | - Ryan R. E. Stanley
- Bedford Institute of OceanographyFisheries and Oceans CanadaDartmouthNova ScotiaCanada
| | - Kyle Matheson
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundlandCanada
| | - Cynthia H. McKenzie
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundlandCanada
| | - Lorraine C. Hamilton
- Aquatic Biotechnology LaboratoryBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Ian R. Bradbury
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundlandCanada
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Wringe BF, Jeffery NW, Stanley RRE, Hamilton LC, Anderson EC, Fleming IA, Grant C, Dempson JB, Veinott G, Duffy SJ, Bradbury IR. Extensive hybridization following a large escape of domesticated Atlantic salmon in the Northwest Atlantic. Commun Biol 2018; 1:108. [PMID: 30271988 PMCID: PMC6123692 DOI: 10.1038/s42003-018-0112-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 07/16/2018] [Indexed: 11/09/2022] Open
Abstract
Domestication is rife with episodes of interbreeding between cultured and wild populations, potentially challenging adaptive variation in the wild. In Atlantic salmon, Salmo salar, the number of domesticated individuals far exceeds wild individuals, and escape events occur regularly, yet evidence of the magnitude and geographic scale of interbreeding resulting from individual escape events is lacking. We screened juvenile Atlantic salmon using 95 single nucleotide polymorphisms following a single, large aquaculture escape in the Northwest Atlantic and report the landscape-scale detection of hybrid and feral salmon (27.1%, 17/18 rivers). Hybrids were reproductively viable, and observed at higher frequency in smaller wild populations. Repeated annual sampling of this cohort revealed decreases in the presence of hybrid and feral offspring over time. These results link previous observations of escaped salmon in rivers with reports of population genetic change, and demonstrate the potential negative consequences of escapes from net-pen aquaculture on wild populations.
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Affiliation(s)
- Brendan F Wringe
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, A1C 5S7, Canada
| | - Nicholas W Jeffery
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
- Faculty of Computer Science, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Ryan R E Stanley
- Science Branch, Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, B2Y 4A2, Canada
| | - Lorraine C Hamilton
- Aquatic Biotechnology Laboratory, Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, B2Y 4A2, Canada
| | - Eric C Anderson
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, CA, 95060, USA
| | - Ian A Fleming
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, A1C 5S7, Canada
| | - Carole Grant
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
| | - J Brian Dempson
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
| | - Geoff Veinott
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
| | - Steven J Duffy
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
| | - Ian R Bradbury
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada.
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, A1C 5S7, Canada.
- Faculty of Computer Science, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
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Faust E, Halvorsen KT, Andersen P, Knutsen H, André C. Cleaner fish escape salmon farms and hybridize with local wrasse populations. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171752. [PMID: 29657779 PMCID: PMC5882703 DOI: 10.1098/rsos.171752] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
The genetic impact of farmed fish escaping aquaculture is a highly debated issue. However, non-target species, such as cleaner fish used to remove sea lice from farmed fish, are rarely considered. Here, we report that wild corkwing wrasse (Symphodus melops), which are transported long distances to be used as cleaner fish in salmon farms, escape and hybridize with local populations. Recently, increasing numbers of corkwing wrasse have been reported in Flatanger in Norway, north of its described distribution range, an area heavily relying on the import of cleaner fish from Skagerrak. Using genetic markers identified with 2bRAD sequencing, we show that, although the Flatanger population largely is a result of a northward range expansion, there is also evidence of considerable gene flow from southern populations in Skagerrak and Kattegat. Of the 40 corkwing wrasses sampled in Flatanger, we discovered two individuals with clear southern genotypes, one first-generation hybrid, and 12 potential second-generation hybrids. In summary, we provide evidence that corkwing wrasse escape from fish farms and hybridize with local populations at the leading edge of an ongoing range expansion. Although the magnitude and significance of escapees warrant further investigation, these results should be taken into consideration in the use of translocated cleaner fish.
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Affiliation(s)
- Ellika Faust
- Department of Marine Sciences - Tjärnö, University of Gothenburg, 45296 Strömstad, Sweden
| | | | - Per Andersen
- Marine senior advisor Nord-Trøndelag, 7770 Flatanger, Norway
| | - Halvor Knutsen
- Institute of Marine Research, Flødevigen, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö, University of Gothenburg, 45296 Strömstad, Sweden
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