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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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2
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Geraerts M, Vangestel C, Artois T, Fernandes JMDO, Jorissen MWP, Chocha Manda A, Danadu Mizani C, Smeets K, Snoeks J, Sonet G, Tingbao Y, Van Steenberge M, Vreven E, Lunkayilakio Wamuini S, Vanhove MPM, Huyse T. Population genomics of introduced Nile tilapia Oreochromis niloticus (Linnaeus, 1758) in the Democratic Republic of the Congo: Repeated introductions since colonial times with multiple sources. Mol Ecol 2022; 31:3304-3322. [PMID: 35460297 DOI: 10.1111/mec.16479] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
During colonial times, Nile tilapia Oreochromis niloticus (Linnaeus, 1758) was introduced into non-native parts of the Congo Basin (Democratic Republic of the Congo, DRC) for the first time. Currently, it is the most farmed cichlid in the DRC, and is present throughout the Congo Basin. Although Nile tilapia has been reported as an invasive species, documentation of historical introductions into this basin and its consequences are scant. Here, we study the genetic consequences of these introductions by genotyping 213 Nile tilapia from native and introduced regions, focusing on the Congo Basin. Additionally, 48 specimens from 16 other tilapia species were included to test for hybridization. Using RAD sequencing (27,611 single nucleotide polymorphisms), we discovered genetic admixture with other tilapia species in several morphologically identified Nile tilapia from the Congo Basin, reflecting their ability to interbreed and the potential threat they pose to the genetic integrity of native tilapias. Nile tilapia populations from the Upper Congo and those from the Middle-Lower Congo are strongly differentiated. The former show genetic similarity to Nile tilapia from the White Nile, while specimens from the Benue Basin and Lake Kariba are similar to Nile tilapia from the Middle-Lower Congo, suggesting independent introductions using different sources. We conclude that the presence of Nile tilapia in the Congo Basin results from independent introductions, reflecting the dynamic aquaculture history, and that their introduction probably leads to genetic interactions with native tilapias, which could lower their fitness. We therefore urge avoiding further introductions of Nile tilapia in non-native regions and to use native tilapias in future aquaculture efforts.
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Affiliation(s)
- Mare Geraerts
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Carl Vangestel
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Terrestrial Ecology Unit, Ghent University, Ghent, Belgium
| | - Tom Artois
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | | | - Michiel W P Jorissen
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Auguste Chocha Manda
- Unité de recherche en Biodiversité et Exploitation durable des Zones Humides (BEZHU), Faculté des Sciences Agronomiques, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Célestin Danadu Mizani
- Département d'Ecologie et Biodiversité des Ressources Aquatique, Centre de Surveillance de la Biodiversité (CSB), Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Karen Smeets
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Jos Snoeks
- Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Gontran Sonet
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Yang Tingbao
- Institute of Aquatic Economic Animals and Key Laboratory for Improved Variety Reproduction of Aquatic Economic Animals, Zhongshan University, Ghangzhou, China
| | - Maarten Van Steenberge
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Emmanuel Vreven
- Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Soleil Lunkayilakio Wamuini
- Département de Biologie, I.S.P. Mbanza-Ngungu, Mbanza-Ngungu, Democratic Republic of the Congo.,Functional and Evolutionary Morphology Laboratory, University of Liège, Liège, Belgium
| | - Maarten P M Vanhove
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tine Huyse
- Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
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3
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Ottenburghs J. The genic view of hybridization in the Anthropocene. Evol Appl 2021; 14:2342-2360. [PMID: 34745330 PMCID: PMC8549621 DOI: 10.1111/eva.13223] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/24/2022] Open
Abstract
Human impact is noticeable around the globe, indicating that a new era might have begun: the Anthropocene. Continuing human activities, including land-use changes, introduction of non-native species and rapid climate change, are altering the distributions of countless species, often giving rise to human-mediated hybridization events. While the interbreeding of different populations or species can have detrimental effects, such as genetic extinction, it can be beneficial in terms of adaptive introgression or an increase in genetic diversity. In this paper, I first review the different mechanisms and outcomes of anthropogenic hybridization based on literature from the last five years (2016-2020). The most common mechanisms leading to the interbreeding of previously isolated taxa include habitat change (51% of the studies) and introduction of non-native species (34% intentional and 19% unintentional). These human-induced hybridization events most often result in introgression (80%). The high incidence of genetic exchange between the hybridizing taxa indicates that the application of a genic view of speciation (and introgression) can provide crucial insights on how to address hybridization events in the Anthropocene. This perspective considers the genome as a dynamic collection of genetic loci with distinct evolutionary histories, giving rise to a heterogenous genomic landscape in terms of genetic differentiation and introgression. First, understanding this genomic landscape can lead to a better selection of diagnostic genetic markers to characterize hybrid populations. Second, describing how introgression patterns vary across the genome can help to predict the likelihood of negative processes, such as demographic and genetic swamping, as well as positive outcomes, such as adaptive introgression. It is especially important to not only quantify how much genetic material introgressed, but also what has been exchanged. Third, comparing introgression patterns in pre-Anthropocene hybridization events with current human-induced cases might provide novel insights into the likelihood of genetic swamping or species collapse during an anthropogenic hybridization event. However, this comparative approach remains to be tested before it can be applied in practice. Finally, the genic view of introgression can be combined with conservation genomic studies to determine the legal status of hybrids and take appropriate measures to manage anthropogenic hybridization events. The interplay between evolutionary and conservation genomics will result in the constant exchange of ideas between these fields which will not only improve our knowledge on the origin of species, but also how to conserve and protect them.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and ConservationWageningen University & ResearchWageningenThe Netherlands
- Forest Ecology and Forest ManagementWageningen University & ResearchWageningenThe Netherlands
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Muniz AC, Lemos-Filho JP, Souza HA, Marinho RC, Buzatti RS, Heuertz M, Lovato MB. The protected tree Dimorphandra wilsonii (Fabaceae) is a population of inter-specific hybrids: recommendations for conservation in the Brazilian Cerrado/Atlantic Forest ecotone. ANNALS OF BOTANY 2020; 126:191-203. [PMID: 32277237 PMCID: PMC7304468 DOI: 10.1093/aob/mcaa066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 04/09/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUNDS AND AIMS Dimorphandra wilsonii Rizzini, a critically endangered and protected tree, has a restricted distribution in the ecotone between the Cerrado and the Atlantic Forest in south-eastern Brazil. In this area, it co-occurs with D. mollis Benth., a common tree from the Cerrado, and D. exaltata Schott., a rare tree from the Atlantic Forest. Previous studies of D. wilsonii indicated heterozygosity excess at the individual level. Field observation of some intermediate phenotypes between D. wilsonii and both congeners suggests hybridization of D. wilsonii with D. mollis and/or D. exaltata. Here, we tested the hypothesis that D. wilsonii may have originated from hybridization between D. exaltata and D. mollis. We also performed cytogenetic analysis to examine if the heterozygosity excess could be explained by polyploidy in D. wilsonii. METHODS We evaluated the genetic diversity and population structure of D. wilsonii using 11 nuclear simple sequence repeats (SSRs) genotyped in 152 individuals sampled across the taxon's range. We performed comparative genetic analyses using overlapping SSR markers between D. wilsonii and previously published SSR data in D. mollis and D. exaltata to subsequently perform a series of allelic comparisons, multivariate and Bayesian analysis. KEY RESULTS Our results suggest that D. wilsonii individuals are most likely to correspond to F1 hybrids between D. exaltata and D. mollis. Cytogenetic analysis indicated that D. wilsonii is diploid with the same chromosome number as D. mollis (2n = 2x = 28). CONCLUSIONS Our study raises questions about the taxonomic status and the evolutionary future of D. wilsonii. We suggest that the conservation and management strategy for D. wilsonii should be revised and that it should take into account both parental Dimorphandra species in the ecotone, with special emphasis on the threatened D. exaltata. Finally, this study highlights the value of genetic information for the design of conservation strategies.
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Affiliation(s)
- André Carneiro Muniz
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP, Belo Horizonte, Brazil
| | - José Pires Lemos-Filho
- Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Helena Augusta Souza
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP, Belo Horizonte, Brazil
| | | | - Renata Santiago Buzatti
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP, Belo Horizonte, Brazil
| | | | - Maria Bernadete Lovato
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP, Belo Horizonte, Brazil
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5
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Oswald KJ, Spinks E, Duktig GS, Baker JS, Kibbey MR, Zimmerman B, Tucker H, Boucher CE, Cincotta DA, Starnes WC, Kiss AJ, Wright JJ, Carlson DM, Bangs MR, Roberts MA, Quattro JM. Drainage History, Evolution, and Conservation of Tonguetied Minnow (Exoglossum laurae), a Rare and Imperiled Teays River Endemic. COPEIA 2020. [DOI: 10.1643/ci-18-118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Kenneth J. Oswald
- Ohio Northern University, Department of Biological and Allied Health Sciences, 525 South Main Street, Ada, Ohio 45810; (KJO) . Send reprint requests to KJO
| | - Emily Spinks
- Northern Kentucky University, Honors Program, Nunn Drive, Highland Heights, Kentucky 41099
| | - Garrett S. Duktig
- Ohio Northern University, Department of Biological and Allied Health Sciences, 525 South Main Street, Ada, Ohio 45810; (KJO) . Send reprint requests to KJO
| | - Justin S. Baker
- Ohio State University, Museum of Biological Diversity, 1315 Kinnear Road, Columbus, Ohio 43212
| | - Marc R. Kibbey
- Ohio State University, Museum of Biological Diversity, 1315 Kinnear Road, Columbus, Ohio 43212
| | - Brian Zimmerman
- Ohio State University, Museum of Biological Diversity, 1315 Kinnear Road, Columbus, Ohio 43212
| | - Holly Tucker
- Ohio Environmental Protection Agency, Division of Surface Water, 50 West Town Street, Columbus, Ohio 43215
| | - Charles E. Boucher
- Ohio Environmental Protection Agency, Division of Surface Water, 50 West Town Street, Columbus, Ohio 43215
| | - Daniel A. Cincotta
- West Virginia Division of Natural Resources, Wildlife Diversity Unit, Ward Road, Elkins, West Virginia 26241
| | - Wayne C. Starnes
- North Carolina Museum of Natural Sciences, Ichthyology Division, 11 West Jones Street, Raleigh, North Carolina 27601
| | - Andor J. Kiss
- Miami University, Department of Biological Sciences, 700 East High Street, Oxford, Ohio 45056
| | - Jeremy J. Wright
- New York State Museum, Division of Ichthyology, 222 Madison Avenue, Albany, New York 12230
| | - Douglas M. Carlson
- New York Department of Environmental Conservation, Bureau of Fisheries, 317 Washington Street, Watertown, New York 13601
| | - Max R. Bangs
- Auburn University, School of Fisheries and Allied Aquacultures, 203 Swingle Hall, Auburn, Alabama 36849
| | - Mark A. Roberts
- University of South Carolina, Department of Biological Sciences, 631 Sumter Street, Columbia, South Carolina 29208
| | - Joseph M. Quattro
- University of South Carolina, Department of Biological Sciences, 631 Sumter Street, Columbia, South Carolina 29208
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Harrington RC, Simmons JW, Near TJ. The Geographic Distribution of the Imperiled Barrens Darter, Etheostoma forbesi, and Threats of Hybridization with the Closely Related Fringed Darter, Etheostoma crossopterum. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2020. [DOI: 10.3374/014.061.0101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Thomas J. Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106; and Peabody Museum of Natural History, Yale University, New Haven, CT 06520-8118 USA
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