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Côte J, Poulet N, Blanc L, Grenouillet G. Disentangling the effects of different human disturbances on multifaceted biodiversity indices in freshwater fish. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2845. [PMID: 36922403 DOI: 10.1002/eap.2845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/29/2022] [Accepted: 12/15/2022] [Indexed: 06/02/2023]
Abstract
Evaluating the effects of anthropogenic pressures on several biodiversity metrics can inform the management and monitoring of biodiversity loss. However, the type of disturbances can lead to different responses in different metrics. In this study, we aimed at disentangling the effects of different types of anthropogenic disturbances on freshwater fish communities. We calculated diversity indices for 1109 stream fish communities across France by computing richness and evenness components for ecological, morphological, and phylogenetic diversity, and used null models to estimate standardized effect sizes. We used generalized linear mixed models to assess the relative effects of environmental and anthropogenic drivers in driving those diversity indices. Our results demonstrated that all diversity indices exhibited significant responses to both climatic conditions and anthropogenic disturbances. While we observed a decrease of ecological and phylogenetic richness with the intensity of disturbance, a weak increase in morphological richness and evenness was apparent. Overall, our results demonstrated the importance of disentangling various types of disturbances when assessing human-induced ecological impacts and highlighted that different facets of diversity are not impacted identically by anthropogenic disturbances in stream fish communities. This calls for further work seeking to integrate biodiversity responses to human disturbances into a multifaceted framework, and could have beneficial implications when planning conservation action in freshwater ecosystems.
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Affiliation(s)
- Jessica Côte
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, Université de Toulouse, CNRS, IRD, Université Toulouse III - Paul Sabatier, Toulouse, France
| | - Nicolas Poulet
- Pôle Ecohydraulique, Office Français de La Biodiversité, Institut des Mécaniques des Fluides, Toulouse, France
| | - Laurence Blanc
- Office français de la biodiversité, Direction régionale Occitanie, Toulouse, France
| | - Gaël Grenouillet
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, Université de Toulouse, CNRS, IRD, Université Toulouse III - Paul Sabatier, Toulouse, France
- Institut Universitaire de France, Paris, France
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2
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Strong bidirectional gene flow between fish lineages separated for over 100,000 years. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01476-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractRestoring levels of genetic diversity in small and declining populations is increasingly being considered in biodiversity conservation. Evidence-based genetic management requires assessment of risks and benefits of crossing populations. Because risks are challenging to assess experimentally, e.g. through multi-generational crosses, decision-support approaches utilize proxy risk factors such as time since separation of lineages. However, the paucity of empirical datasets on fitness consequences of longer separation times tends to favour crossing lineages with conservatively short separations, restricting wildlife managers’ options. Here, we assessed the genetic outcomes of interbreeding in the wild between lineages of a threatened Australian freshwater fish (Macquarie perch) separated by an estimated 119,000–385,000 years of evolution in distinct environments. Fish belonging to the Murray-Darling Basin (MDB) lineage escaped from Cataract Dam—into which they were translocated in ~ 1915—into the Cataract River, where they interbred with the local Hawkesbury-Nepean Basin (HNB) lineage. Analyses of reduced-representation genomic data revealed no evidence of genetic incompatibilities during interbreeding of the two lineages in the Cataract River: assignment to genotypic clusters indicated a spectrum of hybrid types including second generation hybrids and backcrosses to both parental lineages. Thus, no adverse effects were detected from genetic mixing of populations separated by > 100,000 years. We are not advocating purposely crossing the two lineages for management purposes under present cost–benefit considerations, because there are currently sufficient intra-lineage source populations to beneficially mix. Instead, this study presents a useful calibration point: two morphologically different lineages evolved in different habitats for 119,000–385,000 years can successfully interbreed.
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3
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Redak CA, Williams AS, Garner JT, Halanych KM, Whelan NV. Assessing genomic diversity, connectivity, and riverscape genetics hypotheses in the endangered Rough Hornsnail, Pleurocera foremani, following habitat disruption. J Hered 2021; 112:635-645. [PMID: 34673971 PMCID: PMC8683363 DOI: 10.1093/jhered/esab065] [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: 02/03/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
The southeastern United States is home to some of the richest biodiversity in the world. Over the last 200 years, however, rapid industrialization and urbanization have threatened many natural areas, including freshwater habitats. River impoundments have also rapidly altered freshwater habitats, often resulting in species extirpation or extinction. The Coosa River in Alabama experienced one of the largest faunal declines in modern history after impoundment, making it an ideal system for studying how invertebrate species are affected by reservoir creation. One such species, the Rough Hornsnail, Pleurocera foremani, is an endangered freshwater snail in the family Pleuroceridae. We sampled all known localities of P. foremani and used 2bRAD-seq to measure genetic diversity. We assessed riverscape genomic patterns across the current range of P. foremani and measured gene flow within and between impoundments. We also investigated the degree to which P. foremani displays an isolation by distance pattern and conforms to broad hypotheses that have been put forth for population genetics of riverine species like the Mighty Headwater Hypothesis that predicts greater genetic diversity in headwater reaches compared with mainstem populations. Like most other freshwater species, a pattern of isolation by distance was observed in P. foremani. We also found that Coosa River dams are a barrier to gene flow, and genetic fragmentation of P. foremani is likely to increase. However, gene flow appeared common within reservoirs and tributaries. Additionally, we found that spatial genetic structure of P. foremani deviates from what is expected under the Mighty Headwaters Hypothesis, adding to a growing body of research suggesting that the majority of genetic diversity in low-dispersing gastropods is found in mainstem populations.
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Affiliation(s)
- Caitlin A Redak
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Ashantye' S Williams
- Southeast Conservation Genetics Lab, Warm Springs Fish Technology Center, United States Fish and Wildlife Service, Auburn, AL, United States of America
| | - Jeffrey T Garner
- Alabama Department of Conservation and Natural Resources, Florence, AL, United States of America
| | - Kenneth M Halanych
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Nathan V Whelan
- Southeast Conservation Genetics Lab, Warm Springs Fish Technology Center, United States Fish and Wildlife Service, Auburn, AL, United States of America.,School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL, United States of America
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4
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Lutz ML, Tonkin Z, Yen JD, Johnson G, Ingram BA, Sharley J, Lyon J, Chapple DG, Sunnucks P, Pavlova A. Using multiple sources during reintroduction of a locally extinct population benefits survival and reproduction of an endangered freshwater fish. Evol Appl 2021; 14:950-964. [PMID: 33897813 PMCID: PMC8061264 DOI: 10.1111/eva.13173] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 11/26/2022] Open
Abstract
Through using different sources, population reintroductions can create genetically diverse populations at low risk of harmful inbreeding and well equipped for adaptation to future environments. Genetic variation from one source can mask locally nonoptimal alleles from another, thereby enhancing adaptive potential and population persistence. We assessed the outcomes in survival, growth and reproduction of using two differentiated sources (genetically diverse Yarra and moderately diverse Dartmouth) for translocations and stocking to reintroduce the endangered Australian freshwater Macquarie perch Macquaria australasica into the Ovens River. For stocking, same- and different-population parents ("cross-types") were used during hatchery production. Genetic samples and data on individual fish were collected over three years of monitoring the Ovens. We genetically assigned Ovens fish to their broodstock parents and tested whether cross-type and genetic dissimilarity between parents are associated with offspring survival, and whether cross-type and parental dissimilarity or individual genetic diversity are associated with somatic growth rates of stocked fish. We genetically identified translocated fish and assessed local recruit ancestry. Of 296 Ovens fish, 31.1% were inferred to be stocked, 1.3% translocated and 67.6% locally born. Cross-type strongly predicted survival of stocked offspring: those with two Yarra parents had the highest survival, followed by offspring with two-population, then Dartmouth, ancestry. Of the Ovens recruits, 59.5% had Yarra, 33.5% two-population and 7.0% Dartmouth ancestry, despite 67% of stocked and 98% of translocated fish originating from Dartmouth. Offspring with two Yarra parents grew faster than offspring of Dartmouth or two-population ancestry. Although Dartmouth fish appear to be less fit in the Ovens compared to Yarra fish, possibly due to deleterious variation or genetic or plastic maladaptation, they contribute to the reintroduced population through local interbreeding with Yarra fish and relatively high survival of stocked offspring of two-population ancestry. Thus, combining compatible stocks is likely to benefit restoration of other wildlife populations.
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Affiliation(s)
- Maiko L. Lutz
- School of Biological SciencesMonash UniversityClaytonVic.Australia
| | - Zeb Tonkin
- Arthur Rylah Institute for Environmental Research (ARI)HeidelbergVic.Australia
| | - Jian D.L. Yen
- Arthur Rylah Institute for Environmental Research (ARI)HeidelbergVic.Australia
- School of BioSciencesThe University of MelbourneParkvilleVic.Australia
| | - Glen Johnson
- Department of Environment, Land, Water and PlanningWodongaVic.Australia
| | | | - Joanne Sharley
- Arthur Rylah Institute for Environmental Research (ARI)HeidelbergVic.Australia
| | - Jarod Lyon
- Arthur Rylah Institute for Environmental Research (ARI)HeidelbergVic.Australia
| | - David G. Chapple
- School of Biological SciencesMonash UniversityClaytonVic.Australia
| | - Paul Sunnucks
- School of Biological SciencesMonash UniversityClaytonVic.Australia
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5
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Brauer CJ, Beheregaray LB. Recent and rapid anthropogenic habitat fragmentation increases extinction risk for freshwater biodiversity. Evol Appl 2020; 13:2857-2869. [PMID: 33294027 PMCID: PMC7691462 DOI: 10.1111/eva.13128] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/16/2022] Open
Abstract
Anthropogenic habitat fragmentation is often implicated as driving the current global extinction crisis, particularly in freshwater ecosystems. The genetic signal of recent population isolation can be confounded by the complex spatial arrangement of dendritic river systems. Consequently, many populations may presently be managed separately based on an incorrect assumption that they have evolved in isolation. Integrating landscape genomics data with models of connectivity that account for landscape structure, we show that the cumulative effects of multiple in-stream barriers have contributed to the recent decline of a freshwater fish from the Murray-Darling Basin, Australia. In addition, individual-based eco-evolutionary simulations further demonstrate that contemporary inferences about population isolation are consistent with the 160-year time frame since construction of in-stream barriers began in the region. Our findings suggest that the impact of very recent fragmentation may be often underestimated for freshwater biodiversity. We argue that proactive conservation measures to reconnect many riverine populations are urgently needed.
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Affiliation(s)
- Chris J. Brauer
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityAdelaideSAAustralia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityAdelaideSAAustralia
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6
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Landínez-García RM, Narváez JC, Márquez EJ. Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci. PeerJ 2020; 8:e10327. [PMID: 33240645 PMCID: PMC7666565 DOI: 10.7717/peerj.10327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 10/19/2020] [Indexed: 11/29/2022] Open
Abstract
Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.
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Affiliation(s)
- Ricardo M Landínez-García
- Facultad de Ciencias, Escuela de Biociencias, Laboratorio de Biología Molecular y Celular, Universidad Nacional de Colombia-Sede Medellín, Medellín, Colombia
| | - Juan Carlos Narváez
- Grupo de Biodiversidad y Ecología Aplicada, Laboratorio de Genética Molecular, Universidad del Magdalena, Santa Marta, Magdalena, Colombia
| | - Edna J Márquez
- Facultad de Ciencias, Escuela de Biociencias, Laboratorio de Biología Molecular y Celular, Universidad Nacional de Colombia-Sede Medellín, Medellín, Colombia
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7
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Valenzuela‐Aguayo F, McCracken GR, Manosalva A, Habit E, Ruzzante DE. Human-induced habitat fragmentation effects on connectivity, diversity, and population persistence of an endemic fish, Percilia irwini, in the Biobío River basin (Chile). Evol Appl 2020; 13:794-807. [PMID: 32211068 PMCID: PMC7086057 DOI: 10.1111/eva.12901] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/14/2019] [Accepted: 11/05/2019] [Indexed: 01/15/2023] Open
Abstract
An understanding of how genetic variability is distributed in space is fundamental for the conservation and maintenance of diversity in spatially fragmented and vulnerable populations. While fragmentation can occur from natural barriers, it can also be exacerbated by anthropogenic activities such as hydroelectric power plant development. Whatever the source, fragmentation can have significant ecological effects, including disruptions of migratory processes and gene flow among populations. In Chile, the Biobío River basin exhibits a high degree of habitat fragmentation due to the numerous hydroelectric power plants in operation, the number of which is expected to increase following new renewable energy use strategies. Here, we assessed the effects of different kinds of barriers on the genetic structure of the endemic freshwater fish Percilia irwini, knowledge that is critically needed to inform conservation strategies in light of current and anticipated further fragmentation initiatives in the system. We identified eight genetic units throughout the entire Biobío system with high effective sizes. A reduced effective size estimate was, however, observed in a single population located between two impassable barriers. Both natural waterfalls and human-made dams were important drivers of population differentiation in this system; however, dams affect genetic diversity differentially depending on their mode of operation. Evidence of population extirpation was found in two river stretches limited by upstream and downstream dams. Significant gene flow in both directions was found among populations not separated by natural or anthropogenic barriers. Our results suggest a significant vulnerability of P. irwini populations to future dam development and demonstrate the importance of studying basin-wide data sets with genetic metrics to understand the strength and direction of anthropogenic impacts on fish populations.
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Affiliation(s)
- Francisca Valenzuela‐Aguayo
- Laboratorio de Ecología y Conservación de PecesDepartamento de Sistemas AcuáticosFacultad de Ciencias Ambientales y Centro EULAUniversidad de ConcepciónConcepciónChile
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | | | - Aliro Manosalva
- Laboratorio de Ecología y Conservación de PecesDepartamento de Sistemas AcuáticosFacultad de Ciencias Ambientales y Centro EULAUniversidad de ConcepciónConcepciónChile
| | - Evelyn Habit
- Laboratorio de Ecología y Conservación de PecesDepartamento de Sistemas AcuáticosFacultad de Ciencias Ambientales y Centro EULAUniversidad de ConcepciónConcepciónChile
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8
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Alcaraz C, Gholami Z. Diversity and structure of fragmented populations of a threatened endemic cyprinodontid ( Aphanius sophiae) inferred from genetics and otolith morphology: Implications for conservation and management. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Zeinab Gholami
- Department of Biology University of Isfahan Isfahan Iran
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology & GeoBio‐Center LMU Ludwig‐Maximilians‐University Munich Germany
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9
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Whelan NV, Galaska MP, Sipley BN, Weber JM, Johnson PD, Halanych KM, Helms BS. Riverscape genetic variation, migration patterns, and morphological variation of the threatened Round Rocksnail, Leptoxis ampla. Mol Ecol 2019; 28:1593-1610. [PMID: 30697854 DOI: 10.1111/mec.15032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/10/2019] [Accepted: 01/23/2019] [Indexed: 12/14/2022]
Abstract
Within riverine systems, headwater populations are hypothesized to harbour higher amounts of genetic distinctiveness than populations in the main stem of a river and display increased genetic diversity in large, downstream habitats. However, these hypotheses were mostly developed with insects and fish, and they have not been tested on many invertebrate lineages. Pleuroceridae gastropods are of particular ecological importance to rivers of eastern North America, sometimes comprising over 90% of macroinvertebrate biomass. Yet, virtually nothing is known of pleurocerid landscape genetics, including whether genetic diversity follows predictions made by hypotheses developed on more mobile species. Moreover, the commonly repeated hypothesis that intraspecific morphological variation in gastropods results from ecophenotypic plasticity has not been well tested on pleurocerids. Using 2bRAD-seq to discover single nucleotide polymorphisms, we show that the threatened, Cahaba River endemic pleurocerid, Leptoxis ampla, has limited gene flow among populations and that migration is downstream-biased, conflicting with previous hypotheses. Both tributary and main stem populations harbour unique genomic profiles, and genetic diversity was highest in downstream populations. Furthermore, L. ampla shell morphology was more correlated with genetic differences among individuals and populations than habitat characteristics. We anticipate similar genetic and demographic patterns to be seen in other pleurocerids, and hypotheses about gene flow and population demographics that were based on more mobile taxa often, but not always, apply to freshwater gastropods. From a conservation standpoint, genetic structure of L. ampla populations suggests distinctive genetic diversity is lost with localized extirpation, a phenomenon common across the range of Pleuroceridae.
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Affiliation(s)
- Nathan V Whelan
- Southeast Conservation Genetics Lab, Warm Springs Fish Technology Center, United States Fish and Wildlife Service, Auburn, Alabama.,School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, Alabama
| | - Matthew P Galaska
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania
| | - Breanna N Sipley
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - Jennifer M Weber
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - Paul D Johnson
- Alabama Department of Conservation and Natural Resources, Alabama Aquatic Biodiversity Center, Marion, Alabama
| | | | - Brian S Helms
- Department of Biological and Environmental Sciences, Troy University, Troy, Alabama
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10
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Brauer CJ, Unmack PJ, Smith S, Bernatchez L, Beheregaray LB. On the roles of landscape heterogeneity and environmental variation in determining population genomic structure in a dendritic system. Mol Ecol 2018; 27:3484-3497. [DOI: 10.1111/mec.14808] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Chris J. Brauer
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide South Australia Australia
| | - Peter J. Unmack
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory Australia
| | - Steve Smith
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide South Australia Australia
- Department of Integrative Biology and Evolution University of Veterinary Medicine Vienna Austria
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes Université Laval Québec Québec Quebec Canada
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide South Australia Australia
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11
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Fourtune L, Prunier JG, Paz-Vinas I, Loot G, Veyssière C, Blanchet S. Inferring Causalities in Landscape Genetics: An Extension of Wright's Causal Modeling to Distance Matrices. Am Nat 2018; 191:491-508. [PMID: 29570400 DOI: 10.1086/696233] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Identifying landscape features that affect functional connectivity among populations is a major challenge in fundamental and applied sciences. Landscape genetics combines landscape and genetic data to address this issue, with the main objective of disentangling direct and indirect relationships among an intricate set of variables. Causal modeling has strong potential to address the complex nature of landscape genetic data sets. However, this statistical approach was not initially developed to address the pairwise distance matrices commonly used in landscape genetics. Here, we aimed to extend the applicability of two causal modeling methods-that is, maximum-likelihood path analysis and the directional separation test-by developing statistical approaches aimed at handling distance matrices and improving functional connectivity inference. Using simulations, we showed that these approaches greatly improved the robustness of the absolute (using a frequentist approach) and relative (using an information-theoretic approach) fits of the tested models. We used an empirical data set combining genetic information on a freshwater fish species (Gobio occitaniae) and detailed landscape descriptors to demonstrate the usefulness of causal modeling to identify functional connectivity in wild populations. Specifically, we demonstrated how direct and indirect relationships involving altitude, temperature, and oxygen concentration influenced within- and between-population genetic diversity of G. occitaniae.
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12
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Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish. Heredity (Edinb) 2018; 120:515-532. [PMID: 29326479 PMCID: PMC5943333 DOI: 10.1038/s41437-017-0008-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 11/08/2022] Open
Abstract
Habitat loss and fragmentation often result in small, isolated populations vulnerable to environmental disturbance and loss of genetic diversity. Low genetic diversity can increase extinction risk of small populations by elevating inbreeding and inbreeding depression, and reducing adaptive potential. Due to their linear nature and extensive use by humans, freshwater ecosystems are especially vulnerable to habitat loss and fragmentation. Although the effects of fragmentation on genetic structure have been extensively studied in migratory fishes, they are less understood in low-mobility species. We estimated impacts of instream barriers on genetic structure and diversity of the low-mobility river blackfish (Gadopsis marmoratus) within five streams separated by weirs or dams constructed 45-120 years ago. We found evidence of small-scale (<13 km) genetic structure within reaches unimpeded by barriers, as expected for a fish with low mobility. Genetic diversity was lower above barriers in small streams only, regardless of barrier age. In particular, one isolated population showed evidence of a recent bottleneck and inbreeding. Differentiation above and below the barrier (FST = 0.13) was greatest in this stream, but in other streams did not differ from background levels. Spatially explicit simulations suggest that short-term barrier effects would not be detected with our data set unless effective population sizes were very small (<100). Our study highlights that, in structured populations, the ability to detect short-term genetic effects from barriers is reduced and requires more genetic markers compared to panmictic populations. We also demonstrate the importance of accounting for natural population genetic structure in fragmentation studies.
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13
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Attard CRM, Brauer CJ, Sandoval-Castillo J, Faulks LK, Unmack PJ, Gilligan DM, Beheregaray LB. Ecological disturbance influences adaptive divergence despite high gene flow in golden perch (Macquaria ambigua): Implications for management and resilience to climate change. Mol Ecol 2017; 27:196-215. [PMID: 29165848 DOI: 10.1111/mec.14438] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 10/31/2017] [Accepted: 11/04/2017] [Indexed: 01/01/2023]
Abstract
Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming this necessitates ecological genomic studies of high dispersal, generalist species. Here we perform one such study on golden perch (Macquaria ambigua) in the Murray-Darling Basin (MDB), Australia, using a genome-wide SNP data set. The MDB spans across arid to wet and temperate to subtropical environments, with low to high ecological disturbance in the form of low to high hydrological variability. We found high gene flow across the basin and three populations with low neutral differentiation. Genotype-environment association analyses detected adaptive divergence predominantly linked to an arid region with highly variable riverine flow, and candidate loci included functions related to fat storage, stress and molecular or tissue repair. The high connectivity of golden perch in the MDB will likely allow locally adaptive traits in its most arid and hydrologically variable environment to spread and be selected in localities that are predicted to become arid and hydrologically variable in future climates. High connectivity in golden perch is likely due to their generalist life history and efforts of fisheries management. Our study adds to growing evidence of adaptation in the face of gene flow and highlights the importance of considering ecological disturbance and adaptive divergence in biodiversity management.
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Affiliation(s)
- Catherine R M Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Leanne K Faulks
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.,Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Nagano, Japan
| | - Peter J Unmack
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
| | - Dean M Gilligan
- New South Wales Department of Primary Industries, Batemans Bay Fisheries Centre, Batemans Bay, NSW, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
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14
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Reduced genetic diversity and alteration of gene flow in a fiddler crab due to mangrove degradation. PLoS One 2017; 12:e0182987. [PMID: 28837577 PMCID: PMC5570428 DOI: 10.1371/journal.pone.0182987] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/27/2017] [Indexed: 11/19/2022] Open
Abstract
The fiddler crab Austruca occidentalis is a dominant species in mangrove forests along the East African coast. It enhances soil aeration and, through its engineering activities, makes otherwise-inaccessible food available for other marine organisms. Despite its importance, the habitat of A. occidentalis is threatened by human activities. Clearing the mangroves for salt farming and selective logging of mangroves trees continue to jeopardise mangrove ecosystems in the Western Indian Ocean. This study aims to use partial mitochondrial COI gene sequences and nuclear microsatellites to determine whether salt farming activities in mangroves have a negative impact on the genetic diversity and gene flow of A. occidentalis collected along the Tanzania coast. The level of genetic diversity for both mitochondrial DNA and nuclear microsatellites are relatively lower in samples from salt ponds compared to natural mangrove sites. Analysis of molecular variance (AMOVA) among all populations showed low but significant differentiation (COI: Fst = 0.022, P < 0.05; microsatellites: Fst = 0.022, P < 0.001). A hierarchical AMOVA indicates lower but significant genetic differentiation among populations from salt ponds and natural mangroves sites (COI: Fct = 0.033, P < 0.05; microsatellites: Fct = 0.018, P = < 0.01). These results indicate that salt farming has a significant negative impact on the genetic diversity of A. occidentalis. Since higher genetic diversity contributes to a stable population, restoring the cleared habitats might be the most effective measures for the conservation of genetic diversity and hence adaptive potential to environmental change in this species.
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15
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Brown AP, Greenway R, Morgan S, Quackenbush CR, Giordani L, Arias-Rodriguez L, Tobler M, Kelley JL. Genome-scale data reveal that endemic Poecilia populations from small sulphidic springs display no evidence of inbreeding. Mol Ecol 2017; 26:4920-4934. [PMID: 28731545 DOI: 10.1111/mec.14249] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 04/04/2017] [Accepted: 06/21/2017] [Indexed: 12/27/2022]
Abstract
Populations with limited ranges can be highly vulnerable to changes in their environment and are, thus, of high conservation concern. Populations that experience human-induced range reductions are often highly inbred and lack genetic diversity, but it is unknown whether this is also the case for populations with naturally small ranges. The fishes Poecilia sulphuraria (listed as critically endangered) and Poecilia thermalis, which are endemic to small hydrogen sulphide-rich springs in southern Mexico, are examples of such populations with inherently small habitats. We used geometric morphometrics and population genetics to quantify phenotypic and genetic variation within and among two populations of P. sulphuraria and one population of P. thermalis. Principal component analyses revealed phenotypic and genetic differences among the populations. Evidence for inbreeding was low compared to populations that have undergone habitat reduction. The genetic data were also used to infer the demographic history of these populations to obtain estimates for effective population sizes and migration rates. Effective population sizes were large given the small habitats of these populations. Our results imply that these three endemic extremophile populations should each be considered separately for conservation purposes. Additionally, this study suggests that populations in naturally small habitats may have lower rates of inbreeding and higher genetic diversity than expected, and therefore may be better equipped to handle environmental perturbations than anticipated. We caution, however, that the inferred lack of inbreeding and the large effective population sizes could potentially be a result of colonization by genetically diverse ancestors.
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Affiliation(s)
- Anthony P Brown
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Samuel Morgan
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Corey R Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | | | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, Tabasco, México
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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16
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Pavlova A, Beheregaray LB, Coleman R, Gilligan D, Harrisson KA, Ingram BA, Kearns J, Lamb AM, Lintermans M, Lyon J, Nguyen TTT, Sasaki M, Tonkin Z, Yen JDL, Sunnucks P. Severe consequences of habitat fragmentation on genetic diversity of an endangered Australian freshwater fish: A call for assisted gene flow. Evol Appl 2017; 10:531-550. [PMID: 28616062 PMCID: PMC5469170 DOI: 10.1111/eva.12484] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/29/2017] [Indexed: 12/15/2022] Open
Abstract
Genetic diversity underpins the ability of populations to persist and adapt to environmental changes. Substantial empirical data show that genetic diversity rapidly deteriorates in small and isolated populations due to genetic drift, leading to reduction in adaptive potential and fitness and increase in inbreeding. Assisted gene flow (e.g. via translocations) can reverse these trends, but lack of data on fitness loss and fear of impairing population "uniqueness" often prevents managers from acting. Here, we use population genetic and riverscape genetic analyses and simulations to explore the consequences of extensive habitat loss and fragmentation on population genetic diversity and future population trajectories of an endangered Australian freshwater fish, Macquarie perch Macquaria australasica. Using guidelines to assess the risk of outbreeding depression under admixture, we develop recommendations for population management, identify populations requiring genetic rescue and/or genetic restoration and potential donor sources. We found that most remaining populations of Macquarie perch have low genetic diversity, and effective population sizes below the threshold required to retain adaptive potential. Our simulations showed that under management inaction, smaller populations of Macquarie perch will face inbreeding depression within a few decades, but regular small-scale translocations will rapidly rescue populations from inbreeding depression and increase adaptive potential through genetic restoration. Despite the lack of data on fitness loss, based on our genetic data for Macquarie perch populations, simulations and empirical results from other systems, we recommend regular and frequent translocations among remnant populations within catchments. These translocations will emulate the effect of historical gene flow and improve population persistence through decrease in demographic and genetic stochasticity. Increasing population genetic connectivity within each catchment will help to maintain large effective population sizes and maximize species adaptive potential. The approach proposed here could be readily applicable to genetic management of other threatened species to improve their adaptive potential.
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Affiliation(s)
- Alexandra Pavlova
- School of Biological SciencesClayton Campus, Monash UniversityClaytonVICAustralia
| | | | - Rhys Coleman
- Applied ResearchMelbourne WaterDocklandsVICAustralia
| | - Dean Gilligan
- Freshwater Ecosystems ResearchNSW Department of Primary Industries – FisheriesBatemans BayNSWAustralia
| | - Katherine A. Harrisson
- School of Biological SciencesClayton Campus, Monash UniversityClaytonVICAustralia
- Department of Environment, Land Water and PlanningArthur Rylah Institute, Land, Fire and EnvironmentHeidelbergVICAustralia
- Department of Ecology Environment and EvolutionSchool of Life Sciences, La Trobe UniversityBundoora, Victoria3083Australia
| | - Brett A. Ingram
- Department of Economic DevelopmentJobs, Transport and ResourcesFisheries VictoriaAlexandraVICAustralia
| | - Joanne Kearns
- Department of Environment, Land Water and PlanningArthur Rylah Institute, Land, Fire and EnvironmentHeidelbergVICAustralia
| | - Annika M. Lamb
- School of Biological SciencesClayton Campus, Monash UniversityClaytonVICAustralia
| | - Mark Lintermans
- Institute for Applied EcologyUniversity of CanberraCanberraACTAustralia
| | - Jarod Lyon
- Department of Environment, Land Water and PlanningArthur Rylah Institute, Land, Fire and EnvironmentHeidelbergVICAustralia
| | - Thuy T. T. Nguyen
- Agriculture VictoriaAgriBio, Centre for AgriBioscienceBundooraVICAustralia
| | - Minami Sasaki
- School of Biological SciencesFlinders UniversityAdelaideSAAustralia
| | - Zeb Tonkin
- Department of Environment, Land Water and PlanningArthur Rylah Institute, Land, Fire and EnvironmentHeidelbergVICAustralia
| | - Jian D. L. Yen
- School of Physics and AstronomyClayton Campus, Monash UniversityClaytonVICAustralia
| | - Paul Sunnucks
- School of Biological SciencesClayton Campus, Monash UniversityClaytonVICAustralia
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17
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Pavlova A, Gan HM, Lee YP, Austin CM, Gilligan DM, Lintermans M, Sunnucks P. Purifying selection and genetic drift shaped Pleistocene evolution of the mitochondrial genome in an endangered Australian freshwater fish. Heredity (Edinb) 2017; 118:466-476. [PMID: 28051058 PMCID: PMC5520527 DOI: 10.1038/hdy.2016.120] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 09/20/2016] [Accepted: 11/02/2016] [Indexed: 11/08/2022] Open
Abstract
Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB). Phylogenetic analysis resolved basin-level clades, supporting incipient speciation previously inferred from differentiation in allozymes, microsatellites and mitochondrial control region. The estimated time of lineage divergence suggested an early- to mid-Pleistocene split between SB and the common ancestor of HNB+MDB, followed by mid-to-late Pleistocene splitting between HNB and MDB. These divergence estimates are more recent than previous ones. Our analyses suggested that evolutionary drivers differed between inland MDB and coastal HNB. In the cooler and more climatically variable MDB, mitogenomes evolved under strong purifying selection, whereas in the warmer and more climatically stable HNB, purifying selection was relaxed. Evidence for relaxed selection in the HNB includes elevated transfer RNA and 16S ribosomal RNA polymorphism, presence of potentially mildly deleterious mutations and a codon (ATP6113) displaying signatures of positive selection (ratio of nonsynonymous to synonymous substitution rates (dN/dS) >1, radical change of an amino-acid property and phylogenetic conservation across the Percichthyidae). In addition, the difference could be because of stronger genetic drift in the smaller and historically more subdivided HNB with low per-population effective population sizes.
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Affiliation(s)
- A Pavlova
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - H M Gan
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Y P Lee
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - C M Austin
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - D M Gilligan
- NSW Department of Primary Industries, Batemans Bay, New South Wales, Australia
| | - M Lintermans
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - P Sunnucks
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
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18
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Lean J, Hammer MP, Unmack PJ, Adams M, Beheregaray LB. Landscape genetics informs mesohabitat preference and conservation priorities for a surrogate indicator species in a highly fragmented river system. Heredity (Edinb) 2017; 118:374-384. [PMID: 27876805 PMCID: PMC5345605 DOI: 10.1038/hdy.2016.111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 09/27/2016] [Accepted: 09/27/2016] [Indexed: 11/09/2022] Open
Abstract
Poor dispersal species represent conservative benchmarks for biodiversity management because they provide insights into ecological processes influenced by habitat fragmentation that are less evident in more dispersive organisms. Here we used the poorly dispersive and threatened river blackfish (Gadopsis marmoratus) as a surrogate indicator system for assessing the effects of fragmentation in highly modified river basins and for prioritizing basin-wide management strategies. We combined individual, population and landscape-based approaches to analyze genetic variation in samples spanning the distribution of the species in Australia's Murray-Darling Basin, one of the world's most degraded freshwater systems. Our results indicate that G. marmoratus displays the hallmark of severe habitat fragmentation with notably scattered, small and demographically isolated populations with very low genetic diversity-a pattern found not only between regions and catchments but also between streams within catchments. By using hierarchically nested population sampling and assessing relationships between genetic uniqueness and genetic diversity across populations, we developed a spatial management framework that includes the selection of populations in need of genetic rescue. Landscape genetics provided an environmental criterion to identify associations between landscape features and ecological processes. Our results further our understanding of the impact that habitat quality and quantity has on habitat specialists with similarly low dispersal. They should also have practical applications for prioritizing both large- and small-scale conservation management actions for organisms inhabiting highly fragmented ecosystems.
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Affiliation(s)
- J Lean
- Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
| | - M P Hammer
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia, Australia
- Curator of Fishes, Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory, Australia
| | - P J Unmack
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - M Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - L B Beheregaray
- Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
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19
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Brauer CJ, Hammer MP, Beheregaray LB. Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin. Mol Ecol 2016; 25:5093-5113. [DOI: 10.1111/mec.13830] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/15/2016] [Accepted: 08/23/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Chris J. Brauer
- Molecular Ecology Laboratory School of Biological Sciences Flinders University Adelaide SA 5042 Australia
| | - Michael P. Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory Darwin NT 0801 Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory School of Biological Sciences Flinders University Adelaide SA 5042 Australia
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20
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Harrisson KA, Yen JDL, Pavlova A, Rourke ML, Gilligan D, Ingram BA, Lyon J, Tonkin Z, Sunnucks P. Identifying environmental correlates of intraspecific genetic variation. Heredity (Edinb) 2016; 117:155-64. [PMID: 27273322 PMCID: PMC4981683 DOI: 10.1038/hdy.2016.37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 11/08/2022] Open
Abstract
Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).
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Affiliation(s)
- K A Harrisson
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - J D L Yen
- School of Physics & Astronomy, Monash University, Clayton, Victoria, Australia
| | - A Pavlova
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - M L Rourke
- Department of Primary Industries, DPI Fisheries, Narrandera, New South Wales, Australia
| | - D Gilligan
- Department of Primary Industries, DPI Fisheries, Batemans Bay Fisheries Office, Batemans Bay, New South Wales, Australia
| | - B A Ingram
- Fisheries Victoria, Department of Economic Development, Jobs, Transport and Resources, Alexandra, Victoria, Australia
| | - J Lyon
- Arthur Rylah Institute, Department of Environment, Land, Water & Planning, Heidelberg, Victoria, Australia
| | - Z Tonkin
- Arthur Rylah Institute, Department of Environment, Land, Water & Planning, Heidelberg, Victoria, Australia
| | - P Sunnucks
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
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21
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Cole TL, Hammer MP, Unmack PJ, Teske PR, Brauer CJ, Adams M, Beheregaray LB. Range-wide fragmentation in a threatened fish associated with post-European settlement modification in the Murray–Darling Basin, Australia. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0868-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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22
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Sousa-Santos C, Robalo JI, Pereira AM, Branco P, Santos JM, Ferreira MT, Sousa M, Doadrio I. Broad-scale sampling of primary freshwater fish populations reveals the role of intrinsic traits, inter-basin connectivity, drainage area and latitude on shaping contemporary patterns of genetic diversity. PeerJ 2016; 4:e1694. [PMID: 26966653 PMCID: PMC4782715 DOI: 10.7717/peerj.1694] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 01/26/2016] [Indexed: 11/24/2022] Open
Abstract
Background. Worldwide predictions suggest that up to 75% of the freshwater fish species occurring in rivers with reduced discharge could be extinct by 2070 due to the combined effect of climate change and water abstraction. The Mediterranean region is considered to be a hotspot of freshwater fish diversity but also one of the regions where the effects of climate change will be more severe. Iberian cyprinids are currently highly endangered, with over 68% of the species raising some level of conservation concern. Methods. During the FISHATLAS project, the Portuguese hydrographical network was extensively covered (all the 34 river basins and 47 sub-basins) in order to contribute with valuable data on the genetic diversity distribution patterns of native cyprinid species. A total of 188 populations belonging to 16 cyprinid species of Squalius, Luciobarbus, Achondrostoma, Iberochondrostoma, Anaecypris and Pseudochondrostoma were characterized, for a total of 3,678 cytochrome b gene sequences. Results. When the genetic diversity of these populations was mapped, it highlighted differences among populations from the same species and between species with identical distribution areas. Factors shaping the contemporary patterns of genetic diversity were explored and the results revealed the role of latitude, inter-basin connectivity, migratory behaviour, species maximum size, species range and other species intrinsic traits in determining the genetic diversity of sampled populations. Contrastingly, drainage area and hydrological regime (permanent vs. temporary) seem to have no significant effect on genetic diversity. Species intrinsic traits, maximum size attained, inter-basin connectivity and latitude explained over 30% of the haplotype diversity variance and, generally, the levels of diversity were significantly higher for smaller sized species, from connected and southerly river basins. Discussion. Targeting multiple co-distributed species of primary freshwater fish allowed us to assess the relative role of historical versus contemporary factors affecting genetic diversity. Since different patterns were detected for species with identical distribution areas we postulate that contemporary determinants of genetic diversity (species’ intrinsic traits and landscape features) must have played a more significant role than historical factors. Implications for conservation in a context of climate change and highly disturbed habitats are detailed, namely the need to focus management and conservation actions on intraspecific genetic data and to frequently conduct combined genetic and demographic surveys.
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Affiliation(s)
| | | | | | - Paulo Branco
- CEF-Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal; CERis-Civil Engineering Research and Innovation for Sustainability, Instituto Superior Técnico, Lisbon, Portugal
| | - José Maria Santos
- CEF-Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa , Lisbon , Portugal
| | - Maria Teresa Ferreira
- CEF-Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa , Lisbon , Portugal
| | - Mónica Sousa
- Instituto da Conservação da Natureza e das Florestas, I.P. , Lisbon , Portugal
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23
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Gouskov A, Reyes M, Wirthner-Bitterlin L, Vorburger C. Fish population genetic structure shaped by hydroelectric power plants in the upper Rhine catchment. Evol Appl 2016; 9:394-408. [PMID: 26834832 PMCID: PMC4721079 DOI: 10.1111/eva.12339] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/02/2015] [Indexed: 01/20/2023] Open
Abstract
The Rhine catchment in Switzerland has been transformed by a chain of hydroelectric power stations. We addressed the impact of fragmentation on the genetic structure of fish populations by focusing on the European chub (Squalius cephalus). This fish species is not stocked and copes well with altered habitats, enabling an assessment of the effects of fragmentation per se. Using microsatellites, we genotyped 2133 chub from 47 sites within the catchment fragmented by 37 hydroelectric power stations, two weirs and the Rhine Falls. The shallow genetic population structure reflected drainage topology and was affected significantly by barriers to migration. The effect of power stations equipped with fishpasses on genetic differentiation was detectable, albeit weaker than that of man‐made barriers without fishpasses. The Rhine Falls as the only long‐standing natural obstacle (formed 14 000 to 17 000 years ago) also had a strong effect. Man‐made barriers also exacerbated the upstream decrease in allelic diversity in the catchment, particularly when lacking fishpasses. Thus, existing fishpasses do have the desired effect of mitigating fragmentation, but barriers still reduce population connectivity in a fish that traverses fishpasses better than many other species. Less mobile species are likely to be affected more severely.
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Affiliation(s)
- Alexandre Gouskov
- Institute of Integrative Biology ETH Zürich Zürich Switzerland; Aquatic Ecology Eawag Dübendorf Switzerland
| | | | | | - Christoph Vorburger
- Institute of Integrative Biology ETH Zürich Zürich Switzerland; Aquatic Ecology Eawag Dübendorf Switzerland
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24
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Bracamonte SE, Smith S, Hammer M, Pavey SA, Sunnucks P, Beheregaray LB. Characterization of MHC class IIB for four endangered Australian freshwater fishes obtained from ecologically divergent populations. FISH & SHELLFISH IMMUNOLOGY 2015; 46:468-476. [PMID: 26093210 DOI: 10.1016/j.fsi.2015.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/04/2015] [Accepted: 06/07/2015] [Indexed: 06/04/2023]
Abstract
Genetic diversity is an essential aspect of species viability, and assessments of neutral genetic diversity are regularly implemented in captive breeding and conservation programs. Despite their importance, information from adaptive markers is rarely included in such programs. A promising marker of significance in fitness and adaptive potential is the major histocompatibility complex (MHC), a key component of the adaptive immune system. Populations of Australian freshwater fishes are generally declining in numbers due to human impacts and the introduction of exotic species, a scenario of particular concern for members of the family Percichthyidae, several of which are listed as nationally vulnerable or endangered, and hence subject to management plans, captive breeding, and restoration plans. We used a next-generation sequencing approach to characterize the MHC IIB locus and provide a conservative description of its levels of diversity in four endangered percichthyids: Gadopsis marmoratus, Macquaria australasica, Nannoperca australis, and Nannoperca obscura. Evidence is presented for a duplicated MHC IIB locus, positively selected sites and recombination of MHC alleles. Relatively moderate levels of diversity were detected in the four species, as well as in different ecotypes within each species. Phylogenetic analyses revealed genus specific clustering of alleles and no allele sharing among species. There were also no shared alleles observed between two ecotypes within G. marmoratus and within M. australasica, which might be indicative of ecologically-driven divergence and/or long divergence times. This represents the first characterization and assessment of MHC diversity for Percichthyidae, and also for Australian freshwater fishes in general, providing key genetic resources for a vertebrate group of increasing conservation concern.
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Affiliation(s)
- Seraina E Bracamonte
- Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia; Department of Integrative Biology and Evolution, University of Veterinary Medicine, 1160 Vienna, Austria
| | - Steve Smith
- Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia; Department of Integrative Biology and Evolution, University of Veterinary Medicine, 1160 Vienna, Austria
| | - Michael Hammer
- Evolutionary Biology Unit, South Australian Museum, North Terrace Adelaide, South Australia 5000 and Curator of Fishes, Museum and Art Gallery of the Northern Territory, PO Box 4646, Darwin, Northern Territory 0801, Australia
| | - Scott A Pavey
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec QC G1V 0A6, Canada
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne 3800, Victoria, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia.
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25
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Perea S, Doadrio I. Phylogeography, historical demography and habitat suitability modelling of freshwater fishes inhabiting seasonally fluctuating Mediterranean river systems: a case study using the Iberian cyprinid Squalius valentinus. Mol Ecol 2015; 24:3706-22. [PMID: 26085305 DOI: 10.1111/mec.13274] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 06/08/2015] [Accepted: 06/12/2015] [Indexed: 11/27/2022]
Abstract
The Mediterranean freshwater fish fauna has evolved under constraints imposed by the seasonal weather/hydrological patterns that define the Mediterranean climate. These conditions have influenced the genetic and demographic structure of aquatic communities since their origins in the Mid-Pliocene. Freshwater species in Mediterranean-type climates will likely constitute genetically well-differentiated populations, to varying extents depending on basin size, as a consequence of fragmentation resulting from drought/flood cycles. We developed an integrative framework to study the spatial patterns in genetic diversity, demographic trends, habitat suitability modelling and landscape genetics, to evaluate the evolutionary response of Mediterranean-type freshwater fish to seasonal fluctuations in weather. To test this evolutionary response, the model species used was Squalius valentinus, an endemic cyprinid of the Spanish Levantine area, where seasonal weather fluctuations are extreme, although our findings may be extrapolated to other Mediterranean-type species. Our results underscore the significant role of the Mediterranean climate, along with Pleistocene glaciations, in diversification of S. valentinus. We found higher nuclear diversity in larger drainage basins, but higher mitochondrial diversity correlated to habitat suitability rather than basin size. We also found strong correlation between genetic structure and climatic factors associated with Mediterranean seasonality. Demographic and migration analyses suggested population expansion during glacial periods that also contributed to the current genetic structure of S. valentinus populations. The inferred models support the significant contribution of precipitation and temperature to S. valentinus habitat suitability and allow recognizing areas of habitat stability. We highlight the importance of stable habitat conditions, fostered by typical karstic springs found on the Mediterranean littoral coasts, for the preservation of freshwater species inhabiting seasonally fluctuating river systems.
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Affiliation(s)
- S Perea
- Museo Nacional de Ciencias Naturales, CSIC, Biodiversity and Evolutionary Biology Department, C/José Gutiérrez Abascal, 2. 28006, Madrid, Spain
| | - I Doadrio
- Museo Nacional de Ciencias Naturales, CSIC, Biodiversity and Evolutionary Biology Department, C/José Gutiérrez Abascal, 2. 28006, Madrid, Spain
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Hill E, Ingram BA, Rourke M, Mitchell J, Strugnell JM. Genetic diversity and population structure of the threatened freshwater catfish, Tandanus tandanus, in Victoria, Australia. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0660-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Haponski AE, Stepien CA. A population genetic window into the past and future of the walleye Sander vitreus: relation to historic walleye and the extinct "blue pike" S. v. "glaucus". BMC Evol Biol 2014; 14:133. [PMID: 24941945 PMCID: PMC4229939 DOI: 10.1186/1471-2148-14-133] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 06/05/2014] [Indexed: 11/20/2022] Open
Abstract
Background Conserving genetic diversity and local adaptations are management priorities for wild populations of exploited species, which increasingly are subject to climate change, habitat loss, and pollution. These constitute growing concerns for the walleye Sander vitreus, an ecologically and economically valuable North American temperate fish with large Laurentian Great Lakes' fisheries. This study compares genetic diversity and divergence patterns across its widespread native range using mitochondrial (mt) DNA control region sequences and nine nuclear DNA microsatellite (μsat) loci, examining historic and contemporary influences. We analyze the genetic and morphological characters of a putative endemic variant– “blue pike” S. v. “glaucus” –described from Lakes Erie and Ontario, which became extinct. Walleye with turquoise-colored mucus also are evaluated, since some have questioned whether these are related to the “blue pike”. Results Walleye populations are distinguished by considerable genetic divergence (mean FST mtDNA = 0.32 ± 0.01, μsat = 0.13 ± 0.00) and substantial diversity across their range (mean heterozygosity mtDNA = 0.53 ± 0.02, μsat = 0.68 ± 0.03). Southern populations markedly differ, possessing unique haplotypes and alleles, especially the Ohio/New River population that houses the oldest haplotype and has the most pronounced divergence. Northern formerly glaciated populations have greatest diversity in Lake Erie (mean heterozygosity mtDNA = 0.79 ± 0.00, μsat = 0.72 ± 0.01). Genetic diversity was much less in the historic Lake Erie samples from 1923–1949 (mean heterozygosity mtDNA = 0.05 ± 0.01, μsat = 0.47 ± 0.06) than today. The historic “blue pike” had no unique haplotypes/alleles and there is no evidence that it comprised a separate taxon from walleye. Turquoise mucus walleye also show no genetic differentiation from other sympatric walleye and no correspondence to the “blue pike”. Conclusions Contemporary walleye populations possess high levels of genetic diversity and divergence, despite habitat degradation and exploitation. Genetic and previously published tagging data indicate that natal homing and spawning site philopatry led to population structure. Population patterns were shaped by climate change and drainage connections, with northern ones tracing to post-glacial recolonization. Southerly populations possess unique alleles and may provide an important genetic reservoir. Allelic frequencies of Lake Erie walleye from ~70–90 years ago significantly differed from those today, suggesting population recovery after extensive habitat loss, pollution, and exploitation. The historic “blue pike” is indistinguishable from walleye, indicating that taxonomic designation is not warranted.
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Affiliation(s)
| | - Carol A Stepien
- The Great Lakes Genetics/Genomics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, 6200 Bayshore Road, Toledo, OH 43616, USA.
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Hansen MM, Limborg MT, Ferchaud AL, Pujolar JM. The effects of Medieval dams on genetic divergence and demographic history in brown trout populations. BMC Evol Biol 2014; 14:122. [PMID: 24903056 PMCID: PMC4106231 DOI: 10.1186/1471-2148-14-122] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/30/2014] [Indexed: 12/22/2022] Open
Abstract
Background Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600–800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis of 44 microsatellite loci we investigated if the lake populations have been naturally genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Results Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence times ca. 600–800 years bp, providing strong evidence for establishment of dams in the Medieval as the factor causing divergence. Bayesian cluster analysis showed influence of stocked trout in several reference populations, but not in the focal lake and anadromous populations. Estimates of effective population size using a linkage disequilibrium method ranged from 244 to > 1,000 in all but one anadromous population, but were lower (153 and 252) in the lake populations. Conclusions We show that genetic divergence of lake-dwelling trout in two Danish lakes reflects establishment of water mills and impassable dams ca. 600–800 years ago rather than a natural genetic population structure. Although effective population sizes of the two lake populations are not critically low they may ultimately limit response to selection and thereby future adaptation. Our results demonstrate that populations may have been affected by anthropogenic disturbance over longer time scales than normally assumed.
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Affiliation(s)
- Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
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29
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Brauer CJ, Unmack PJ, Hammer MP, Adams M, Beheregaray LB. Catchment-scale conservation units identified for the threatened Yarra pygmy perch (Nannoperca obscura) in highly modified river systems. PLoS One 2013; 8:e82953. [PMID: 24349405 PMCID: PMC3862729 DOI: 10.1371/journal.pone.0082953] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/29/2013] [Indexed: 11/19/2022] Open
Abstract
Habitat fragmentation caused by human activities alters metapopulation dynamics and decreases biological connectivity through reduced migration and gene flow, leading to lowered levels of population genetic diversity and to local extinctions. The threatened Yarra pygmy perch, Nannoperca obscura, is a poor disperser found in small, isolated populations in wetlands and streams of southeastern Australia. Modifications to natural flow regimes in anthropogenically-impacted river systems have recently reduced the amount of habitat for this species and likely further limited its opportunity to disperse. We employed highly resolving microsatellite DNA markers to assess genetic variation, population structure and the spatial scale that dispersal takes place across the distribution of this freshwater fish and used this information to identify conservation units for management. The levels of genetic variation found for N. obscura are amongst the lowest reported for a fish species (mean heterozygosity of 0.318 and mean allelic richness of 1.92). We identified very strong population genetic structure, nil to little evidence of recent migration among demes and a minimum of 11 units for conservation management, hierarchically nested within four major genetic lineages. A combination of spatial analytical methods revealed hierarchical genetic structure corresponding with catchment boundaries and also demonstrated significant isolation by riverine distance. Our findings have implications for the national recovery plan of this species by demonstrating that N. obscura populations should be managed at a catchment level and highlighting the need to restore habitat and avoid further alteration of the natural hydrology.
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Affiliation(s)
- Chris J. Brauer
- Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Peter J. Unmack
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Michael P. Hammer
- School of Earth and Environmental Sciences, University of Adelaide, South Australia, Australia
- Curator of Fishes, Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - Mark Adams
- School of Earth and Environmental Sciences, University of Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
- * E-mail:
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Todd EV, Blair D, Farley S, Farrington L, FitzSimmons NN, Georges A, Limpus CJ, Jerry DR. Contemporary genetic structure reflects historical drainage isolation in an Australian snapping turtle,Elseya albagula. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Erica V. Todd
- School of Marine and Tropical Biology; James Cook University; Townsville; QLD; 4810; Australia
| | - David Blair
- School of Marine and Tropical Biology; James Cook University; Townsville; QLD; 4810; Australia
| | - Sharon Farley
- Institute for Applied Ecology; University of Canberra; Canberra; ACT; 2601; Australia
| | - Lachlan Farrington
- Institute for Applied Ecology; University of Canberra; Canberra; ACT; 2601; Australia
| | - Nancy N. FitzSimmons
- Institute for Applied Ecology; University of Canberra; Canberra; ACT; 2601; Australia
| | - Arthur Georges
- Institute for Applied Ecology; University of Canberra; Canberra; ACT; 2601; Australia
| | - Colin J. Limpus
- Aquatic Threatened Species Unit; Department of Environment and Heritage Protection; Brisbane; QLD; 4001; Australia
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Koster WM, Dawson DR, Morrongiello JR, Crook DA. Spawning season movements of Macquarie perch (Macquaria australasica) in the Yarra River, Victoria. AUST J ZOOL 2013. [DOI: 10.1071/zo13054] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Macquarie perch (Macquaria australasica) is a threatened fish species that inhabits rivers and impoundments in south-eastern Australia. Previous studies have shown that Macquarie perch in impoundments exhibit synchronised upstream spawning migrations to shallow, fast-flowing habitats in the lower reaches of inflowing streams. There has been little study of movement behaviours of entirely riverine populations of Macquarie perch despite this being the species’ natural habitat. Here, radio-telemetry is used to test the hypothesis that riverine populations exhibit synchronised migrations during the spawning season. Thirty Macquarie perch in the Yarra River, Victoria, a translocated population outside of the species’ natural range, were radio-tagged before the late spring–early summer spawning season and their movements followed over a 10-month period (May 2011 to February 2012). Tagged fish typically occupied restricted reaches of stream (<450 m). Sixteen of the fish undertook occasional upstream or downstream movements (~250–1000 m) away from their usual locations, particularly associated with large flow variations during the spawning season. There was no evidence of synchronised migratory behaviour or movement of multiple fish to specific locations or habitats during the spawning season. Whilst further research over more years is needed to comprehensively document the spawning-related behaviours of riverine Macquarie perch, our study demonstrates that management of riverine populations of this threatened species cannot necessarily be based on the model of spawning behaviour developed for lacustrine populations.
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Baguette M, Blanchet S, Legrand D, Stevens VM, Turlure C. Individual dispersal, landscape connectivity and ecological networks. Biol Rev Camb Philos Soc 2012; 88:310-26. [DOI: 10.1111/brv.12000] [Citation(s) in RCA: 385] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 10/18/2012] [Accepted: 10/25/2012] [Indexed: 11/28/2022]
Affiliation(s)
| | - Simon Blanchet
- USR CNRS 2936; Station d'Ecologie Expérimentale du CNRS à Moulis; 2 route du CNRS; F-09200; Saint Girons; France
| | - Delphine Legrand
- USR CNRS 2936; Station d'Ecologie Expérimentale du CNRS à Moulis; 2 route du CNRS; F-09200; Saint Girons; France
| | - Virginie M. Stevens
- USR CNRS 2936; Station d'Ecologie Expérimentale du CNRS à Moulis; 2 route du CNRS; F-09200; Saint Girons; France
| | - Camille Turlure
- F.R.S.-FNRS; Universite Catholique de Louvain, Earth and Life Institute, Biodiversity Research Centre; Croix du Sud 4; B-1348; Louvain-la-Neuve; Belgium
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Coscia I, Vogiatzi E, Kotoulas G, Tsigenopoulos CS, Mariani S. Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic. Heredity (Edinb) 2012; 108:537-46. [PMID: 22126850 PMCID: PMC3331784 DOI: 10.1038/hdy.2011.120] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 10/17/2011] [Accepted: 10/27/2011] [Indexed: 11/08/2022] Open
Abstract
Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here, we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 expressed sequence tag-linked markers, as well as a portion of the mitochondrial DNA (mtDNA) control region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, although the potential 'surfing effect' of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu.
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Affiliation(s)
- I Coscia
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Dublin, Ireland
| | - E Vogiatzi
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology and Genetics (IMBG), Crete, Greece
- Department of Molecular Biology and Genetics, Democritian University of Thrace, Alexandroupolis, Greece
| | - G Kotoulas
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology and Genetics (IMBG), Crete, Greece
| | - C S Tsigenopoulos
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology and Genetics (IMBG), Crete, Greece
| | - S Mariani
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Dublin, Ireland
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