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Springer AL, Gompert Z. Considerable genetic diversity and structure despite narrow endemism and limited ecological specialization in the Hayden's ringlet, Coenonympha haydenii. Mol Ecol 2024; 33:e17310. [PMID: 38441401 DOI: 10.1111/mec.17310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/26/2023] [Accepted: 02/15/2024] [Indexed: 03/26/2024]
Abstract
Understanding the processes that underlie the development of population genetic structure is central to the study of evolution. Patterns of genetic structure, in turn, can reveal signatures of isolation by distance (IBD), barriers to gene flow, or even the genesis of speciation. However, it is unclear how severe range restriction might impact the processes that dominate the development of genetic structure. In narrow endemic species, is population structure likely to be adaptive in nature, or rather the result of genetic drift? In this study, we investigated patterns of genetic diversity and structure in the narrow endemic Hayden's ringlet butterfly. Specifically, we asked to what degree genetic structure in the Hayden's ringlet can be explained by IBD, isolation by resistance (IBR) (in the form of geographic or ecological barriers to migration between populations), and isolation by environment (in the form of differences in host plant availability and preference). We employed a genotyping-by-sequencing (GBS) approach coupled with host preference assays, Bayesian modelling, and population genomic analyses to answer these questions. Our results suggest that despite their restricted range, levels of genetic diversity in the Hayden's ringlet are comparable to those seen in more widespread butterfly species. Hayden's ringlets showed a strong preference for feeding on grasses relative to sedges, but neither larval preference nor potential host availability at sampling sites correlated with genetic structure. We conclude that geography, in the form of IBR and simple IBD, was the major driver of contemporary patterns of differentiation in this narrow endemic species.
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Affiliation(s)
- Amy L Springer
- Department of Biology, Utah State University, Logan, Utah, USA
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah, USA
- Ecology Center, Utah State University, Logan, Utah, USA
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2
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Hui TCY, Tang Q, Ng EYX, Chong JL, Slade EM, Rheindt FE. Small-Mammal Genomics Highlights Viaducts as Potential Dispersal Conduits for Fragmented Populations. Animals (Basel) 2024; 14:426. [PMID: 38338069 PMCID: PMC10854910 DOI: 10.3390/ani14030426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Wildlife crossings are implemented in many countries to facilitate the dispersal of animals among habitats fragmented by roads. However, the efficacy of different types of habitat corridors remains poorly understood. We used a comprehensive sampling regime in two lowland dipterocarp forest areas in peninsular Malaysia to sample pairs of small mammal individuals in three treatment types: (1) viaduct sites, at which sampling locations were separated by a highway but connected by a vegetated viaduct; (2) non-viaduct sites, at which sampling locations were separated by a highway and not connected by a viaduct; and (3) control sites, at which there was no highway fragmenting the forest. For four small mammal species, the common tree shrew Tupaia glis, Rajah's spiny rat Maxomys rajah, Whitehead's spiny rat Maxomys whiteheadi and dark-tailed tree rat Niviventer cremoriventer, we used genome-wide markers to assess genetic diversity, gene flow and genetic structure. The differences in genetic distance across sampling settings among the four species indicate that they respond differently to the presence of highways and viaducts. Viaducts connecting forests separated by highways appear to maintain higher population connectivity than forest fragments without viaducts, at least in M. whiteheadi, but apparently not in the other species.
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Affiliation(s)
- Tabitha C. Y. Hui
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
| | - Qian Tang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
| | - Elize Y. X. Ng
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Hobart, TAS 7005, Australia
| | - Ju Lian Chong
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Terengganu, Malaysia;
| | - Eleanor M. Slade
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Frank E. Rheindt
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
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3
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Haugen H, Dervo BK, Østbye K, Heggenes J, Devineau O, Linløkken A. Genetic diversity, gene flow, and landscape resistance in a pond-breeding amphibian in agricultural and natural forested landscapes in Norway. Evol Appl 2024; 17:e13633. [PMID: 38283603 PMCID: PMC10810167 DOI: 10.1111/eva.13633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/23/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024] Open
Abstract
Genetic diversity is a key part of biodiversity, threatened by human activities that lead to loss of gene flow and reduction of effective population sizes. Gene flow is a result of both landscape connectivity and demographic processes determining the number of dispersing individuals in space and time. Thus, the effect of human impact on processes determining the level of genetic diversity must be interpreted in the context of basic ecological conditions affecting survival and recruitment. When the intensity of human impact and habitat suitability correlate, the effect on genetic diversity and gene flow may be challenging to predict. We compared genetic diversity, gene flow and landscape resistance in two contrasting landscapes in Norway for the pond-breeding amphibian Triturus cristatus: a highly human-impacted, agricultural landscape with ecologically productive habitats, and a forested landscape with less productive habitats and lower levels of human impact. Our results show that genetic diversity was higher and gene flow lower within the forested landscape. Microclimatic moisture conditions and vegetation cover were important determinants of landscape resistance to gene flow within both landscapes. There were indications that landscape resistance was increased by minor roads in the forested landscape, which was not the case for the agricultural landscape, suggesting a higher vulnerability to human interference within the landscape matrix for the populations in less productive habitats. Our findings suggest that the effect of human impact on genetic diversity may not be straightforward but modulated by the ecological conditions underlying local demographic processes. Populations within both landscapes seem to be vulnerable to loss of genetic diversity, but due to different mechanisms. This has implications for the choice of relevant management actions, that is, increasing population stability may be more relevant within an agricultural landscape still permeable for dispersal, while conserving dispersal corridors may be more appropriate in the forested landscape, to avoid isolation and increased genetic drift.
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Affiliation(s)
- Hanne Haugen
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
| | - Børre K. Dervo
- Norwegian Institute for Nature Research (NINA)OsloNorway
| | - Kjartan Østbye
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
- Department of BiosciencesCenter for Ecological and Evolutionary Synthesis (CEES)University of OsloOsloNorway
| | - Jan Heggenes
- Department of Natural Sciences and Environmental HealthUniversity of South‐Eastern NorwayUniversity of South‐Eastern NorwayNotoddenNorway
| | - Olivier Devineau
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
| | - Arne Linløkken
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
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4
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Kimble SJA, Unger SD, Williams RN. Genetically derived effective population size estimates of herpetofaunal species should be used with caution. J Wildl Manage 2022. [DOI: 10.1002/jwmg.22340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | - Shem D. Unger
- Department of Biology Wingate University Wingate NC 28174 USA
| | - Rod N. Williams
- Department of Forestry and Natural Resources Purdue University West Lafayette IN 47907 USA
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He Q, Yan S, Garber PA, Ren B, Qi X, Zhou J. Habitat restoration is the greatest challenge for population recovery of Hainan gibbons (Nomascus hainanus). Integr Zool 2022. [PMID: 36064198 DOI: 10.1111/1749-4877.12684] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Hainan gibbons are among the world's most critically endangered primates, with a remaining population of only 35 individuals distributed across 5 social groups in the Bawangling Branch of the Hainan Tropical Rainforest National Park, China. Habitat conversion and forest fragmentation over the past 40 years have reduced their geographical distribution by 95%. In the absence of a quantitative assessment of the availability of remaining suitable habitat, it is unclear whether this species can survive to the end of this century. We used behavioral observations, ArcGIS, remote sensing, stereo optical imagery, and MaxEnt modeling to identify patterns of Hainan gibbon range use and compare changes in the distribution of suitable forest types and areas of forest fragmentation over the past 20 years (2000-2020). The results indicate that the combined range of the 5 extant Hainan gibbon groups totaled 14.89 km2 . The home range of the smallest group (Group E, 3 individuals) was 1.51 km2 , which likely represents the minimum home range size for this species. The remaining area of highly suitable and moderately suitable habitat totals 26.9 km2 . However, habitat connectivity across the gibbon range is very low (less than 0.5), limiting the ability of Hainan gibbons to move between forest patches. The results of this study indicate that the availability of suitable habitat in Bawangling is insufficient to allow for future Hainan gibbon population growth. Therefore, immediate action must be taken to restore, reforest, and establish ecological corridors to reconnect areas of suitable habitat for these critically endangered gibbons.
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Affiliation(s)
- Qingqing He
- School of Karst Science, Guizhou Normal University, Guiyang, China
| | - Shasha Yan
- School of Karst Science, Guizhou Normal University, Guiyang, China
| | - Paul A Garber
- Department of Anthropology, University of Illinois, Urbana, Illinois, USA
| | - Baoping Ren
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Xvming Qi
- Bawangling Branch, Hainan Tropic Rainforest National Park Administration, China
| | - Jiang Zhou
- School of Karst Science, Guizhou Normal University, Guiyang, China
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6
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Giuntini S, Pedruzzi L. Sex and the patch: the influence of habitat fragmentation on terrestrial vertebrates’ mating strategies. ETHOL ECOL EVOL 2022. [DOI: 10.1080/03949370.2022.2059787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Silvia Giuntini
- Dipartimento di Biologia, Università di Pisa, Via Alessandro Volta 6, Pisa 56126, Italy
- Environmental Analysis and Management Unit, Guido Tosi Research Group, Department of Theoretical and Applied Sciences, Università degli Studi dell’Insubria, Varese, Italy
| | - Luca Pedruzzi
- Dipartimento di Biologia, Università di Pisa, Via Alessandro Volta 6, Pisa 56126, Italy
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Willi Y, Kristensen TN, Sgrò CM, Weeks AR, Ørsted M, Hoffmann AA. Conservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species. Proc Natl Acad Sci U S A 2022; 119:e2105076119. [PMID: 34930821 PMCID: PMC8740573 DOI: 10.1073/pnas.2105076119] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
About 50 y ago, Crow and Kimura [An Introduction to Population Genetics Theory (1970)] and Ohta and Kimura [Genet. Res. 22, 201-204 (1973)] laid the foundations of conservation genetics by predicting the relationship between population size and genetic marker diversity. This work sparked an enormous research effort investigating the importance of population dynamics, in particular small population size, for population mean performance, population viability, and evolutionary potential. In light of a recent perspective [J. C. Teixeira, C. D. Huber, Proc. Natl. Acad. Sci. U.S.A. 118, 10 (2021)] that challenges some fundamental assumptions in conservation genetics, it is timely to summarize what the field has achieved, what robust patterns have emerged, and worthwhile future research directions. We consider theory and methodological breakthroughs that have helped management, and we outline some fundamental and applied challenges for conservation genetics.
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Affiliation(s)
- Yvonne Willi
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Torsten N Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - Carla M Sgrò
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Andrew R Weeks
- School of BioSciences, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
- Cesar Australia, Brunswick, VIC 3056, Australia
| | - Michael Ørsted
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
- Department of Biology, Aarhus University, Aarhus 8000, Denmark
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia;
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Charles van Zanten T, Craig Simpson S. Managing the Health of Captive Groups of Reptiles and Amphibians. Vet Clin North Am Exot Anim Pract 2021; 24:609-645. [PMID: 34366012 DOI: 10.1016/j.cvex.2021.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Managing the health of reptile and amphibian collections is centered on providing appropriate environmental parameters, husbandry conditions, and nutrition as well as maintaining good welfare and careful collection planning. Disease transmission is reduced through quarantine, appropriate diagnostic testing, and annual veterinary health assessment."
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Affiliation(s)
- Trent Charles van Zanten
- Conservation, Research and Veterinary Services, Wildlife Reserves Singapore, Jurong Bird Park, 2 Jurong Hill, Singapore 628925.
| | - Shane Craig Simpson
- The Unusual Pet Vets, 210 Karingal Drive, Frankston, Victoria 3199, Australia
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Ribeiro SE, de Almeida-Rocha JM, Weber MM, Kajin M, Lorini ML, Cerqueira R. Do anthropogenic matrix and life-history traits structure small mammal populations? A meta-analytical approach. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01352-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Perrin A, Khimoun A, Faivre B, Ollivier A, de Pracontal N, Théron F, Loubon M, Leblond G, Duron O, Garnier S. Habitat fragmentation differentially shapes neutral and immune gene variation in a tropical bird species. Heredity (Edinb) 2021; 126:148-162. [PMID: 32934360 PMCID: PMC7853120 DOI: 10.1038/s41437-020-00366-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/30/2020] [Accepted: 08/30/2020] [Indexed: 01/11/2023] Open
Abstract
Habitat fragmentation is a major cause of biodiversity loss, responsible for an alteration of intraspecific patterns of neutral genetic diversity and structure. Although neutral genetic variation can be informative for demographic inferences, it may be a poor predictor of adaptive genetic diversity and thus of the consequences of habitat fragmentation on selective evolutionary processes. In this context, we contrasted patterns of genetic diversity and structure of neutral loci (microsatellites) and immune genes (i.e., toll-like receptors) in an understorey bird species, the wedge-billed woodcreeper Glyphorynchus spirurus. The objectives were (1) to investigate forest fragmentation effects on population genetic diversity, (2) to disentangle the relative role of demography (genetic drift and migration) and selection, and (3) to assess whether immunogenetic patterns could be associated with variation of ectoparasite (i.e., ticks) pressures. Our results revealed an erosion of neutral genetic diversity and a substantial genetic differentiation among fragmented populations, resulting from a decrease in landscape connectivity and leading to the divergence of distinct genetic pools at a small spatial scale. Patterns of genetic diversity observed for TLR4 and TLR5 were concordant with neutral genetic patterns, whereas those observed for TLR3 and TLR21 were discordant. This result underlines that the dominant evolutionary force shaping immunogenetic diversity (genetic drift vs. selection) may be different depending on loci considered. Finally, tick prevalence was higher in fragmented environments. We discussed the hypothesis that pathogen selective pressures may contribute to maintain adaptive genetic diversity despite the negative demographic effect of habitat fragmentation on neutral genetic diversity.
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Affiliation(s)
- Antoine Perrin
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France.
| | - Aurélie Khimoun
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Bruno Faivre
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Anthony Ollivier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Nyls de Pracontal
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Franck Théron
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Maxime Loubon
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Gilles Leblond
- SARL BIOS, Route de Davidon, Duzer, 97115, Sainte-Rose, France
| | - Olivier Duron
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France
| | - Stéphane Garnier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
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11
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Ecological corridors for the amphibians and reptiles in the Natura 2000 sites of Romania. Sci Rep 2020; 10:19464. [PMID: 33173154 PMCID: PMC7655805 DOI: 10.1038/s41598-020-76596-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/30/2020] [Indexed: 11/08/2022] Open
Abstract
Landscape heterogeneity and fragmentation are key challenges for biodiversity conservation. As Earth’s landscape is increasingly dominated by anthropogenic land use, it is clear that broad-scale systems of nature reserves connected by corridors are needed to enable the dispersal of flora and fauna. The European Union currently supports a continent-wide network of protected areas, the Natura 2000 program, but this program lacks the necessary connectivity component. To examine whether a comprehensive network could be built in order to protect amphibians and reptiles, two taxonomic groups sensitive to environmental changes due to their physiological constrains and low dispersal capacity, we used species’ distribution maps, the sites of community interest (SCIs) in Romania, and landscape resistance rasters. Except Vipera ursinii rakosiensis, all amphibians and reptiles had corridors mapped that, when assembled, provided linkages for up to 27 species. Natura 2000 species were not good candidates for umbrella species as these linkages covered only 17% of the corridors for all species. Important Areas for Connectivity were identified in the Carpathian Mountains and along the Danube River, further confirming these regions as hot spots for biodiversity in Europe, where successful linkages are most likely. In the end, while such corridors may not be created just for amphibians and reptiles, they can easily be incorporated into more complex linkages with corridors for more charismatic species, therefore enhancing the corridors’ value in terms of quality and structure.
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12
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Almeida-Rocha JM, Soares LASS, Andrade ER, Gaiotto FA, Cazetta E. The impact of anthropogenic disturbances on the genetic diversity of terrestrial species: A global meta-analysis. Mol Ecol 2020; 29:4812-4822. [PMID: 33058295 DOI: 10.1111/mec.15688] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 10/01/2020] [Accepted: 10/08/2020] [Indexed: 01/22/2023]
Abstract
Human activities are primarily responsible for habitat loss and changes in natural environments around the world. It has been suggested that populations inhabiting human-modified landscapes experience reduced gene flow, inbreeding depression, and loss of alleles due to genetic drift. However, empirical evidence shows the contrasting effects of anthropogenic disturbances on the genetic diversity of species. We performed a meta-analysis of 61 studies that compared the genetic diversity of plant and/or animal populations in disturbed and more preserved areas (316 paired comparisons) to investigate the genetic responses to different disturbance types. There is a negative effect (effect size: -0.45; 95% confidence interval: -0.61, -0.29) of disturbances on genetic diversity, in which the most detrimental effects are caused by the loss of connectivity and forest cover. The methodological approach can explain part of the heterogeneity among the genetic responses detected by primary studies: (a) studies using the number of effective alleles did not detect genetic erosion, while all other indices revealed negative responses to disturbances; and (b) only studies performed with transferred or a combination of transferred and specific microsatellites detected negative responses. The effects on animal populations are more detrimental than in plant populations. Only plant species with a shrub life form, self-incompatible reproductive systems, and biotic pollination and seed dispersal showed negative responses to disturbances. Despite heterogeneity among studies, there is an overall negative effect of disturbances on genetic diversity, which indicates that remaining populations inhabiting human-modified landscapes have reduced evolutionary potential and are prone to local extinction.
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Affiliation(s)
| | - Leiza A S S Soares
- Applied Ecology and Conservation Lab, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Edyla R Andrade
- Applied Ecology and Conservation Lab, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Fernanda A Gaiotto
- Applied Ecology and Conservation Lab, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil.,Laboratório de Marcadores Moleculares, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Eliana Cazetta
- Applied Ecology and Conservation Lab, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
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13
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Pabijan M, Palomar G, Antunes B, Antoł W, Zieliński P, Babik W. Evolutionary principles guiding amphibian conservation. Evol Appl 2020; 13:857-878. [PMID: 32431739 PMCID: PMC7232768 DOI: 10.1111/eva.12940] [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: 10/30/2019] [Revised: 02/05/2020] [Accepted: 02/18/2020] [Indexed: 12/18/2022] Open
Abstract
The Anthropocene has witnessed catastrophic amphibian declines across the globe. A multitude of new, primarily human-induced drivers of decline may lead to extinction, but can also push species onto novel evolutionary trajectories. If these are recognized by amphibian biologists, they can be engaged in conservation actions. Here, we summarize how principles stemming from evolutionary concepts have been applied for conservation purposes, and address emerging ideas at the vanguard of amphibian conservation science. In particular, we examine the consequences of increased drift and inbreeding in small populations and their implications for practical conservation. We then review studies of connectivity between populations at the landscape level, which have emphasized the limiting influence of anthropogenic structures and degraded habitat on genetic cohesion. The rapid pace of environmental changes leads to the central question of whether amphibian populations can cope either by adapting to new conditions or by shifting their ranges. We gloomily conclude that extinction seems far more likely than adaptation or range shifts for most species. That said, conservation strategies employing evolutionary principles, such as selective breeding, introduction of adaptive variants through translocations, ecosystem interventions aimed at decreasing phenotype-environment mismatch, or genetic engineering, may effectively counter amphibian decline in some areas or for some species. The spread of invasive species and infectious diseases has often had disastrous consequences, but has also provided some premier examples of rapid evolution with conservation implications. Much can be done in terms of setting aside valuable amphibian habitat that should encompass both natural and agricultural areas, as well as designing protected areas to maximize the phylogenetic and functional diversity of the amphibian community. We conclude that an explicit consideration and application of evolutionary principles, although certainly not a silver bullet, should increase effectiveness of amphibian conservation in both the short and long term.
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Affiliation(s)
- Maciej Pabijan
- Institute of Zoology and Biomedical ResearchFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Gemma Palomar
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Bernardo Antunes
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Weronika Antoł
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Piotr Zieliński
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Wiesław Babik
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
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14
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Catullo RA, Llewelyn J, Phillips BL, Moritz CC. The Potential for Rapid Evolution under Anthropogenic Climate Change. Curr Biol 2019; 29:R996-R1007. [DOI: 10.1016/j.cub.2019.08.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Thompson LM, Klütsch CFC, Manseau M, Wilson PJ. Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction. Ecol Evol 2019; 9:7030-7046. [PMID: 31380031 PMCID: PMC6662424 DOI: 10.1002/ece3.5269] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 11/12/2022] Open
Abstract
With increasing human activities and associated landscape changes, distributions of terrestrial mammals become fragmented. These changes in distribution are often associated with reduced population sizes and loss of genetic connectivity and diversity (i.e., genetic erosion) which may further diminish a species' ability to respond to changing environmental conditions and lead to local population extinctions. We studied threatened boreal caribou (Rangifer tarandus caribou) populations across their distribution in Ontario/Manitoba (Canada) to assess changes in genetic diversity and connectivity in areas of high and low anthropogenic activity. Using data from >1,000 caribou and nine microsatellite loci, we assessed population genetic structure, genetic diversity, and recent migration rates using a combination of network and population genetic analyses. We used Bayesian clustering analyses to identify population genetic structure and explored spatial and temporal variation in those patterns by assembling networks based on R ST and F ST as historical and contemporary genetic edge distances, respectively. The Bayesian clustering analyses identified broad-scale patterns of genetic structure and closely aligned with the R ST network. The F ST network revealed substantial contemporary genetic differentiation, particularly in areas presenting contemporary anthropogenic disturbances and habitat fragmentation. In general, relatively lower genetic diversity and greater genetic differentiation were detected along the southern range limit, differing from areas in the northern parts of the distribution. Moreover, estimation of migration rates suggested a northward movement of animals away from the southern range limit. The patterns of genetic erosion revealed in our study suggest ongoing range retraction of boreal caribou in central Canada.
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Affiliation(s)
- Laura M. Thompson
- Natural Resources DNA Profiling and Forensic CentreTrent UniversityPeterboroughOntarioCanada
- Present address:
U.S. Geological SurveyNational Climate Adaptation Science CenterRestonVirginia
| | - Cornelya F. C. Klütsch
- Natural Resources DNA Profiling and Forensic CentreTrent UniversityPeterboroughOntarioCanada
- Present address:
Division of Environmental Research in the Barents RegionNorwegian Institute of Bioeconomy Research (NIBIO)SvanvikNorway
| | - Micheline Manseau
- Natural Resources DNA Profiling and Forensic CentreTrent UniversityPeterboroughOntarioCanada
- Natural Resources InstituteUniversity of ManitobaWinnipegManitobaCanada
- Landscape Science and TechnologyEnvironment and Climate Change CanadaOttawaOntarioCanada
| | - Paul J. Wilson
- Natural Resources DNA Profiling and Forensic CentreTrent UniversityPeterboroughOntarioCanada
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16
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DeCandia AL, Brzeski KE, Heppenheimer E, Caro CV, Camenisch G, Wandeler P, Driscoll C, vonHoldt BM. Urban colonization through multiple genetic lenses: The city-fox phenomenon revisited. Ecol Evol 2019; 9:2046-2060. [PMID: 30847091 PMCID: PMC6392345 DOI: 10.1002/ece3.4898] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022] Open
Abstract
Urbanization is driving environmental change on a global scale, creating novel environments for wildlife to colonize. Through a combination of stochastic and selective processes, urbanization is also driving evolutionary change. For instance, difficulty in traversing human-modified landscapes may isolate newly established populations from rural sources, while novel selective pressures, such as altered disease risk, toxicant exposure, and light pollution, may further diverge populations through local adaptation. Assessing the evolutionary consequences of urban colonization and the processes underlying them is a principle aim of urban evolutionary ecology. In the present study, we revisited the genetic effects of urbanization on red foxes (Vulpes vulpes) that colonized Zurich, Switzerland. Through use of genome-wide single nucleotide polymorphisms and microsatellite markers linked to the major histocompatibility complex (MHC), we expanded upon a previous neutral microsatellite study to assess population structure, characterize patterns of genetic diversity, and detect outliers associated with urbanization. Our results indicated the presence of one large evolutionary cluster, with substructure evident between geographic sampling areas. In urban foxes, we observed patterns of neutral and functional diversity consistent with founder events and reported increased differentiation between populations separated by natural and anthropogenic barriers. We additionally reported evidence of selection acting on MHC-linked markers and identified outlier loci with putative gene functions related to energy metabolism, behavior, and immunity. We concluded that demographic processes primarily drove patterns of diversity, with outlier tests providing preliminary evidence of possible urban adaptation. This study contributes to our overall understanding of urban colonization ecology and emphasizes the value of combining datasets when examining evolutionary change in an increasingly urban world.
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Affiliation(s)
- Alexandra L. DeCandia
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
| | - Kristin E. Brzeski
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
- School of Forest Resources and Environmental ScienceMichigan Technological UniversityHoughtonMichigan
| | | | - Catherine V. Caro
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | | | - Carlos Driscoll
- Laboratory of Comparative Behavioral GenomicsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthRockvilleMaryland
| | - Bridgett M. vonHoldt
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
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17
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Pflüger FJ, Signer J, Balkenhol N. Habitat loss causes non-linear genetic erosion in specialist species. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2018.e00507] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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18
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Schlaepfer DR, Braschler B, Rusterholz HP, Baur B. Genetic effects of anthropogenic habitat fragmentation on remnant animal and plant populations: a meta-analysis. Ecosphere 2018. [DOI: 10.1002/ecs2.2488] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Daniel R. Schlaepfer
- School of Forestry and Environmental Studies; Yale University; New Haven Connecticut 06511 USA
| | - Brigitte Braschler
- Section of Conservation Biology; Department of Environmental Sciences; University of Basel; CH-4056 Basel Switzerland
| | - Hans-Peter Rusterholz
- Section of Conservation Biology; Department of Environmental Sciences; University of Basel; CH-4056 Basel Switzerland
| | - Bruno Baur
- Section of Conservation Biology; Department of Environmental Sciences; University of Basel; CH-4056 Basel Switzerland
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19
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Genetic polymorphism and structure of wild and zoo populations of the fosa (Eupleridae, Carnivora), the largest living carnivoran of Madagascar. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Land-use change impact on mycorrhizal symbiosis in female and male plants of wild Carica papaya (Caricaceae). Symbiosis 2018. [DOI: 10.1007/s13199-018-0549-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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21
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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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22
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Cosgrove AJ, McWhorter TJ, Maron M. Consequences of impediments to animal movements at different scales: A conceptual framework and review. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12699] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Anita J. Cosgrove
- School of Earth and Environmental Sciences The University of Queensland St Lucia Qld Australia
| | - Todd J. McWhorter
- School of Animal and Veterinary Sciences The University of Adelaide Adelaide SA Australia
| | - Martine Maron
- School of Earth and Environmental Sciences The University of Queensland St Lucia Qld Australia
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23
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Faucher L, Hénocq L, Vanappelghem C, Rondel S, Quevillart R, Gallina S, Godé C, Jaquiéry J, Arnaud JF. When new human-modified habitats favour the expansion of an amphibian pioneer species: Evolutionary history of the natterjack toad (Bufo calamita) in a coal basin. Mol Ecol 2017; 26:4434-4451. [PMID: 28667796 DOI: 10.1111/mec.14229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/17/2017] [Accepted: 06/05/2017] [Indexed: 11/29/2022]
Abstract
Human activities affect microevolutionary dynamics by inducing environmental changes. In particular, land cover conversion and loss of native habitats decrease genetic diversity and jeopardize the adaptive ability of populations. Nonetheless, new anthropogenic habitats can also promote the successful establishment of emblematic pioneer species. We investigated this issue by examining the population genetic features and evolutionary history of the natterjack toad (Bufo [Epidalea] calamita) in northern France, where populations can be found in native coastal habitats and coalfield habitats shaped by European industrial history, along with an additional set of European populations located outside this focal area. We predicted contrasting patterns of genetic structure, with newly settled coalfield populations departing from migration-drift equilibrium. As expected, coalfield populations showed a mosaic of genetically divergent populations with short-range patterns of gene flow, and native coastal populations indicated an equilibrium state with an isolation-by-distance pattern suggestive of postglacial range expansion. However, coalfield populations exhibited (i) high levels of genetic diversity, (ii) no evidence of local inbreeding or reduced effective population size and (iii) multiple maternal mitochondrial lineages, a genetic footprint depicting independent colonization events. Furthermore, approximate Bayesian computations suggested several evolutionary trajectories from ancient isolation in glacial refugia during the Pleistocene, with biogeographical signatures of recent expansion probably confounded by human-mediated mixing of different lineages. From an evolutionary and conservation perspective, this study highlights the ecological value of industrial areas, provided that ongoing regional gene flow is ensured within the existing lineage boundaries.
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Affiliation(s)
- Leslie Faucher
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Laura Hénocq
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Cédric Vanappelghem
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France.,Conservatoire d'espaces naturels du Nord et du Pas de Calais, Lillers, France
| | - Stéphanie Rondel
- Centre Permanent d'Initiatives pour l'Environnement - Chaîne des Terrils, Loos-en-Gohelle, France
| | - Robin Quevillart
- Groupe ornithologique et naturaliste du Nord - Pas-de-Calais, Lille, France
| | - Sophie Gallina
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Cécile Godé
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Julie Jaquiéry
- UMR CNRS 6553 - ECOBIO, Université de Rennes 1, Rennes Cedex, France
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24
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Lourenço A, Álvarez D, Wang IJ, Velo-Antón G. Trapped within the city: integrating demography, time since isolation and population-specific traits to assess the genetic effects of urbanization. Mol Ecol 2017; 26:1498-1514. [DOI: 10.1111/mec.14019] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/04/2017] [Accepted: 01/05/2017] [Indexed: 01/05/2023]
Affiliation(s)
- André Lourenço
- Departamento de Biologia da Faculdade de Ciências da Universidade do Porto; Rua Campo Alegre 4169-007 Porto Portugal
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Instituto de Ciências Agrárias de Vairão; Rua Padre Armando Quintas 7 4485-661 Vairão Portugal
| | - David Álvarez
- Ecology Unit; Department of Organisms and Systems Biology; University of Oviedo; C/ Catedrático Rodrigo Uría 33071 Oviedo Spain
| | - Ian J. Wang
- Department of Environmental Science, Policy and Management; University of California; 130 Mulford Hall #3114 Berkeley CA 94705 USA
| | - Guillermo Velo-Antón
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Instituto de Ciências Agrárias de Vairão; Rua Padre Armando Quintas 7 4485-661 Vairão Portugal
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25
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Munshi‐South J, Zolnik CP, Harris SE. Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations. Evol Appl 2016; 9:546-64. [PMID: 27099621 PMCID: PMC4831458 DOI: 10.1111/eva.12357] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/27/2015] [Indexed: 12/16/2022] Open
Abstract
Urbanization results in pervasive habitat fragmentation and reduces standing genetic variation through bottlenecks and drift. Loss of genomewide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genomewide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genomewide variation was estimated as a proxy for evolutionary potential using more than 10 000 single nucleotide polymorphism (SNP) markers generated by ddRAD-Seq. We found that genomewide variation is inversely related to urbanization as measured by percent impervious surface cover, and to a lesser extent, human population density. We also report that urbanization results in enhanced genomewide differentiation between populations in cities. There was no pattern of isolation by distance among these populations, but an isolation by resistance model based on impervious surface significantly explained patterns of genetic differentiation. Isolation by environment modeling also indicated that urban populations deviate much more strongly from global allele frequencies than suburban or rural populations. This study is the first to examine loss of genomewide SNP variation along an urban-to-rural gradient and quantify urbanization as a driver of population genomic patterns.
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Affiliation(s)
- Jason Munshi‐South
- Department of Biological Sciences and the Louis Calder Center—Biological Field StationFordham UniversityArmonkNYUSA
| | - Christine P. Zolnik
- Department of Biological Sciences and the Louis Calder Center—Biological Field StationFordham UniversityArmonkNYUSA
| | - Stephen E. Harris
- Ph.D. Program in EcologyEvolutionary Biology and Behaviorthe Graduate Center of the City University of New YorkNew YorkNYUSA
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26
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Roth S, Jehle R. High genetic diversity of common toad (Bufo bufo) populations under strong natural fragmentation on a Northern archipelago. Ecol Evol 2016; 6:1626-36. [PMID: 27087930 PMCID: PMC4801968 DOI: 10.1002/ece3.1957] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 02/02/2023] Open
Abstract
The last decades have shown a surge in studies focusing on the interplay between fragmented habitats, genetic variation, and conservation. In the present study, we consider the case of a temperate pond-breeding anuran (the common toad Bufo bufo) inhabiting a naturally strongly fragmented habitat at the Northern fringe of the species' range: islands offshore the Norwegian coast. A total of 475 individuals from 19 populations (three mainland populations and 16 populations on seven adjacent islands) were genetically characterized using nine microsatellite markers. As expected for a highly fragmented habitat, genetic distances between populations were high (pairwise F st values ranging between 0.06 and 0.33), with however little differences between populations separated by ocean and populations separated by terrestrial habitat (mainland and on islands). Despite a distinct cline in genetic variation from mainland populations to peripheral islands, the study populations were characterized by overall high genetic variation, in line with effective population sizes derived from single-sample estimators which were on average about 20 individuals. Taken together, our results reinforce the notion that spatial and temporal scales of fragmentation need to be considered when studying the interplay between landscape fragmentation and genetic erosion.
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Affiliation(s)
- Steffen Roth
- The Natural History Collections University Museum of Bergen Bergen N-5020 Norway
| | - Robert Jehle
- School of Environment and Life Sciences University of Salford Salford M5 4WT UK
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