A Rapid, Strong, and Convergent Genetic Response to Urban Habitat Fragmentation in Four Divergent and Widespread Vertebrates
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{"title"=>"A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates", "type"=>"journal", "authors"=>[{"first_name"=>"Kathleen Semple", "last_name"=>"Delaney", "scopus_author_id"=>"8297100900"}, {"first_name"=>"Seth P.D.", "last_name"=>"Riley", "scopus_author_id"=>"56258717000"}, {"first_name"=>"Robert N.", "last_name"=>"Fisher", "scopus_author_id"=>"7403556431"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-77958526424", "pui"=>"359839095", "doi"=>"10.1371/journal.pone.0012767", "isbn"=>"1932-6203", "sgr"=>"77958526424", "pmid"=>"20862274"}, "id"=>"70725246-171c-38ba-9d41-a8429f269001", "abstract"=>"Background: Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding. Methodology/Principal Findings: We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation. Conclusions/Significance: Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.", "link"=>"http://www.mendeley.com/research/rapid-strong-convergent-genetic-response-urban-habitat-fragmentation-four-divergent-widespread-verte", "reader_count"=>272, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>11, "Student > Doctoral Student"=>13, "Researcher"=>51, "Student > Ph. D. Student"=>62, "Student > Postgraduate"=>11, "Other"=>18, "Student > Master"=>54, "Student > Bachelor"=>29, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>2, "Professor"=>14}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>11, "Student > Doctoral Student"=>13, "Researcher"=>51, "Student > Ph. D. Student"=>62, "Student > Postgraduate"=>11, "Other"=>18, "Student > Master"=>54, "Student > Bachelor"=>29, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>2, "Professor"=>14}, "reader_count_by_subject_area"=>{"Unspecified"=>9, "Engineering"=>1, "Environmental Science"=>51, "Biochemistry, Genetics and Molecular Biology"=>12, "Agricultural and Biological Sciences"=>187, "Medicine and Dentistry"=>1, "Psychology"=>1, "Social Sciences"=>2, "Computer Science"=>4, "Earth and Planetary Sciences"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>2}, "Psychology"=>{"Psychology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>187}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Unspecified"=>{"Unspecified"=>9}, "Environmental Science"=>{"Environmental Science"=>51}}, "reader_count_by_country"=>{"Romania"=>1, "United States"=>10, "Sri Lanka"=>1, "United Kingdom"=>1, "Switzerland"=>1, "Portugal"=>2, "Russia"=>1, "Canada"=>2, "China"=>1, "Brazil"=>5, "Italy"=>1, "South Africa"=>1, "Nigeria"=>1, "France"=>1}, "group_count"=>7}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/829945"], "description"=>"a<p>Mantel test correlations between genetic distance (F<sub>ST</sub>) and geographic distance (GD).</p>b<p>Partial Mantel tests for partial correlations between the presence of Highway 23 only (HWY), the presence of major roads including Highway 23 (RDS), and the age of isolation between patches (patch age; AGE) while controlling for geographic distance.</p>", "links"=>[], "tags"=>["mantel"], "article_id"=>500321, "categories"=>["Evolutionary Biology", "Ecology"], "users"=>["Kathleen Semple Delaney", "Seth P. D. Riley", "Robert N. Fisher"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012767.t002", "stats"=>{"downloads"=>1, "page_views"=>29, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mantel_and_partial_Mantel_tests_with_genetic_distance_and_landscape_features_/500321", "title"=>"Mantel and partial Mantel tests with genetic distance and landscape features.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-16 00:05:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/413145", "https://ndownloader.figshare.com/files/413182", "https://ndownloader.figshare.com/files/413216", "https://ndownloader.figshare.com/files/413243", "https://ndownloader.figshare.com/files/413275", "https://ndownloader.figshare.com/files/413307"], "description"=>"<div><h3>Background</h3><p>Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding.</p><h3>Methodology/Principal Findings</h3><p>We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation.</p><h3>Conclusions/Significance</h3><p>Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.</p></div>", "links"=>[], "tags"=>["convergent", "fragmentation", "divergent", "vertebrates"], "article_id"=>141621, "categories"=>["Evolutionary Biology", "Ecology"], "users"=>["Kathleen Semple Delaney", "Seth P. D. Riley", "Robert N. Fisher"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0012767.s001", "https://dx.doi.org/10.1371/journal.pone.0012767.s002", "https://dx.doi.org/10.1371/journal.pone.0012767.s003", "https://dx.doi.org/10.1371/journal.pone.0012767.s004", "https://dx.doi.org/10.1371/journal.pone.0012767.s005", "https://dx.doi.org/10.1371/journal.pone.0012767.s006"], "stats"=>{"downloads"=>39, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Rapid_Strong_and_Convergent_Genetic_Response_to_Urban_Habitat_Fragmentation_in_Four_Divergent_and_Widespread_Vertebrates/141621", "title"=>"A Rapid, Strong, and Convergent Genetic Response to Urban Habitat Fragmentation in Four Divergent and Widespread Vertebrates", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-09-16 00:27:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/829729"], "description"=>"<p>Each column represents one individual and colors correspond to the percentage of assignment to each cluster. Patch names (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012767#pone-0012767-g001\" target=\"_blank\">Fig. 1a</a>) are on the X-axis organized from west (left) to east (right). A black triangle indicates the location of the 23 freeway.</p>", "links"=>[], "tags"=>["clustering", "reveals"], "article_id"=>500105, "categories"=>["Evolutionary Biology", "Ecology"], "users"=>["Kathleen Semple Delaney", "Seth P. D. Riley", "Robert N. Fisher"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012767.g002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_clustering_analysis_reveals_the_most_likely_K_/500105", "title"=>"Genetic clustering analysis reveals the most likely K.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-16 00:01:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/829977"], "description"=>"a<p>Patch isolation values (PROX) decrease with increasing isolation of patches.</p>b<p>Patch age was calculated as the number of years since the patch was 100% isolated from other open natural space.</p>", "links"=>[], "tags"=>["metrics", "samples", "genotyped"], "article_id"=>500347, "categories"=>["Evolutionary Biology", "Ecology"], "users"=>["Kathleen Semple Delaney", "Seth P. D. Riley", "Robert N. Fisher"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012767.t001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Patch_metrics_area_isolation_and_age_and_the_number_of_samples_genotyped_by_species_/500347", "title"=>"Patch metrics (area, isolation, and age) and the number of samples genotyped by species.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-16 00:05:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/829869"], "description"=>"<p>A. wrentits (H<sub>e</sub>: R<sup>2</sup> = 0.698, p = 0.051, d.f. = 7; N<sub>A</sub>: R<sup>2</sup> = 0.55, p = 0.035, d.f. = 7) and B. three lizard species (R<sub>LR</sub>: side-blotched lizard R<sup>2</sup> = 0.4, p = 0.03, d.f. = 10; western skink R<sup>2</sup> = 0.33, p = 0.05, d.f. = 9; western fence lizard R<sup>2</sup> = 0.52, p = 0.002, d.f. = 8). <sup>a</sup> Patch proximity is the inverse of patch isolation.</p>", "links"=>[], "tags"=>["ecology", "ecology/evolutionary ecology", "ecology/global change ecology", "evolutionary biology/evolutionary ecology"], "article_id"=>500237, "categories"=>["Evolutionary Biology", "Ecology"], "users"=>["Kathleen Semple Delaney", "Seth P. D. Riley", "Robert N. Fisher"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012767.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_genetic_diversity_heterozygosity_number_of_effective_alleles_and_relatedness_and_patch_proximity_a_log_transformed_/500237", "title"=>"Relationship between genetic diversity (heterozygosity, number of effective alleles, and relatedness) and patch proximity<sup>a</sup> (log transformed).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-16 00:03:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/829540"], "description"=>"<p>A. Sampling sites (mist-net and pitfall locations), roads, and habitat patches (S = small, L = large, C = core) within the study area (Sample sizes are shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012767#pone-0012767-t001\" target=\"_blank\">Table 1</a>). B. Mean genetic divergence mapped on the Simi Hills landscape for all four species, and separately for C. wrentits, D. side-blotched lizards, E. western skinks, and F. western fence lizards.</p>", "links"=>[], "tags"=>["ecology", "ecology/evolutionary ecology", "ecology/global change ecology", "evolutionary biology/evolutionary ecology"], "article_id"=>499902, "categories"=>["Evolutionary Biology", "Ecology"], "users"=>["Kathleen Semple Delaney", "Seth P. D. Riley", "Robert N. Fisher"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012767.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Study_area_and_genetic_divergence_/499902", "title"=>"Study area and genetic divergence.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-16 02:45:02"}

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Relative Metric

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