Signatures of Rapid Evolution in Urban and Rural Transcriptomes of White-Footed Mice (Peromyscus leucopus) in the New York Metropolitan Area
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{"title"=>"Signatures of Rapid Evolution in Urban and Rural Transcriptomes of White-Footed Mice (Peromyscus leucopus) in the New York Metropolitan Area", "type"=>"journal", "authors"=>[{"first_name"=>"Stephen E.", "last_name"=>"Harris", "scopus_author_id"=>"55838624300"}, {"first_name"=>"Jason", "last_name"=>"Munshi-South", "scopus_author_id"=>"56089114300"}, {"first_name"=>"Craig", "last_name"=>"Obergfell", "scopus_author_id"=>"8400962300"}, {"first_name"=>"Rachel", "last_name"=>"O'Neill", "scopus_author_id"=>"35453942200"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84883181072", "sgr"=>"84883181072", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0074938", "pmid"=>"24015321", "isbn"=>"1646660625", "pui"=>"369686916"}, "id"=>"f709deb7-390c-3849-b14d-f698a7fc7080", "abstract"=>"Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscusleucopus, is a common resident of NYC's forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar \"urban adapter.\" We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.", "link"=>"http://www.mendeley.com/research/signatures-rapid-evolution-urban-rural-transcriptomes-whitefooted-mice-peromyscus-leucopus-new-york-7", "reader_count"=>99, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>5, "Researcher"=>15, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>36, "Student > Postgraduate"=>4, "Other"=>4, "Student > Master"=>13, "Student > Bachelor"=>11, "Lecturer"=>2, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>5, "Researcher"=>15, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>36, "Student > Postgraduate"=>4, "Other"=>4, "Student > Master"=>13, "Student > Bachelor"=>11, "Lecturer"=>2, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>9, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>80, "Medicine and Dentistry"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>80}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>9}}, "reader_count_by_country"=>{"United States"=>7}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1184329"], "description"=>"<p>(a) Comparison of brain transcriptome to liver and gonad. (b) Comparison of liver to brain and gonad. (c) Comparison of gonad to liver and brain.</p>", "links"=>[], "tags"=>["pairwise", "comparisons"], "article_id"=>783776, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Stephen E. Harris", "Jason Munshi-South", "Craig Obergfell", "Rachel O’Neill"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0074938.g004", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Over_represented_GO_terms_from_pairwise_tissue_comparisons_FDR_8804_0_05_/783776", "title"=>"Over-represented GO terms from pairwise tissue comparisons (FDR ≤0.05).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-28 02:18:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1184326"], "description"=>"<p>Number of assembled <i>P</i><i>. leucopus</i> contigs from four different tissue types that had significant hits with known proteins on BLASTX, and GO term annotations from reference databases using Blast2Go; Blue = Total number of contigs, Red = BLASTX hits, Green = number of annotated contigs.</p>", "links"=>[], "tags"=>[], "article_id"=>783774, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Stephen E. Harris", "Jason Munshi-South", "Craig Obergfell", "Rachel O’Neill"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0074938.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Annotation_of_final_reference_transcriptome_/783774", "title"=>"Annotation of final reference transcriptome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-28 02:18:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1184356", "https://ndownloader.figshare.com/files/1184357", "https://ndownloader.figshare.com/files/1184358", "https://ndownloader.figshare.com/files/1184359", "https://ndownloader.figshare.com/files/1184360"], "description"=>"<div><p>Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, <i>Peromyscus</i><i>leucopus</i>, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban <i>P</i><i>. leucopus</i> to examine evolutionary changes in protein-coding regions for an exemplar “urban adapter.” We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of <i>P</i><i>. leucopus</i>. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.</p> </div>", "links"=>[], "tags"=>["signatures", "transcriptomes", "white-footed", "mice", "york"], "article_id"=>783802, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Stephen E. Harris", "Jason Munshi-South", "Craig Obergfell", "Rachel O’Neill"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0074938.s001", "https://dx.doi.org/10.1371/journal.pone.0074938.s002", "https://dx.doi.org/10.1371/journal.pone.0074938.s003", "https://dx.doi.org/10.1371/journal.pone.0074938.s004", "https://dx.doi.org/10.1371/journal.pone.0074938.s005"], "stats"=>{"downloads"=>17, "page_views"=>49, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Signatures_of_Rapid_Evolution_in_Urban_and_Rural_Transcriptomes_of_White_Footed_Mice_Peromyscus_leucopus_in_the_New_York_Metropolitan_Area/783802", "title"=>"Signatures of Rapid Evolution in Urban and Rural Transcriptomes of White-Footed Mice (<i>Peromyscus leucopus</i>) in the New York Metropolitan Area", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-08-28 02:18:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1184332"], "description"=>"<p>Each circle represents one unique assembled contig. (a) Pairwise comparisons for all urban populations. (b) Pairwise comparisons for urban to rural populations. The dashed line denotes <i>p</i><sub>N</sub> / <i>p</i><sub>S</sub> = 1, and circles above the line (<i>p</i><sub>N</sub> / <i>p</i><sub>S</sub> > 1) indicate candidates for positive selection. The solid line shows the slope for <i>p</i><sub>N</sub> / <i>p</i><sub>S</sub> = 0.5.</p>", "links"=>[], "tags"=>["snp", "substitutions", "plotted", "synonymous", "354"], "article_id"=>783779, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Stephen E. Harris", "Jason Munshi-South", "Craig Obergfell", "Rachel O’Neill"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0074938.g005", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Non_synonymous_p_N_SNP_substitutions_plotted_vs_synonymous_p_S_substitutions_for_354_genes_/783779", "title"=>"Non-synonymous (<i>p</i><sub>N</sub>) SNP substitutions plotted vs. synonymous (<i>p</i><sub>S</sub>) substitutions for 354 genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-28 02:18:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1184349"], "description"=>"<p>Urban populations are in shades of blue; light blue = male; dark blue = female. Rural population in orange and brown; orange = male; brown = female. Areas shaded red on the map indicate degree of urbanization (i.e. impermeable surface cover such as roads and rooftops) and green areas indicate vegetation cover from the 2006 National Landcover Database (CP = Central Park; NYBG = New York Botanical Gardens; RR = Ridgewood Reservoir; FM = Flushing Meadows-Willow Lake; HP = Harriman State Park).</p>", "links"=>[], "tags"=>["individuals", "populations", "nyc"], "article_id"=>783796, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Stephen E. Harris", "Jason Munshi-South", "Craig Obergfell", "Rachel O’Neill"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0074938.g006", "stats"=>{"downloads"=>1, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Location_and_number_of_individuals_collected_from_five_populations_in_the_NYC_metropolitan_area_/783796", "title"=>"Location and number of individuals collected from five populations in the NYC metropolitan area.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-28 02:18:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1184318"], "description"=>"<p>Number and distribution of contigs from <i>P</i><i>. leucopus</i> transcriptome (Newbler cDNA assembly) that aligned to each chromosome of the. (a) <i>Rattus norvegicus</i>. Blue = total number of genes per chromosome for <i>Rattus</i>. Red = number of aligned <i>Peromyscus</i> isotigs per <i>Rattus</i> chromosome. (b) <i>Mus musculus</i>. Blue = total number of genes per chromosome for <i>Mus</i>. Red = number of aligned <i>Peromyscus</i> isotigs per <i>Mus</i> chromosome.</p>", "links"=>[], "tags"=>["alignment", "rodent"], "article_id"=>783766, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Stephen E. Harris", "Jason Munshi-South", "Craig Obergfell", "Rachel O’Neill"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0074938.g002", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transcriptome_alignment_to_reference_rodent_genomes_/783766", "title"=>"Transcriptome alignment to reference rodent genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-28 02:18:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1184315"], "description"=>"<p>Inset: Zoomed-in view of frequency of longer assembled contigs from 1,500–3,000 bp. Blue line = Newbler cDNA, Red line = Newbler genome, Green line = Cap3.</p>", "links"=>[], "tags"=>["contig", "lengths", "transcriptome"], "article_id"=>783762, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Stephen E. Harris", "Jason Munshi-South", "Craig Obergfell", "Rachel O’Neill"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0074938.g001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_of_contig_lengths_for_three_transcriptome_assembly_methods_/783762", "title"=>"Frequency of contig lengths for three transcriptome assembly methods.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-28 02:18:18"}

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Relative Metric

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