Replicate Phylogenies and Post-Glacial Range Expansion of the Pitcher-Plant Mosquito, Wyeomyia smithii, in North America
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{"title"=>"Replicate Phylogenies and Post-Glacial Range Expansion of the Pitcher-Plant Mosquito, Wyeomyia smithii, in North America", "type"=>"journal", "authors"=>[{"first_name"=>"Clayton", "last_name"=>"Merz", "scopus_author_id"=>"36721923900"}, {"first_name"=>"Julian M.", "last_name"=>"Catchen", "scopus_author_id"=>"8879140800"}, {"first_name"=>"Victor", "last_name"=>"Hanson-Smith", "scopus_author_id"=>"37018207100"}, {"first_name"=>"Kevin J.", "last_name"=>"Emerson", "scopus_author_id"=>"15072561600"}, {"first_name"=>"William E.", "last_name"=>"Bradshaw", "scopus_author_id"=>"7005486622"}, {"first_name"=>"Christina M.", "last_name"=>"Holzapfel", "scopus_author_id"=>"7006509279"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84883651377", "sgr"=>"84883651377", "pui"=>"369769965", "isbn"=>"1932-6203", "pmid"=>"24039746", "doi"=>"10.1371/journal.pone.0072262"}, "id"=>"fe16da43-2674-3410-ac7a-db2bd7597790", "abstract"=>"Herein we tested the repeatability of phylogenetic inference based on high throughput sequencing by increased taxon sampling using our previously published techniques in the pitcher-plant mosquito, Wyeomyia smithii in North America. We sampled 25 natural populations drawn from different localities nearby 21 previous collection localities and used these new data to construct a second, independent phylogeny, expressly to test the reproducibility of phylogenetic patterns. Comparison of trees between the two data sets based on both maximum parsimony and maximum likelihood with Bayesian posterior probabilities showed close correspondence in the grouping of the most southern populations into clear clades. However, discrepancies emerged, particularly in the middle of W. smithii's current range near the previous maximum extent of the Laurentide Ice Sheet, especially concerning the most recent common ancestor to mountain and northern populations. Combining all 46 populations from both studies into a single maximum parsimony tree and taking into account the post-glacial historical biogeography of associated flora provided an improved picture of W. smithii's range expansion in North America. In a more general sense, we propose that extensive taxon sampling, especially in areas of known geological disruption is key to a comprehensive approach to phylogenetics that leads to biologically meaningful phylogenetic inference.", "link"=>"http://www.mendeley.com/research/replicate-phylogenies-postglacial-range-expansion-pitcherplant-mosquito-wyeomyia-smithii-north-ameri", "reader_count"=>43, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>12, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>1, "Student > Master"=>7, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>12, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>1, "Student > Master"=>7, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>36}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>36}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>4}}, "reader_count_by_country"=>{"Canada"=>1, "Austria"=>2, "United States"=>3, "Brazil"=>1, "Spain"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1194586", "https://ndownloader.figshare.com/files/1194587"], "description"=>"<div><p>Herein we tested the repeatability of phylogenetic inference based on high throughput sequencing by increased taxon sampling using our previously published techniques in the pitcher-plant mosquito, <i>Wyeomyia smithii</i> in North America. We sampled 25 natural populations drawn from different localities nearby 21 previous collection localities and used these new data to construct a second, independent phylogeny, expressly to test the reproducibility of phylogenetic patterns. Comparison of trees between the two data sets based on both maximum parsimony and maximum likelihood with Bayesian posterior probabilities showed close correspondence in the grouping of the most southern populations into clear clades. However, discrepancies emerged, particularly in the middle of <i>W. smithii</i>'s current range near the previous maximum extent of the Laurentide Ice Sheet, especially concerning the most recent common ancestor to mountain and northern populations. Combining all 46 populations from both studies into a single maximum parsimony tree and taking into account the post-glacial historical biogeography of associated flora provided an improved picture of <i>W. smithii</i>'s range expansion in North America. In a more general sense, we propose that extensive taxon sampling, especially in areas of known geological disruption is key to a comprehensive approach to phylogenetics that leads to biologically meaningful phylogenetic inference.</p></div>", "links"=>[], "tags"=>["replicate", "phylogenies", "post-glacial", "pitcher-plant", "america"], "article_id"=>791456, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Clayton Merz", "Julian M. Catchen", "Victor Hanson-Smith", "Kevin J. Emerson", "William E. Bradshaw", "Christina M. Holzapfel"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0072262.s001", "https://dx.doi.org/10.1371/journal.pone.0072262.s002"], "stats"=>{"downloads"=>3, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Replicate_Phylogenies_and_Post_Glacial_Range_Expansion_of_the_Pitcher_Plant_Mosquito_Wyeomyia_smithii_in_North_America/791456", "title"=>"Replicate Phylogenies and Post-Glacial Range Expansion of the Pitcher-Plant Mosquito, <i>Wyeomyia smithii</i>, in North America", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-09-06 02:12:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1194583"], "description"=>"<p><b>Left</b>, phylogenetic tree from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072262#pone.0072262-Emerson1\" target=\"_blank\">[1]</a> using 21 populations and 54 bp reads. <b>Right</b>, phylogenetic tree from the current study using 25 populations and 80 bp reads. Colors and abbreviations as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072262#pone-0072262-g001\" target=\"_blank\">Figure 1</a>. Nodal values show bootstrap support >50%.</p>", "links"=>[], "tags"=>["parsimony"], "article_id"=>791453, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Clayton Merz", "Julian M. Catchen", "Victor Hanson-Smith", "Kevin J. Emerson", "William E. Bradshaw", "Christina M. Holzapfel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0072262.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Replicability_of_maximum_parsimony_trees_/791453", "title"=>"Replicability of maximum parsimony trees.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-06 02:12:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1194584"], "description"=>"<p>The tree is based on 54>50% support. Color codes are the same as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072262#pone-0072262-g001\" target=\"_blank\">Figures 1</a>–<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072262#pone-0072262-g002\" target=\"_blank\">2</a>. There are two major monophyletic groupings: one consisting of populations along the Gulf and North Carolina Coasts, the other consisting of all more northern and mountain populations. The mainland Maryland population (MD2) shares a most recent common ancestor with all more northern and mountain populations. Phylogenetic results generally follow latitude except for the mountain populations (NCmt, PA). There are six well supported clades (bootstrap>70) that include two or more populations: Gulf Coast (MS, AL, FL: black), North Carolina Coast (NC: red), North Carolina mountains (NCmt: green), Pocono Mountains (PA: brown), northeast (ME, NS, NL: blue), and northwest (WI2–3, wON, MB, SK: purple). The North Carolina mountain populations (NCmt) split into two clades: one in the Savannah River drainage leading to the Atlantic Ocean (NCmt1–2), the other in the Tennessee River drainage (NCmt3–5) leading to the Gulf of Mexico.</p>", "links"=>[], "tags"=>["parsimony", "bootstrap", "46"], "article_id"=>791454, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Clayton Merz", "Julian M. Catchen", "Victor Hanson-Smith", "Kevin J. Emerson", "William E. Bradshaw", "Christina M. Holzapfel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0072262.g003", "stats"=>{"downloads"=>3, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_parsimony_with_bootstrap_support_for_the_combined_46_populations_/791454", "title"=>"Maximum parsimony with bootstrap support for the combined 46 populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-06 02:12:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1194582"], "description"=>"<p><b>Left</b>, phylogenetic tree from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072262#pone.0072262-Emerson1\" target=\"_blank\">[1]</a> using 21 populations and 54 bp reads <b>Right</b>, phylogenetic tree from the current study using 25 populations and 80 bp reads. Branches leading to <i>W. mitchellii</i> and <i>W. vanduzeei</i> are abbreviated to clarify presentation. Color code indicates region of geographic origin. Numbers show nodal support as aLRT-SH scores. Two-letter abbreviations identify each state or province. Where two or more sites come from the same state or province, they are identified by number. Latitudes, longitudes, altitudes, and acronyms connecting the specific localities with earlier studies from this lab are provided in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072262#pone.0072262.s001\" target=\"_blank\">Table S1</a>. The scale bars indicate substitutions per site.</p>", "links"=>[], "tags"=>[], "article_id"=>791452, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Clayton Merz", "Julian M. Catchen", "Victor Hanson-Smith", "Kevin J. Emerson", "William E. Bradshaw", "Christina M. Holzapfel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0072262.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Replicability_of_maximum_likelihood_trees_/791452", "title"=>"Replicability of maximum likelihood trees.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-06 02:12:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1194585"], "description"=>"<p>Arrows indicate directions of range expansion based on <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072262#pone-0072262-g003\" target=\"_blank\">Figure 3</a>. Maximum extent of the Laurentide Ice Sheet at the last glacial maximum is plotted as a dotted line <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072262#pone.0072262-Colgan1\" target=\"_blank\">[6]</a>. Two-letter abbreviations identify each state or province. Color codes are the same as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072262#pone-0072262-g001\" target=\"_blank\">Figures 1</a>–<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072262#pone-0072262-g003\" target=\"_blank\">3</a>. Map symbols represented by a triangle show mountain populations in the southern Appalachians of North Carolina (green) or in the Pocono Mountains of Pennsylvania (brown). The filled orange symbol with the star indicates the mainland Maryland population (MD2). Numbers associated with each node or branch tip represent maximum parsimony bootstrap support for that clade. There are no support numbers for the QC, eON and neWI or the NJ, MA, and Eastern Shore MD populations (open circles) because they do not constitute a monophyletic grouping. e, eastern Ontario (ON1); w, western Ontario (ON2).</p>", "links"=>[], "tags"=>["46-population", "glacial"], "article_id"=>791455, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Clayton Merz", "Julian M. Catchen", "Victor Hanson-Smith", "Kevin J. Emerson", "William E. Bradshaw", "Christina M. Holzapfel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0072262.g004", "stats"=>{"downloads"=>1, "page_views"=>40, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeography_of_Wyeomyia_smithii_based_on_the_combined_46_population_tree_Fig_3_on_historical_biogeography_and_on_the_timing_of_glacial_events_/791455", "title"=>"Phylogeography of <i>Wyeomyia smithii</i> based on the combined 46-population tree (<b>Fig. 3</b>), on historical biogeography, and on the timing of glacial events.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-06 02:12:01"}

PMC Usage Stats | Further Information

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Relative Metric

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