Molecular Biogeography: Towards an Integrated Framework for Conserving Pan-African Biodiversity
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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/950008"], "description"=>"<p>Ecological affinity was inferred from a haplogroup's index of specialisation (IS); Arrows (red for the <i>Scriptus</i> group and blue for the <i>Sylvaticus</i> group) summarise the core ecoregions of each haplogroup into their appropriate core biomes (shaded), which were then translated into key biogeographic regions by the inclusion of geography. Haplogroups are colour-coded as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000454#pone-0000454-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["habitation", "23", "bushbuck", "inference", "affinities", "biogeographic", "regions", "defined", "molecular"], "article_id"=>620322, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Michael W. Bruford"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000454.g003", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ecoregional_habitation_of_23_bushbuck_haplogroups_the_inference_of_ecological_affinities_and_the_identification_of_key_biogeographic_regions_as_defined_by_molecular_data_/620322", "title"=>"Ecoregional habitation of 23 bushbuck haplogroups, the inference of ecological affinities and the identification of key biogeographic regions as defined by molecular data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-05-23 00:05:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/467468", "https://ndownloader.figshare.com/files/467500", "https://ndownloader.figshare.com/files/467517"], "description"=>"<div><h3>Background</h3><p>Biogeographic models partition ecologically similar species assemblages into discrete ecoregions. However, the history, relationship and interactions between these regions and their assemblages have rarely been explored.</p><h3>Methodology/Principal Findings</h3><p>Here we develop a taxon-based approach that explicitly utilises molecular information to compare ecoregion history and status, which we exemplify using a continentally distributed mammalian species: the African bushbuck (<em>Tragelaphus scriptus</em>). We reveal unprecedented levels of genetic diversity and structure in this species and show that ecoregion biogeographic history better explains the distribution of molecular variation than phenotypic similarity or geography. We extend these data to explore ecoregion connectivity, identify core habitats and infer ecological affinities from them.</p><h3>Conclusions/Significance</h3><p>This analysis defines 28 key biogeographic regions for sub-Saharan Africa, and provides a valuable framework for the incorporation of genetic and biogeographic information into a more widely applicable model for the conservation of continental biodiversity.</p></div>", "links"=>[], "tags"=>["molecular", "conserving", "pan-african", "biodiversity"], "article_id"=>152167, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Michael W. Bruford"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0000454.s001", "https://dx.doi.org/10.1371/journal.pone.0000454.s002", "https://dx.doi.org/10.1371/journal.pone.0000454.s003"], "stats"=>{"downloads"=>4, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Molecular_Biogeography_Towards_an_Integrated_Framework_for_Conserving_Pan_African_Biodiversity/152167", "title"=>"Molecular Biogeography: Towards an Integrated Framework for Conserving Pan-African Biodiversity", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-05-23 00:36:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/949738"], "description"=>"<p>Part A. An unrooted median joining network of 485 control region sequences, overlaid onto a topographical map of Africa. 320 haplotypes are arranged according to original sampling location, thus describing the approximate geographic range of each terminal haplogroup. The size of each circle is scaled to haplotype frequency. A dashed white line separates <i>Scriptus</i> and <i>Sylvaticus</i> haplotypes. Relationships between intermediate-level haplogroups (thick red links) were unresolved by CR data and were inferred from a cytochrome <i>b</i> network (data not shown). Thick black links join terminal haplogroups nested within intermediate haplogroups and thin black links join individual haplotypes within terminal haplogroups. Inset panels B and C show the comparitive distribution of biogeographic provinces <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000454#pone.0000454-Udvardy1\" target=\"_blank\">[3]</a> and ecoregions <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000454#pone.0000454-Olson2\" target=\"_blank\">[7]</a> respectively.</p>", "links"=>[], "tags"=>["relationships", "23", "bushbuck", "haplogroups", "toplogy"], "article_id"=>620055, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Michael W. Bruford"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000454.g001", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pan_African_relationships_among_23_bushbuck_haplogroups_in_relation_to_toplogy_and_habitat_heterogeneity_/620055", "title"=>"Pan-African relationships among 23 bushbuck haplogroups in relation to toplogy and habitat heterogeneity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-05-23 00:00:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/949896"], "description"=>"<p>Nodal support for haplogroups is displayed and nodes with less than 50% support were collapsed. Haplogroups are determined by monophyly and distribution. Haplogroups are colour coded as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000454#pone-0000454-g001\" target=\"_blank\">Figure 1</a>. The picture panel shows the general phenotype of each intermediate-level haplogroup. The <i>decula</i> terminal haplogroup is depicted to show the loss of patterning in this subspecies. The bottom panel displays the timing of evolutionary events with equivalent changes in the global temperature (as measured by changes in the oxygen isotope 18) adapted from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000454#pone.0000454-Zachos1\" target=\"_blank\">[55]</a>.</p>", "links"=>[], "tags"=>["phylogenetic", "90", "cytochrome", "haplotypes", "assuming", "hky", "nucleotide"], "article_id"=>620217, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Michael W. Bruford"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000454.g002", "stats"=>{"downloads"=>3, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Linearised_phylogenetic_tree_for_90_cytochrome_b_haplotypes_obtained_by_maximum_likelihood_assuming_an_HKY_model_for_nucleotide_substitution_/620217", "title"=>"Linearised phylogenetic tree for 90 cytochrome <i>b</i> haplotypes obtained by maximum likelihood assuming an HKY model for nucleotide substitution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-05-23 00:03:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/950068"], "description"=>"<p>The shaded grey area marks the threshold distinguishing specialist from generalist haplogroups and the dashed red line denotes the onset of major diversification events. Boxes denote early generalists; circles, late generalists; and triangles, late specialists. Haplogroups are colour coded as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000454#pone-0000454-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["specialization"], "article_id"=>620395, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Michael W. Bruford"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000454.g004", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_evolution_of_specialization_through_time_in_bushbuck_/620395", "title"=>"The evolution of specialization through time in bushbuck.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-05-23 00:06:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/950138"], "description"=>"<p>The test statistic reported is the proportion of variance in the data that was accounted for by each model. For AMOVA this may be the proportion of variance among populations (<i>F</i><sub>ST</sub>, in bold case, where #groups = 1) or among groups (<i>F</i><sub>CT</sub>, normal case, where #groups>1). Conditional MMR tests assess the proportion of marginal variation remaining after geography is taken into account. Sequential MMR tests fit the best model to the data and the statistic reported is that proportion of the remaining variation that is attributable to the second model. Models (P, phenotype; B, biogeography; G, geography; M, molecular; Lt, latitude; and Lg, longitude) are listed in the sequential order in which they were fitted to the regression. Significance was denoted *** (p<0.001), ** (p<0.01), * (p<0.05) or NS (not significant) after 10000 (AMOVA) or 9999 (MMR) permutations.</p>", "links"=>[], "tags"=>["molecular", "variance", "multivariate", "matrix", "regressions"], "article_id"=>620463, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Michael W. Bruford"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000454.t001", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_testing_by_analyses_of_molecular_variance_AMOVA_and_multivariate_matrix_regressions_MMR_/620463", "title"=>"Model testing by analyses of molecular variance (AMOVA) and multivariate matrix regressions (MMR).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-05-23 00:07:43"}

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Relative Metric

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