Sensitivity of Metrics of Phylogenetic Structure to Scale, Source of Data and Species Pool of Hummingbird Assemblages along Elevational Gradients
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{"title"=>"Sensitivity of metrics of phylogenetic structure to scale, source of data and species pool of hummingbird assemblages along elevational gradients", "type"=>"journal", "authors"=>[{"first_name"=>"Sebastián", "last_name"=>"González-Caro", "scopus_author_id"=>"55203531200"}, {"first_name"=>"Juan L.", "last_name"=>"Parra", "scopus_author_id"=>"10440758000"}, {"first_name"=>"Catherine H.", "last_name"=>"Graham", "scopus_author_id"=>"7401505218"}, {"first_name"=>"Jimmy A.", "last_name"=>"McGuire", "scopus_author_id"=>"7202221788"}, {"first_name"=>"Carlos Daniel", "last_name"=>"Cadena", "scopus_author_id"=>"55665109000"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84871089414", "sgr"=>"84871089414", "pui"=>"364720840", "isbn"=>"1932-6203", "pmid"=>"22558157", "doi"=>"10.1371/journal.pone.0035472"}, "id"=>"6cc82bd4-3fc7-35ed-9e09-5d247c0bcf64", "abstract"=>"Patterns of phylogenetic structure of assemblages are increasingly used to gain insight into the ecological and evolutionary processes involved in the assembly of co-occurring species. Metrics of phylogenetic structure can be sensitive to scaling issues and data availability. Here we empirically assess the sensitivity of four metrics of phylogenetic structure of assemblages to changes in (i) the source of data, (ii) the spatial grain at which assemblages are defined, and (iii) the definition of species pools using hummingbird (Trochilidae) assemblages along an elevational gradient in Colombia. We also discuss some of the implications in terms of the potential mechanisms driving these patterns. To explore how source of data influence phylogenetic structure we defined assemblages using three sources of data: field inventories, museum specimens, and range maps. Assemblages were defined at two spatial grains: coarse-grained (elevational bands of 800-m width) and fine-grained (1-km(2) plots). We used three different species pools: all species contained in assemblages, all species within half-degree quadrats, and all species either above or below 2000 m elevation. Metrics considering phylogenetic relationships among all species within assemblages showed phylogenetic clustering at high elevations and phylogenetic evenness in the lowlands, whereas those metrics considering only the closest co-occurring relatives showed the opposite trend. This result suggests that using multiple metrics of phylogenetic structure should provide greater insight into the mechanisms shaping assemblage structure. The source and spatial grain of data had important influences on estimates of both richness and phylogenetic structure. Metrics considering the co-occurrence of close relatives were particularly sensitive to changes in the spatial grain. Assemblages based on range maps included more species and showed less phylogenetic structure than assemblages based on museum or field inventories. Coarse-grained assemblages included more distantly related species and thus showed a more even phylogenetic structure than fine-grained assemblages. Our results emphasize the importance of carefully selecting the scale, source of data and metric used in analysis of the phylogenetic structure of assemblages.", "link"=>"http://www.mendeley.com/research/sensitivity-metrics-phylogenetic-structure-scale-source-data-species-pool-hummingbird-assemblages-al", "reader_count"=>121, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>10, "Librarian"=>1, "Researcher"=>23, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>39, "Student > Postgraduate"=>5, "Student > Master"=>16, "Other"=>2, "Student > Bachelor"=>10, "Lecturer"=>1, "Professor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>10, "Librarian"=>1, "Researcher"=>23, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>39, "Student > Postgraduate"=>5, "Student > Master"=>16, "Other"=>2, "Student > Bachelor"=>10, "Lecturer"=>1, "Professor"=>6}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>17, "Biochemistry, Genetics and Molecular Biology"=>2, "Materials Science"=>1, "Agricultural and Biological Sciences"=>93, "Medicine and Dentistry"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>93}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>17}}, "reader_count_by_country"=>{"Colombia"=>2, "Sweden"=>1, "United States"=>6, "China"=>2, "Brazil"=>3, "Mexico"=>2, "Chile"=>2, "Switzerland"=>4, "Germany"=>2, "Spain"=>1}, "group_count"=>4}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/645095"], "description"=>"<p>Relationship between PSV and elevation. Assemblages showing statistically significant patterns of phylogenetic evenness are represented with black filled circles, those with phylogenetic clustering in gray circles, and those showing patterns not deviating from the null model in hollow circles. R-squared values (rsqu) and the slope (s) of the linear regression are shown on the lower right corner (* = p<0.05, ** = p<0.01, *** = p<0.001).</p>", "links"=>[], "tags"=>["phylogenetic", "variability"], "article_id"=>315585, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sebastián González-Caro", "Juan L. Parra", "Catherine H. Graham", "Jimmy A. McGuire", "Carlos Daniel Cadena"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035472.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_the_Phylogenetic_Species_Variability_index_PSV_and_elevation_/315585", "title"=>"Relationship between the Phylogenetic Species Variability index (PSV) and elevation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-27 01:33:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/645413"], "description"=>"<p>Relationship between PSC and elevation. Assemblages showing statistically significant patterns of phylogenetic evenness are represented with black filled circles, those with phylogenetic clustering in gray circles, and those showing patterns not deviating from the null model in hollow circles. R-squared values (rsqu) and the slope (s) of the linear regression are shown on the lower right corner (* = p<0.05, ** = p<0.01, *** = p<0.001).</p>", "links"=>[], "tags"=>["phylogenetic", "clustering"], "article_id"=>315910, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sebastián González-Caro", "Juan L. Parra", "Catherine H. Graham", "Jimmy A. McGuire", "Carlos Daniel Cadena"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035472.g006", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_the_Phylogenetic_Species_Clustering_index_PSC_and_elevation_/315910", "title"=>"Relationship between the Phylogenetic Species Clustering index (PSC) and elevation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-27 01:38:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/645582"], "description"=>"<p>Significant <i>P</i>-values are highlighted in bold. Only significant Tukey post-hoc comparisons are mentioned.</p>", "links"=>[], "tags"=>["ancova", "differences", "richness", "indices", "phylogenetic", "spatial", "grains", "sources", "elevation"], "article_id"=>316065, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sebastián González-Caro", "Juan L. Parra", "Catherine H. Graham", "Jimmy A. McGuire", "Carlos Daniel Cadena"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035472.t001", "stats"=>{"downloads"=>2, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_the_ANCOVA_testing_for_differences_in_species_richness_and_in_the_four_indices_of_phylogenetic_structure_when_changing_spatial_grains_and_sources_of_data_using_elevation_as_a_covariable_/316065", "title"=>"Results of the ANCOVA testing for differences in species richness and in the four indices of phylogenetic structure when changing spatial grains and sources of data using elevation as a covariable.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-27 01:41:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/644843"], "description"=>"<p>Relationship between species richness estimated from field inventories and range maps at two different spatial grains. Coarse-grained assemblages are shown in light gray and fine-grained assemblages in dark gray. The line indicates one-to-one correspondence, demonstrating that richness estimated from range maps are higher than those estimated from field inventories.</p>", "links"=>[], "tags"=>["richness", "sources"], "article_id"=>315336, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sebastián González-Caro", "Juan L. Parra", "Catherine H. Graham", "Jimmy A. McGuire", "Carlos Daniel Cadena"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035472.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Species_richness_obtained_from_different_sources_at_different_scales_/315336", "title"=>"Species richness obtained from different sources at different scales.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-27 01:28:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/333178", "https://ndownloader.figshare.com/files/333240", "https://ndownloader.figshare.com/files/333290", "https://ndownloader.figshare.com/files/333346", "https://ndownloader.figshare.com/files/333403", "https://ndownloader.figshare.com/files/333546", "https://ndownloader.figshare.com/files/333626", "https://ndownloader.figshare.com/files/333682", "https://ndownloader.figshare.com/files/333746"], "description"=>"<div><p>Patterns of phylogenetic structure of assemblages are increasingly used to gain insight into the ecological and evolutionary processes involved in the assembly of co-occurring species. Metrics of phylogenetic structure can be sensitive to scaling issues and data availability. Here we empirically assess the sensitivity of four metrics of phylogenetic structure of assemblages to changes in (i) the source of data, (ii) the spatial grain at which assemblages are defined, and (iii) the definition of species pools using hummingbird (Trochilidae) assemblages along an elevational gradient in Colombia. We also discuss some of the implications in terms of the potential mechanisms driving these patterns. To explore how source of data influence phylogenetic structure we defined assemblages using three sources of data: field inventories, museum specimens, and range maps. Assemblages were defined at two spatial grains: coarse-grained (elevational bands of 800-m width) and fine-grained (1-km<sup>2</sup> plots). We used three different species pools: all species contained in assemblages, all species within half-degree quadrats, and all species either above or below 2000 m elevation. Metrics considering phylogenetic relationships among all species within assemblages showed phylogenetic clustering at high elevations and phylogenetic evenness in the lowlands, whereas those metrics considering only the closest co-occurring relatives showed the opposite trend. This result suggests that using multiple metrics of phylogenetic structure should provide greater insight into the mechanisms shaping assemblage structure. The source and spatial grain of data had important influences on estimates of both richness and phylogenetic structure. Metrics considering the co-occurrence of close relatives were particularly sensitive to changes in the spatial grain. Assemblages based on range maps included more species and showed less phylogenetic structure than assemblages based on museum or field inventories. Coarse-grained assemblages included more distantly related species and thus showed a more even phylogenetic structure than fine-grained assemblages. Our results emphasize the importance of carefully selecting the scale, source of data and metric used in analysis of the phylogenetic structure of assemblages.</p> </div>", "links"=>[], "tags"=>["metrics", "phylogenetic", "hummingbird", "assemblages", "elevational", "gradients"], "article_id"=>125801, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sebastián González-Caro", "Juan L. Parra", "Catherine H. Graham", "Jimmy A. McGuire", "Carlos Daniel Cadena"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0035472.s001", "https://dx.doi.org/10.1371/journal.pone.0035472.s002", "https://dx.doi.org/10.1371/journal.pone.0035472.s003", "https://dx.doi.org/10.1371/journal.pone.0035472.s004", "https://dx.doi.org/10.1371/journal.pone.0035472.s005", "https://dx.doi.org/10.1371/journal.pone.0035472.s006", "https://dx.doi.org/10.1371/journal.pone.0035472.s007", "https://dx.doi.org/10.1371/journal.pone.0035472.s008", "https://dx.doi.org/10.1371/journal.pone.0035472.s009"], "stats"=>{"downloads"=>35, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Sensitivity_of_Metrics_of_Phylogenetic_Structure_to_Scale_Source_of_Data_and_Species_Pool_of_Hummingbird_Assemblages_along_Elevational_Gradients/125801", "title"=>"Sensitivity of Metrics of Phylogenetic Structure to Scale, Source of Data and Species Pool of Hummingbird Assemblages along Elevational Gradients", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-04-27 01:36:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/645265"], "description"=>"<p>Relationship between NTI and elevation. Assemblages showing statistically significant patterns of phylogenetic evenness are represented with black filled circles, those with phylogenetic clustering in gray circles, and those showing patterns not deviating from the null model in hollow circles. R-squared values (rsqu) and the slope (s) of the linear regression are shown on the lower right corner (* = p<0.05, ** = p<0.01, *** = p<0.001).</p>", "links"=>[], "tags"=>["nearest", "taxon"], "article_id"=>315758, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sebastián González-Caro", "Juan L. Parra", "Catherine H. Graham", "Jimmy A. McGuire", "Carlos Daniel Cadena"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035472.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_the_Nearest_Taxon_Index_NTI_and_elevation_/315758", "title"=>"Relationship between the Nearest Taxon Index (NTI) and elevation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-27 01:35:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/645627"], "description"=>"<p>Percentages of assemblages showing statistically significant phylogenetic evenness or clustering are indicated.</p>", "links"=>[], "tags"=>["deviation", "richness", "indices", "phylogenetic", "spatial"], "article_id"=>316111, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sebastián González-Caro", "Juan L. Parra", "Catherine H. Graham", "Jimmy A. McGuire", "Carlos Daniel Cadena"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035472.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mean_and_standard_deviation_of_richness_and_of_the_four_indices_of_phylogenetic_structure_for_each_combination_of_spatial_grain_and_source_of_data_used_/316111", "title"=>"Mean and standard deviation of richness and of the four indices of phylogenetic structure for each combination of spatial grain and source of data used.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-27 01:41:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/644979"], "description"=>"<p>Relationship between NRI and elevation. Assemblages showing statistically significant patterns of phylogenetic evenness are represented with black filled circles, those with phylogenetic clustering in gray circles, and those showing patterns not deviating from the null model in hollow circles. R-squared values (rsqu) and the slope (s) of the linear regression are shown on the lower right corner (* = p<0.05, ** = p<0.01, *** = p<0.001).</p>", "links"=>[], "tags"=>["relatedness"], "article_id"=>315472, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sebastián González-Caro", "Juan L. Parra", "Catherine H. Graham", "Jimmy A. McGuire", "Carlos Daniel Cadena"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035472.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_the_Net_Relatedness_Index_NRI_and_elevation_/315472", "title"=>"Relationship between the Net Relatedness Index (NRI) and elevation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-27 01:31:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/644730"], "description"=>"<p>Geographic location of field inventories in the study area. Grids represent the half-degree grains used to define species pools. Color-scale elevation bands are classified according to the elevation categories used in analyses. Cities are indicated with triangles (Bogotá on the east and Manizales on the west).</p>", "links"=>[], "tags"=>["hummingbird"], "article_id"=>315230, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sebastián González-Caro", "Juan L. Parra", "Catherine H. Graham", "Jimmy A. McGuire", "Carlos Daniel Cadena"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035472.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Geographic_location_of_hummingbird_assemblages_/315230", "title"=>"Geographic location of hummingbird assemblages.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-27 01:27:10"}

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Relative Metric

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