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209 results for “Biogeographic history”
Aligned DNA sequence matrix for phylogenetic analyses in the article "Three new species of Torrent Treefrogs (Anura: Hylidae) of the Hyloscirtus bogotensis group from the eastern Andean slopes and the biogeographic history of the genus"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Three new species of Torrent Treefrogs (Anura: Hylidae) of the Hyloscirtus bogotensis group from the Amazon foothills and the biogeographic history of the genus"</p> <p>The matrix is in NEXUS format and has 3259 bp and 25 terminals.</p> <p>Partitions are as follows:</p> <div>charset 12S = 1-955;</div> <div>charset ND1_nonCoding1 = 956-1279;</div> <div>charset ND1_Pos1 = 1280-2240\3;</div> <div>charset ND1_Pos2 = 1281-2241\3;</div> <div>charset ND1_Pos3 = 1282-2242\3;</div> <div>charset ND1_nonCoding2 = 2243-2361;</div> <div>charset cmyc_Pos1 = 2362-2779\3;</div> <div>charset cmyc_Pos2 = 2363-2780\3;</div> <div>charset cmyc_Pos3 = 2364-2781\3;</div> <div>charset Rag1_Pos1 = 2782-3415\3;</div> <div>charset Rag1_Pos2 = 2783-3416\3;</div> <div>charset Rag1_Pos3 = 2784-3417\3;</div>
Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, in the Neotropics and adjacent regions
<p>## Metadata</p> <p>backbone_accessions.tsv - GenBank/INSDC accession numbers for LSU, rpb1 and rpb2 accessions used for the Russulaceae backbone tree including 472 taxa.</p> <p>ITS_sequences_OTUs.tsv - Metadata for all 34,624 ITS sequences used in the study. Columns: "accession": accession ID in analysis – GenBank/INSDC or UNITE accession number for compiled data, lab ID for newly generated data; "specimen": specimen/voucher number, for newly generated sequences; "INSDC_accession": INSDC/GenBank accession for new newly generated data; "taxon": specimen identification; "New": whether ITS sequences was generated in this study (*); "OTU": name of cluster/OTU, if not the sequence accession itself (*); "In_tree": whether sequence is represented in the Russulaceae supertree after filtering steps (*), "lb" long-branch accession removed during tree estimation, "ol" outlier removed during tree estimation; "area": biogeographic area assigned.</p> <p> </p> <p>## Sequences and alignments</p> <p>backbone_concat.fasta - Concatenated LSU-rpb1-rpb2 alignment for 372 backbone taxa.</p> <p>backbone_concat_part.txt - Gene partitions and substitution models applied to the backbone alignment.</p> <p>einsi_clade1_Russula_trimmed.fasta - Alignment of 2,279 representative ITS sequences in the Russula clade; alignment end columns with >90% missing data/gaps were trimmed.</p> <p>einsi_clade2_LactariusMultifurca_trimmed.fasta - Alignment of 621 representative ITS sequences in the Lactarius-Multifurca clade; alignment end columns with >90% missing data/gaps were trimmed.</p> <p>einsi_clade3_Lactifluus_trimmed.fasta - Alignment of 482 representative ITS sequences in the Lactifluus clade; alignment end columns with >90% missing data/gaps were trimmed.</p> <p> </p> <p>## Phylogenetic trees</p> <p>12_make_supertree.R - R script for grafting clade trees onto the backbone tree to produce a supertree.</p> <p>backbone_calibrated.nwk - Time-calibrated Russulaceae backbone phylogeny.</p> <p>backbone_TBE.raxml.support - Russulaceae backbone phylogeny annotated with transfer bootstrap expectation support values.</p> <p>clade1_Russula_TBE.raxml.support - Russula subclade ITS phylogeny (2,279 tips), annotated with transfer bootstrap expectation support values.</p> <p>clade2_LactariusMultifurca_TBE.raxml.support - Lactarius-Multifurca subclade ITS phylogeny (621 tips), annotated with transfer bootstrap expectation support values.</p> <p>clade3_Lactifluus_TBE.raxml.support - Lactifluus subclade ITS phylogeny (482 tips), annotated with transfer bootstrap expectation support values.</p> <p>supertree_calibrated.nwk - Combined Russulaceae supertree, time-calibrated (root age = 1).</p> <p>tree_calibrated_clade1_Russula.nwk - Russula subclade ITS backbone phylogeny, time-calibrated (root age = 1).</p> <p>tree_calibrated_clade2_LactariusMultifurca.nwk - Lactarius-Multifurca subclade ITS backbone phylogeny, time-calibrated (root age = 1).</p> <p>tree_calibrated_clade3_Lactifluus.nwk - Lactifluus subclade ITS backbone phylogeny, time-calibrated (root age = 1).</p> <p> </p> <p>## Biogeographic analysis</p> <p>3_disp_counts.R - R script to count dispersal events between biogeographic areas, based on stochastic mapping output.</p> <p>9_disp_count_time.R - R script to count dispersal events to and from each area through time, based on stochastic mapping output.</p> <p>area_codes.tab - Area letter coding and colours used for biogeographic analysis and plotting.</p> <p>area_shapes.zip - Shapefiles for the nine biogeographic areas defined, based on merged areas from Dinerstein et al. 2017 (https://doi.org/10.1093/biosci/bix014) and Löwenberg-Neto (2014: https://doi.org/10.11646/zootaxa.3802.2.12; 2015: https://doi.org/10.11646/10.11646/zootaxa.3985.4.9).</p> <p>areas_manually_zenodo.csv - Manual assignment of 800 ITS sequences to biogeographic areas based on associated literature records or metadata.</p> <p>corHMM_ER.Rdata - R data archive with input data and results for the corHMM/Mv biogeographic area reconstruction.<br> <br> corHMM_ER_stoch_maps.Rdata - R data archive with results from the corHMM/Mv biogeographic stochastic mapping.</p> <p>disp_counts_focal.tab - Dispersal counts to and from each focal area through time, based on BioGeoBEARS stochastic mapping output.</p> <p>disp_counts_sam_afr.tab - Dispersal counts between Afrotopics and lowland tropical S. America through time, based on BioGeoBEARS stochastic mapping output.</p> <p>disp_matrix_025.txt - Dispersal rates between biogeographic areas (2.5% quantiles), based on stochastic mapping output.</p> <p>disp_matrix_975.txt - Dispersal rates between biogeographic areas (97.5% quantiles), based on stochastic mapping output.</p> <p>disp_matrix_median.txt - Dispersal rates between biogeographic areas (median values), based on stochastic mapping output.</p> <p> </p> <p>## Diversification analysis</p> <p>5_rates_per_area.R - R script to partition diversification rates by biogeographic area, both overall and through time, based on BAMM diversification rates and area stochastic mapping.</p> <p>event_data.txt - Posterior samples of diversification rate regimes estimated with BAMM.</p> <p>div_rates_area_overall.txt - Overall diversification rates per biogeographic area, based on BAMM diversification rates and area stochastic mapping.</p> <p>div_rates_per_area_025.tsv - Diversification rates through time (2.5% quantiles) partitioned by biogeographic area, based on BAMM diversification rates and area stochastic mapping.</p> <p>div_rates_per_area_975.tsv - Diversification rates through time (97.5% quantiles) partitioned by biogeographic area, based on BAMM diversification rates and area stochastic mapping.</p> <p>div_rates_per_area_median.tsv - Diversification rates through time (means) partitioned by biogeographic area, based on BAMM diversification rates and area stochastic mapping.</p> <p>mcmc_out.txt - BAMM posterior sample characteristics.</p>
Fig. 29 in Systematics of the enigmatic South American Streblopus Van Lansberge, 1874 dung beetles and their transatlantic origin: a case study on the role of dispersal events in the biogeographical history of the Scarabaeinae (Coleoptera: Scarabaeidae)
Fig. 29. Current distribution of Streblopus van Lansberge, 1874 and the Old World groups with which it is believed to be more closely related plotted on an Upper Cretaceous palaeomap (~ 80 million years ago). Based particularly on the hypothesis in Tarasov & Génier (2015) that Streblopus is part of a clade otherwise composed uniquely of dung beetle lineages either exclusively distributed in Africa (Circellium, Chalconotus and Gyronotus) or with a distribution largely centred on that continent (Scarabaeini), and on the dating of the origin of the Scarabaeini as 71 million years ago (Gunter et al. 2016), we propose that the lineage that would eventually lead to Streblopus branched off from those groups in Africa some time between 95 and 71 million years ago, and that one of its descendent lineages (the only one living today) dispersed from its original continent to South America during the late Upper Cretaceous or the early Cenozoic. Since Africa and South America have not been connected by land since the Lower Cretaceous, the only way the ancestor of Streblopus could have reached South America was through transoceanic dispersal across the early South Atlantic. That dispersal probably happened by rafting on floating pieces of plants or other debris, as probably occurred with a large number of other organisms. Palaeomap modified from Scotese (2016); distribution area based on Balthasar (1963), Scholtz & Howden (1987), Davis et al. (2008) and our own results.
Fig. 14. Profemora. A‒B. Streblopus opatroides van Lansberge, 1874. A in Systematics of the enigmatic South American Streblopus Van Lansberge, 1874 dung beetles and their transatlantic origin: a case study on the role of dispersal events in the biogeographical history of the Scarabaeinae (Coleoptera: Scarabaeidae)
Fig. 14. Profemora. A‒B. Streblopus opatroides van Lansberge, 1874. A. ♂. B. ♀. C‒D. S. punctatus (Balthasar, 1938). C. ♂. D. ♀. Note the differences between the species and sexes in relation to the overall shape of the profemora and the presence of spurs on the anterior edge in males.
Fig. 12. Pronotum. A. Streblopus opatroides van Lansberge, 1874. B. S in Systematics of the enigmatic South American Streblopus Van Lansberge, 1874 dung beetles and their transatlantic origin: a case study on the role of dispersal events in the biogeographical history of the Scarabaeinae (Coleoptera: Scarabaeidae)
Fig. 12. Pronotum. A. Streblopus opatroides van Lansberge, 1874. B. S. punctatus (Balthasar, 1938). Note the differences in the umbilicate punctation and colour between the species.
Fig. 1. Streblopus opatroides van Lansberge, 1874. A‒B. Ordinary specimens, dorsal view. A in Systematics of the enigmatic South American Streblopus Van Lansberge, 1874 dung beetles and their transatlantic origin: a case study on the role of dispersal events in the biogeographical history of the Scarabaeinae (Coleoptera: Scarabaeidae)
Fig. 1. Streblopus opatroides van Lansberge, 1874. A‒B. Ordinary specimens, dorsal view. A. ♂. B. ♀. C‒D. Lectotype, ♂. C. Dorsal view. D. Attached labels.
Fig. 3 in Systematics of the enigmatic South American Streblopus Van Lansberge, 1874 dung beetles and their transatlantic origin: a case study on the role of dispersal events in the biogeographical history of the Scarabaeinae (Coleoptera: Scarabaeidae)
Fig. 3. Streblopus punctatus (Balthasar, 1938). A‒B. Holotype, ♀. A. Dorsal view. B. Attached labels. C‒D. Ordinary specimens, dorsal view. C. ♂. D. ♀.
Fig. 2 in Molecular phylogeny and biogeographic history of the Neotropical tribe Glandulocaudini (Characiformes: Characidae: Stevardiinae)
Fig. 2. Calibrated Bayesian tree based on concatenated dataset (16S+COI+RAG2, 1,829 bp) showing the relationships within the Glandulocaudini. Numbers at branches are posterior probabilities and bootstrap values. Species/populations from Brazilian crystalline shield are highlighted in brown (upland areas) and species/populations from Brazilian coastal drainages in green (lowland areas).
Data from: Global plant-frugivore trait matching is shaped by climate and biogeographic history
<p>Species interactions are influenced by the trait structure of local multi-trophic communities. However, it remains unclear whether mutualistic interactions, in particular, can drive trait patterns at the global scale, where climatic constraints and biogeographic processes gain importance. Here we evaluate global relationships between traits of frugivorous birds and palms (<em>Arecaceae</em>), and how these relationships are affected, directly or indirectly, by assemblage richness, climate and biogeographic history. We leverage a new and expanded gape size dataset for nearly all avian frugivores, and find a positive relationship between gape size and fruit size, that is, trait matching, which is influenced indirectly by palm richness and climate. We also uncover a latitudinal gradient in trait matching strength, which increases towards the tropics and varies among zoogeographic realms. Taken together, our results suggest trophic interactions have consistent influences on trait structure, but that abiotic, biogeographic and richness effects also play important, though sometimes indirect, roles in shaping the functional biogeography of mutualisms.</p>
Data for: Holocene history of the landscape at the biogeographical and cultural crossroads between Central and Eastern Europe (Western Podillia, Ukraine)
<p><strong>Here, we publish the working data sheets for individual proxies (pollen, plant macrofossils, mollusc and geochemical composition), which was used for paleoecological diagrams in the paper Hájková et al. in Quaternary Science Reviews. </strong></p>
Chameleon biogeographic dispersal associated with extreme life history strategies
<div class="t-landing__text-wall "> <p>This dataset contains data and code that support the results in Weil, S.-S., Gallien, L., Lavergne, S., Börger, L., Hassler, G., Nicolaï, Michaël P. J., Allen, William L. (2022) Chameleon biogeographic dispersal associated with extreme life history strategies (DOI<strong>: </strong><span>10.1111/ecog.06323</span>).</p> <p>We used species distribution, phylogenetic and life history trait data of 181 chameleons to determine the relationship between three traits (coastal distribution, body size, position on the fast/slow life history continuum) and past dispersal probability on an evolutionary timescale using trait-dependent biogeographic models.</p> <p>We found that all three traits were associated with past biogeographical movements. Lineages having coastal distributions and those with large bodies had higher dispersal probabilities. Interestingly, chameleons with either very fast or very slow life history were more successful dispersers than species with an intermediate strategy. Together, the three traits "coastal, large-bodied and extreme life history" form a dispersal syndrome.</p> </div>
Figure 6 in An update on the phylogeny and biogeographical history of Rhipicephalus sanguineus complex
Figure 6. The biogeographic analysis of the Rhipicephalus sanguineus complex with S-DIVA and BBM analysis based on mt 12S rDN.
Figure 3 in An update on the phylogeny and biogeographical history of Rhipicephalus sanguineus complex
Figure 3. Phylogenetic tree of sequences obtained by mt 12S rDNA from this study and sequences of GenBank. Haplotypes obtained from this study are indicated with TRY codes and highlighted in bold.
Figure 4 in An update on the phylogeny and biogeographical history of Rhipicephalus sanguineus complex
Figure 4. Phylogenetic tree of sequences obtained by ITS2 from this study and sequences of GenBank. Haplotypes obtained from this study are indicated with TRY codes and highlighted in bold. Different haplotypes of the same individual are labeled as TRY-1 and TRY-2 on the phylogenetic tree.
Figure 2 in An update on the phylogeny and biogeographical history of Rhipicephalus sanguineus complex
Figure 2. Phylogenetic tree of sequences obtained by mt 16S rDNA from this study and sequences of GenBank. Haplotypes obtained from this study are indicated with TRY codes and highlighted in bold.
Figure 5 in An update on the phylogeny and biogeographical history of Rhipicephalus sanguineus complex
Figure 5. The biogeographic analysis of the Rhipicephalus sanguineus complex with S-DIVA and BBM analysis based on mt 16S rDNA.
Linked collectors and determiners for: Systematics of the enigmatic South American Streblopus Van Lansberge, 1874 dung beetles and their transatlantic origin: a case study on the role of dispersal events in the biogeographical history of the Scarabaeinae (Coleoptera: Scarabaeidae).
Natural history specimen data linked to collectors and determiners held within, "Systematics of the enigmatic South American Streblopus Van Lansberge, 1874 dung beetles and their transatlantic origin: a case study on the role of dispersal events in the biogeographical history of the Scarabaeinae (Coleoptera: Scarabaeidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/1668be17-f285-47ef-98b6-c9d90b8cbd6e">https://bionomia.net/dataset/1668be17-f285-47ef-98b6-c9d90b8cbd6e</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/1668be17-f285-47ef-98b6-c9d90b8cbd6e">https://gbif.org/dataset/1668be17-f285-47ef-98b6-c9d90b8cbd6e</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: From Europe to Caucasus: cryptic diversity and unexpected biogeographic history of a Western Palaearctic moss-inhabiting flea beetle (Chrysomelidae: Mniophila).
Natural history specimen data linked to collectors and determiners held within, "From Europe to Caucasus: cryptic diversity and unexpected biogeographic history of a Western Palaearctic moss-inhabiting flea beetle (Chrysomelidae: Mniophila)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/424d5dfc-58a9-4350-ac78-0195bea07487">https://bionomia.net/dataset/424d5dfc-58a9-4350-ac78-0195bea07487</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/424d5dfc-58a9-4350-ac78-0195bea07487">https://gbif.org/dataset/424d5dfc-58a9-4350-ac78-0195bea07487</a>. Formatted as a Frictionless Data package.
Figure 6 in Phylogenetic relationships and biogeographical history of the genus Rhinoclemmys Fitzinger, 1835 and the monophyly of the turtle family Geoemydidae (Testudines: Testudinoidea)
Figure 6. Time calibration using the program BEAST. The error bar on each node represents the 95% confidence interval calculated by the program. The column on the right shows the time slice of Isthmian closure (3.5–2.5 Mya; Coates & Obando, 1996). Pli + Ple: Pliocene + Pleistocene.
Figure 4 in Phylogenetic relationships and biogeographical history of the genus Rhinoclemmys Fitzinger, 1835 and the monophyly of the turtle family Geoemydidae (Testudines: Testudinoidea)
Figure 4. Strict consensus of three most parsimonious trees produced from 3373 aligned characters (TL = 3337; CI = 0.43; RI = 0.59) using maximum parsimony. Of these, 2315 are constant characters and 798 are potentially parsimony-informative. Numbers above and below branches are bootstrap (> 50%) and Bremer values, respectively.
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