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66 results for “BEAST”
Data from: Computational performance and statistical accuracy of *BEAST and comparisons with other methods
Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common genealogical history, thereby equating gene coalescence with species divergence. The multispecies coalescent is supported by previous studies which found that its predicted distributions fit empirical data, and that concatenation is not a consistent estimator of the species tree. *BEAST, a fully Bayesian implementation of the multispecies coalescent, is popular but computationally intensive, so the increasing size of phylogenetic data sets is both a computational challenge and an opportunity for better systematics. Using simulation studies, we characterize the scaling behavior of *BEAST, and enable quantitative prediction of the impact increasing the number of loci has on both computational performance and statistical accuracy. Follow-up simulations over a wide range of parameters show that the statistical performance of *BEAST relative to concatenation improves both as branch length is reduced and as the number of loci is increased. Finally, using simulations based on estimated parameters from two phylogenomic data sets, we compare the performance of a range of species tree and concatenation methods to show that using *BEAST with tens of loci can be preferable to using concatenation with thousands of loci. Our results provide insight into the practicalities of Bayesian species tree estimation, the number of loci required to obtain a given level of accuracy and the situations in which supermatrix or summary methods will be outperformed by the fully Bayesian multispecies coalescent.
Data from: TipDatingBeast: an R package to assist the implementation of phylogenetic tip-dating tests using BEAST
Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. In this context, BEAST, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce TipDatingBeast, an R package built to assist the implementation of various phylogenetic tip-dating tests using BEAST. TipDatingBeast currently contains two main functions. The first one allows preparing date-randomization analyses, which assess the temporal signal of a dataset. The second function allows performing leave-one-out analyses, which test for the consistency between independent calibration sequences and allow pinpointing those leading to potential bias. We apply those functions to an empirical dataset and supply practical guidance for results interpretation.
Concatenated DNA matrix and BEAST tree used for phylogenetic, dating, biogeographic and diversification analyses of Caribbean Podocarpus
<p><b>Aim </b>The Progression Rule, that older lineages inhabit older islands and colonize newer ones as they emerge, has seldom been tested in the Caribbean due to its geological complexity. Here we use the conifer genus <i>Podocarpus</i> to explore this hypothesis. We infer the evolutionary history, biogeography, and diversification rates of this genus under a hypothesis testing framework.</p> <p><b>Location</b> The Caribbean archipelago (Antilles)</p> <p><b>Methods</b> We present the most comprehensive sampling for Caribbean <i>Podocarpus</i> to date in a Bayesian dated phylogenetic tree using a genotyping by sequencing DNA matrix of 67,589 bp. We inferred ancestral ranges and inter-island divergence patterns using several models available. We explored diversification rates associated with island colonization, and checked for diversification rate shifts in the phylogeny.</p> <p><b>Results</b> Caribbean <i>Podocarpus</i> is the result of colonization from the Andes during the Eocene to Oligocene (ca. 45-31 Ma). Lesser Antillean species originated during the Oligocene from the Andes or the Greater Antilles, depending on the model of choice. Vicariance can explain the divergence of Cuban and Hispaniolan species, with subsequent dispersals into Jamaica. Despite the availability of new habitat opportunities, which might promote cladogenesis, insular <i>Podocarpus</i> did not show higher diversification rates than continental taxa.</p> <p><b>Main</b> <b>conclusions </b>The conditions for progression rule were not met because colonization of younger islands (Lesser Antilles) occurred from the continent, or because suitable habitat in the partially emerged younger islands was likely present at the time older islands (Greater Antilles) were colonized. An improved paleogeographic knowledge of the Caribbean will allow testing this hypothesis in multiple lineages. Our finding that diversification rates did not increase with island colonization might be common in other Caribbean lineages. Genotyping by sequencing proved promising to reveal complex historical assembly processes of vicariance and dispersal at a fine phylogenetic scale.</p> <p> </p>
Supplementary material 2 from: Lindemann-Matthies P (2016) Beasts or beauties? Laypersons' perception of invasive alien plant species in Switzerland and attitudes towards their management. NeoBiota 29: 15-33. https://doi.org/10.3897/neobiota.29.5786
English translation of the questionnaire :
Supplementary material 1 from: Lindemann-Matthies P (2016) Beasts or beauties? Laypersons' perception of invasive alien plant species in Switzerland and attitudes towards their management. NeoBiota 29: 15-33. https://doi.org/10.3897/neobiota.29.5786
Short description of the eight invasive alien plant species :
Figures 31-32 from: Michat MC, Alarie Y, Watts CHS (2019) Dealing with a hairy beast–larval morphology and chaetotaxy of the Australian endemic diving beetle genus Spencerhydrus (Coleoptera, Dytiscidae, Cybistrini). ZooKeys 884: 53-67. https://doi.org/10.3897/zookeys.884.38391
Figures 31-32 Head of Spencerhydrus species 31S. latecinctus, instar II, dorsal aspect 32S. pulchellus, instar III, dorsal aspect. Scale bar: 1.00 mm.
Figures 5-14 from: Michat MC, Alarie Y, Watts CHS (2019) Dealing with a hairy beast–larval morphology and chaetotaxy of the Australian endemic diving beetle genus Spencerhydrus (Coleoptera, Dytiscidae, Cybistrini). ZooKeys 884: 53-67. https://doi.org/10.3897/zookeys.884.38391
Figures 5-14 Head appendages of Spencerhydrus species, instar I 5S. latecinctus, right antenna, dorsal aspect 6S. latecinctus, left antenna, ventral aspect 7S. pulchellus, right antenna, dorsal aspect 8S. pulchellus, left antenna, ventral aspect 9S. latecinctus, right mandible, dorsal aspect 10S. pulchellus, right mandible, dorsal aspect 11S. latecinctus, right maxilla, dorsal aspect 12S. latecinctus, left maxilla, ventral aspect 13S. pulchellus, right maxilla, dorsal aspect 14S. pulchellus, left maxilla, ventral aspect. Numbers and lowercase letters indicate primary setae and pores, respectively. Additional setae and pores not labelled. Abbreviations: A1–4: antennomeres 1–4; AN: antenna; MN: mandible; MP1–3: maxillary palpomeres 1–3; MX: maxilla; PPF: palpifer; SP: spinula. Scale bar: 0.30 mm.
Figures 27-30 from: Michat MC, Alarie Y, Watts CHS (2019) Dealing with a hairy beast–larval morphology and chaetotaxy of the Australian endemic diving beetle genus Spencerhydrus (Coleoptera, Dytiscidae, Cybistrini). ZooKeys 884: 53-67. https://doi.org/10.3897/zookeys.884.38391
Figures 27-30 Urogomphus of Spencerhydrus species, instar I 27S. latecinctus, right urogomphus, dorsal aspect 28S. latecinctus, left urogomphus, ventral aspect 29S. pulchellus, right urogomphus, dorsal aspect 30S. pulchellus, left urogomphus, ventral aspect. Numbers and lowercase letters indicate primary setae and pores, respectively. UR: urogomphus. Scale bar: 0.05 mm.
Figures 23-26 from: Michat MC, Alarie Y, Watts CHS (2019) Dealing with a hairy beast–larval morphology and chaetotaxy of the Australian endemic diving beetle genus Spencerhydrus (Coleoptera, Dytiscidae, Cybistrini). ZooKeys 884: 53-67. https://doi.org/10.3897/zookeys.884.38391
Figures 23-26 Abdominal segment VIII of Spencerhydrus species, instar I 23S. latecinctus, dorsal aspect 24S. pulchellus, dorsal aspect 25S. latecinctus, ventral aspect 26S. pulchellus, ventral aspect. Numbers and lowercase letters indicate primary setae and pores, respectively. Additional setae and pores not labelled. Abbreviation: AB: abdominal segment VIII. Scale bar: 0.50 mm.
Figures 19-22 from: Michat MC, Alarie Y, Watts CHS (2019) Dealing with a hairy beast–larval morphology and chaetotaxy of the Australian endemic diving beetle genus Spencerhydrus (Coleoptera, Dytiscidae, Cybistrini). ZooKeys 884: 53-67. https://doi.org/10.3897/zookeys.884.38391
Figures 19-22 Left metathoracic leg of Spencerhydrus species, instar I 19S. latecinctus, anterior aspect 20S. latecinctus, posterior aspect 21S. pulchellus, anterior aspect 22S. pulchellus, posterior aspect. Numbers and lowercase letters indicate primary setae and pores, respectively. Additional setae and pores not labelled. Abbreviations: CO: coxa; FE: femur; PT: pretarsus; TA: tarsus; TI: tibia; TR: trochanter. Scale bar: 0.20 mm.
Figures 15-18 from: Michat MC, Alarie Y, Watts CHS (2019) Dealing with a hairy beast–larval morphology and chaetotaxy of the Australian endemic diving beetle genus Spencerhydrus (Coleoptera, Dytiscidae, Cybistrini). ZooKeys 884: 53-67. https://doi.org/10.3897/zookeys.884.38391
Figures 15-18 Labium of Spencerhydrus species, instar I 15S. latecinctus, dorsal aspect 16S. latecinctus, ventral aspect 17S. pulchellus, dorsal aspect 18S. pulchellus, ventral aspect. Numbers and lowercase letters indicate primary setae and pores, respectively. Additional setae and pores not labelled. Abbreviations: LA: labium; LP1–2: labial palpomeres 1–2. Scale bar: 0.15 mm.
Figures 1-4 from: Michat MC, Alarie Y, Watts CHS (2019) Dealing with a hairy beast–larval morphology and chaetotaxy of the Australian endemic diving beetle genus Spencerhydrus (Coleoptera, Dytiscidae, Cybistrini). ZooKeys 884: 53-67. https://doi.org/10.3897/zookeys.884.38391
Figures 1-4 Cephalic capsule of Spencerhydrus species, instar I 1S. latecinctus, dorsal aspect 2S. pulchellus, dorsal aspect 3S. latecinctus, ventral aspect 4S. pulchellus, ventral aspect. Numbers and lowercase letters indicate primary setae and pores, respectively. Additional setae not labelled. Color patterns not represented. Abbreviations: EB: egg burster; FR: frontoclypeus; PA: parietal; LC: lamellae clypeales; TP: tentorial pit. Scale bar: 0.70 mm.
Figures 5-6 from: Engel M, Falin Z (2014) Serendipity at the Smithsonian: The 107-year journey of Rhipidocyrtus muiri Falin & Engel, new genus and species (Ripidiinae, Ripidiini), from jungle beast to valid taxon. ZooKeys 424: 101-116. https://doi.org/10.3897/zookeys.424.7853
Figures 5-6 - Photographs of holotype male of Rhipidocyrtus muiri Falin & Engel, gen. et sp. n. from Borneo. 5 Dorsal detail of metathorax. 6 Posterior view of thorax as preserved.
Figures 3-4 from: Engel M, Falin Z (2014) Serendipity at the Smithsonian: The 107-year journey of Rhipidocyrtus muiri Falin & Engel, new genus and species (Ripidiinae, Ripidiini), from jungle beast to valid taxon. ZooKeys 424: 101-116. https://doi.org/10.3897/zookeys.424.7853
Figures 3-4 - Photographs of holotype male of Rhipidocyrtus muiri Falin & Engel, gen. et sp. n. from Borneo. 3 Facial view 4 Right lateral view of head and prothorax.
Figures 13-15 from: Engel M, Falin Z (2014) Serendipity at the Smithsonian: The 107-year journey of Rhipidocyrtus muiri Falin & Engel, new genus and species (Ripidiinae, Ripidiini), from jungle beast to valid taxon. ZooKeys 424: 101-116. https://doi.org/10.3897/zookeys.424.7853
Figures 13-15 - Photographs of slide mounted abdominal structures from holotype male of Rhipidocyrtus muiri Falin & Engel, gen. et sp. n. 13 Splayed abdomen as preserved on slide, numbered ventrites to the left, unnumbered tergites to the right 14 Enlarged detail, ventral view of tegmen 15 Enlarged detail of median lobe.
Figures 7-12 from: Engel M, Falin Z (2014) Serendipity at the Smithsonian: The 107-year journey of Rhipidocyrtus muiri Falin & Engel, new genus and species (Ripidiinae, Ripidiini), from jungle beast to valid taxon. ZooKeys 424: 101-116. https://doi.org/10.3897/zookeys.424.7853
Figures 7-12 - Photographs of slide mounted structures from holotype male of Rhipidocyrtus muiri Falin & Engel, gen. et sp. n. 7 Elytron 8 Hind wing 9 Right antenna 10 Foreleg 11 Mid-leg 12 Hind leg.
Figures 1-2 from: Engel M, Falin Z (2014) Serendipity at the Smithsonian: The 107-year journey of Rhipidocyrtus muiri Falin & Engel, new genus and species (Ripidiinae, Ripidiini), from jungle beast to valid taxon. ZooKeys 424: 101-116. https://doi.org/10.3897/zookeys.424.7853
Figures 1-2 - Photographs of holotype male of Rhipidocyrtus muiri Falin & Engel, gen. et sp. n. from Borneo. 1 Lateral habitus as preserved 2 Dorsal detail of head and thorax as preserved.
BEAST: A Pilot Trial
ClinicalTrials.gov study NCT05416203. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Computational performance and statistical accuracy of *BEAST and comparisons with other methods
Open the record for dataset details and reuse information.
Concatenated DNA matrix and BEAST tree used for phylogenetic, dating, biogeographic and diversification analyses of Caribbean Podocarpus
Open the record for dataset details and reuse information.
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