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7 results for “ASTRAL species tree”
Fig. 1. Species tree reconstruction inferred from ASTRAL-II using 89 specimens and 787 in One in, one out: Generic circumscription within subtribe Manilkarinae (Sapotaceae)
Fig. 1. Species tree reconstruction inferred from ASTRAL-II using 89 specimens and 787 individual gene trees obtained using RAxML. The node labels represent ASTRAL support values. Note that ASTRAL only calculates internal branch length and that tip lines are artificially fixed with the same length for all the specimens. Tip labels include the species names and the collector codes. Branch colors represent the traditional classification: Labramia (dark green), Manilkara (orange), Faucherea (yellow) and Labourdonnaisia (pink). The revised four major genetic clades are highlighted by a colored bar as follows: Labramia (dark green), Manilkara s.str. (orange), Faucherea and Labourdonnaisia (pink), and the Abebaia clade (blue). The main regions are indicated as follows: Afr: Africa; Ame: Americas; Com: Comoros; Ind: Indonesia; Mad: Madagascar; Msc: Mascarenes; Pac: Pacific Asia. RN: Réserves Naturelles; SF: Service Forestier.
Fig. 1. A. ASTRAL and B. wASTRAL-hybrid species trees for the superfamily Elapoidea from the 50 in Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
Fig. 1. A. ASTRAL and B. wASTRAL-hybrid species trees for the superfamily Elapoidea from the 50 % complete dataset, consisting of 4561 loci. Circles on the branch represent a local posterior probability support of 0.95 to 1.0. Abbreviations – AT – Atractaspidinae, CL – Cyclocoridae, EL – Elapidae, LM – Lamprophiinae, MC – Micrelapidae fam. nov., OG – outgroup, PD – Pseudaspidinae, PR – Prosymninae, PS – Psammophiinae, PX – Pseudoxyrhophiinae.
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
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Data from: ASTRAL: genome-scale coalescent-based species tree estimation
<p>Species trees provide insight into basic biology, including the mechanisms of evolution and how it modifies biomolecular function and structure, biodiversity and co-evolution between genes and species. Yet, gene trees often differ from species trees, creating challenges to species tree estimation. One of the most frequent causes for conflicting topologies between gene trees and species trees is incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent. While many methods have been developed to estimate species trees from multiple genes, some which have statistical guarantees under the multi-species coalescent model, existing methods are too computationally intensive for use with genome-scale analyses or have been shown to have poor accuracy under some realistic conditions.</p> <p>Results: We present ASTRAL, a fast method for estimating species trees from multiple genes. ASTRAL is statistically consistent, can run on datasets with thousands of genes and has outstanding accuracy—improving on MP-EST and the population tree from BUCKy, two statistically consistent leading coalescent-based methods. ASTRAL is often more accurate than concatenation using maximum likelihood, except when ILS levels are low or there are too few gene trees.</p>
Data from: ASTRAL: genome-scale coalescent-based species tree estimation
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ASTRAL-Pro: Quartet-based species-tree inference despite paralogy
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Figure 1. Phylogenetic tree reconstruction from ASTRAL, using 638 in A Taxonomic Revision of the Madagascar-Endemic Genus Bemangidia (Sapotaceae), with Description of a Second Species
Figure 1. Phylogenetic tree reconstruction from ASTRAL, using 638 protein-coding genes. Note that ASTRAL calculates only internal branch lengths, and that tip lines are artificially fixed at the same length for all the specimens. The node labels represent ASTRAL support values given as posterior probabilities (PP). Specimen collector's numbers are indicated after the species name, except for Capurodendron and Sapoteae, which appear in Boluda et al. (2022). BioSample numbers for sequence accessions are given in Boluda et al. (2022), except for Bemangidia sp. nov. Randriatafika 813 (BioSample no. SAMN35983425), B. lowryi Gautier 5784 (BioSample no. SAMN35982381), B. lowryi Lowryi et al. 6657 (BioSample no. SAMN35983092), Northia seychellana Bernardi 14641 (BioSample no. SAMN35983402) and Tsebona sp. Andriamiarisoa 2582 (BioSample no. SAMN35983419).
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