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68 results for “taxon sampling”
Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)
<div> <div> <div> <p>Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been key to establishing the suprafamilial backbone of the charadriiform tree, a number of relationships at both deep and shallow taxonomic levels remain poorly resolved. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 353 ingroup taxa (90% of all extant or recently extinct species), 27 loci (15 mitochondrial and 12 nuclear), and 69 morphological characters. We further clarify the timeline of charadriiform evolution by time-scaling this phylogeny using a set of 14 up-to-date and thoroughly vetted fossil calibrations. In addition, we assemble a taxonomically restricted 100-locus dataset specifically designed to resolve outstanding problems in higher-level charadriiform phylogeny. In terms of tree topology, our results are largely congruent with previous studies but indicate that some of the conflicts among earlier analyses reflect a genuine signal of pervasive gene tree discordance. Monophyly of the plovers (Charadriidae), the position of the ibisbill (<em>Ibidorhyncha</em>), and the relationships among the five subfamilies of the gulls (Laridae) could not be resolved even with greatly increased locus and taxon sampling. Moreover, several localized regions of uncertainty persist in shallower parts of the tree, including the interrelationships of the true auks (Alcinae) and anarhynchine plovers. Our node-dating and macroevolutionary rate analyses find support for a Paleocene origin of crown-group shorebirds, as well as exceptionally rapid recent radiations of Old World oystercatchers (Haematopodidae) and select genera of gulls. Our study underscores the challenges involved in estimating a comprehensively sampled and carefully calibrated time tree for a diverse avian clade, and highlights areas in need of further research.</p> </div> </div> </div>
FIGURE 1 in Tackling an intractable problem: Can greater taxon sampling help resolve relationships within the Stenopelmatoidea (Orthoptera: Ensifera)?
FIGURE 1. Representatives of major groups included in our analysis with emphasis on the Stenopelmatoidea. Panel 1: A. Comicus sp. probably calcaris. B. Sia sp. C. Stenopelmatopterus politus. D. Stenopelmatus sp. E. Stenopelmatus sp. F. Oryctopus sp. from India, (not included in analysis). Panel 2: G. Xanthogryllacris punctipennis. H. Penalva flavocalceatus I. Cooloola propator J. Anabropsis sp. K. Lezina concolor. L. Cnemotettix bifasciatus. Photo credits: R. Lakes-Harlan: A; D.B. Weissman: B, C, D, E, J, L; R. Balakrishnan: F; D.C.F. Rentz: G, H, I; G. Wizen: K. Respective family supported by this paper: Schizodactylidae: A. Stenopelmatidae: B, C, D, E, F. Gryllacrididae: G. Anostostomatidae: H, I, J, K, L. The colored boxes around photographs correspond to the same colors denoting families in Figures 2 and 3.
FIGURE S2-3 in Tackling an intractable problem: Can greater taxon sampling help resolve relationships within the Stenopelmatoidea (Orthoptera: Ensifera)?
FIGURE S2-3: Karyotypes of Glaphyrosoma A: Male from Mexico, Nuevo Leon. 2n♂=29 with 1 pair of metacentric and 13 pairs of rod shaped autosomes and a metacentric X. B: Male from Honduras, Cortes, 2n♂=28 with 13 pairs of rod shaped autosomes and a metacentric X and rod shaped Y chromosome.
FIGURE S2-2 in Tackling an intractable problem: Can greater taxon sampling help resolve relationships within the Stenopelmatoidea (Orthoptera: Ensifera)?
FIGURE S2-2: Karyotypes of Cnemotettix. A: Male from California, Monterey Co., 2n♂=27 with 6 pairs of metacentric and 7 pairs of rod shaped autosomes and a metacentric X. B: Male from California, Santa Barbara Co. 2n♂=25 with 7 pairs of metacentric and 5 pairs of rod shaped autosomes and a metacentric X.
FIGURE S2-1 in Tackling an intractable problem: Can greater taxon sampling help resolve relationships within the Stenopelmatoidea (Orthoptera: Ensifera)?
FIGURE S2-1: Karyotypes of North American Stenopelmatinae. A: Male from California, Inyo Co., 2n♂= 25, showing 6 pairs each of metacentric and rod shaped autosomes and a metacentric X. B: Male from California, San Diego Co., 2n♂=23, showing 7 pairs of metacentric and 4 pairs of rod shaped autosomes and a metacentric X.
FIGURE S2–4 in Tackling an intractable problem: Can greater taxon sampling help resolve relationships within the Stenopelmatoidea (Orthoptera: Ensifera)?
FIGURE S2–4. Karyotype of Lezina. There are 4 pairs of metacentric and 10 pairs of telocentric autosomes with a metacentric X chromosome.
Fig. 1 in Phylogenomic analysis with improved taxon sampling corroborates an Alydidae + Hydarinae + Pseudophloeinae clade (Heteroptera: Coreoidea: Alydidae, Coreidae)
Fig. 1 Summary of phylogenetic hypotheses based on previous morphological and molecular cladistic analyses
0.0 0.5 1.0 1.5 uncorrected p in Increased taxon sampling provides new insights into the phylogeny and evolution of the subclass Calcaronea (Porifera, Calcarea)
0.0 0.5 1.0 1.5 uncorrected p-distances (%) Fig. 3 Distribution of intra- and interspecific divergences (uncorrected pdistances) of 18S rRNA in Calcaronea
Fig. 2 in Increased taxon sampling provides new insights into the phylogeny and evolution of the subclass Calcaronea (Porifera, Calcarea)
Fig. 2 Phylogenetic reconstruction using Bayesian inference (PHASE-3, HKY85/ RNA16D + G) of the C-region of 28S rDNA for the subclass Calcaronea. Outgroup taxa not shown. Posterior probability values are shown as the upper half of circles, and the lower half represents bootstrap values (ML). Support values are color-coded
Fig. 1 in Increased taxon sampling provides new insights into the phylogeny and evolution of the subclass Calcaronea (Porifera, Calcarea)
Fig. 1 Phylogenetic reconstruction using Bayesian inference (PHASE-3, REV + G/ RNA16D + G) of 18S rRNA for the subclass Calcaronea. Outgroup taxa not shown. Posterior probabilities values are shown as the upper half of circles, and the lower half represents bootstrap values (ML). Support values are color-coded. Gray branches in the tree represent those without support
Fig. 4 in Increased taxon sampling provides new insights into the phylogeny and evolution of the subclass Calcaronea (Porifera, Calcarea)
Fig. 4 Distribution of intra- and interspecific divergences (uncorrected p- distances) of the C-region of 28S rDNA in Calcaronea
Data from: Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling
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Data from: Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting
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Data from: Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes.
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Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul
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Data from: Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera)
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Data from: Inclusive taxon sampling suggests a single, stepwise origin of ectolecithality in Platyhelminthes
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Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)
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Data from: The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae)
Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) generated using the anchored phylogenomics sequencing method (66 loci, derived from conserved genome regions, for 48 taxa) and Sanger sequencing (seven loci for up to 142 taxa) to tackle this problem. We assess the effects of character sampling, taxon sampling, analytical methods and assumptions in phylogenetic inference of microhylid frogs. The phylogeny of microhylids shows high susceptibility to different analytical methods and datasets used for the analyses. Clades inferred from maximum-likelihood are generally more stable across datasets than those inferred from parsimony. Parsimony trees inferred within a tree-alignment framework are generally better resolved and better supported than those inferred within a similarity-alignment framework, even under the same cost matrix (equally weighted) and same treatment of gaps (as a fifth nucleotide state). We discuss potential causes for these differences in resolution and clade stability among discovery operations. We also highlight the problem that commonly used algorithms for model-based analyses do not explicitly model insertion and deletion events (i.e. gaps are treated as missing data). Our results corroborate the monophyly of Microhylidae and most currently recognized subfamilies but fail to provide support for relationships among subfamilies. Several taxonomic updates are provided, including naming of two new subfamilies, both monotypic.
FIGURE 3 in Tackling an intractable problem: Can greater taxon sampling help resolve relationships within the Stenopelmatoidea (Orthoptera: Ensifera)?
FIGURE 3. Bayesian chronogram estimated in Beast. Clade posterior probabilities> 0.95 are denoted with a black dot. Estimated ages for the most recent common ancestors of clades are indicated at the top left of nodes. Blue bars represent 95% credible intervals around node ages. Asterisks indicate the three nodes that were calibrated using published fossil ages (see methods).
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