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15 results for “Pseudapis”
Data for: Gene tree estimation error with ultraconserved elements: An empirical study on Pseudapis bees
<p>Summarizing individual gene trees to species phylogenies using two-step coalescent methods is now a standard strategy in the field of phylogenomics. However, practical implementations of summary methods suffer from gene tree estimation error, which is caused by various biological and analytical factors. Greatly understudied is the choice of gene tree inference method and downstream effects on species tree estimation for empirical data sets. To better understand the impact of this method choice on gene and species tree accuracy, we compare gene trees estimated through four widely used programs under different model-selection criteria: PhyloBayes, MrBayes, IQ-Tree and RAxML. We study their performance in the phylogenomic framework of > 800 ultraconserved elements from the bee subfamily Nomiinae (Halictidae). Our taxon sampling focuses on the genus <i>Pseudapis</i>, a distinct lineage with diverse morphological features, but contentious morphology-based taxonomic classifications and no molecular phylogenetic guidance. We approximate topological accuracy of gene trees by assessing their ability to recover two uncontroversial, monophyletic groups, and compare branch lengths of individual trees using the stemminess metric (the relative length of internal branches). We further examine different strategies of removing uninformative loci and the collapsing of weakly supported nodes into polytomies. We then summarize gene trees with ASTRAL and compare resulting species phylogenies, including comparisons to concatenation-based estimates. Gene trees obtained with the reversible jump model search in MrBayes were most concordant on average and all Bayesian methods yielded gene trees with better stemminess values. The only gene tree estimation approach whose ASTRAL summary trees consistently produced the most likely correct topology, however, was IQ-Tree with automated model designation (MFP). We discuss these findings and provide practical advice on gene tree estimation for summary methods. Lastly, we establish the first phylogeny-informed classification for <i>Pseudapis</i> s. l. and map the distribution of distinct morphological features of the group.</p>
FIGURES 40a–f. Pseudapis tobiasi Astafurova, 2004 in The type specimens of bees (Hymenoptera, Apoidea) deposited in the Zoological Institute of the Russian Academy of Sciences, St. Petersburg. Contribution II. Family Halictidae, subfamilies Rophitinae, Nomiinae, and Nomioidinae
FIGURES 40a–f. Pseudapis tobiasi Astafurova, 2004. Holotype, male: a—habitus, lateral view; b—head, frontal view; c— mesosoma, dorsal view; d—S5–S6, ventral view; e—labels; f—hind tibia, lateral view.
FIGURE 1. A in Two new species of Pseudapis Kirby, 1900 (Hymenoptera: Halictidae: Nomiinae) from Oman
FIGURE 1. A, Map of Oman showing the collecting locality in the Hajar Mountains (red box) and Dhofar (blue box); B, Geographic distribution of Pseudapis interstitinervis (Strand, 1912) (dots in Africa) and Pseudapis kuhlmanni sp. nov. (dots in the Arabian Peninsula); C, Map of the collecting localities in northern Oman, red dots representing Pseudapis kuhlmanni and blue dot representing P. lisetae sp. nov.; D, Map of collecting localities for Pseudapis kuhlmanni in Dhofar, southern Oman.
FIGURE 6 in Two new species of Pseudapis Kirby, 1900 (Hymenoptera: Halictidae: Nomiinae) from Oman
FIGURE 6. Pseudapis kuhlmanni sp. nov., female. A, head; B, vertex; C, mesosoma; D, propodeum; E, first tergum; F, metasoma.
FIGURE 12 in Two new species of Pseudapis Kirby, 1900 (Hymenoptera: Halictidae: Nomiinae) from Oman
FIGURE 12. Plants foraged by Pseudapis in Oman. A, Acridocarpus orientalis A. Juss (Malpighiaceae); B, Aerva javanica (Burm.f.) Shult (Amaranthaceae); C, Ochradenus aucheri Boiss (Resedaceae); D, Blepharis ciliaris (L.) (Acanthaceae).
FIGURE 4 in Two new species of Pseudapis Kirby, 1900 (Hymenoptera: Halictidae: Nomiinae) from Oman
FIGURE 4. Structures of males; A, Hind leg of P. kuhlmanni sp. nov.; B, Hind leg of P. interstitinervis; C, Apical lobes of sternum V of P. kuhlmanni; D, Apical lobes of sternum V of P. interstitinervis; E, Sternum V and apical membranes of the genitalia of P. kuhlmanni; F, Genitalia of P. kuhlmanni in dorsal view.
FIGURE 9 in Two new species of Pseudapis Kirby, 1900 (Hymenoptera: Halictidae: Nomiinae) from Oman
FIGURE 9. Pseudapis lisetae sp. nov., male. A, head; B, vertex; C, mesosoma; D, propodeum; E, first tergum; F, metasoma.
FIGURE 3 in Two new species of Pseudapis Kirby, 1900 (Hymenoptera: Halictidae: Nomiinae) from Oman
FIGURE 3. Pseudapis kuhlmanni, sp. nov., male. A, habitus; B, head; C, mesosoma; D, propodeum; E, first tergum; F, metasoma.
FIGURE 11 in Two new species of Pseudapis Kirby, 1900 (Hymenoptera: Halictidae: Nomiinae) from Oman
FIGURE 11. Pseudapis lisetae sp. nov., female. A, Head; B, vertex; C, mesosoma; D, propodeum; E, first tergum; F, metasoma.
Data for: Gene tree estimation error with ultraconserved elements: An empirical study on Pseudapis bees
Open the record for dataset details and reuse information.
FIGURE 5 in Two new species of Pseudapis Kirby, 1900 (Hymenoptera: Halictidae: Nomiinae) from Oman
FIGURE 5. Pseudapis kuhlmanni sp. nov., female. A, dorsal view; B, lateral view.
FIGURE 10 in Two new species of Pseudapis Kirby, 1900 (Hymenoptera: Halictidae: Nomiinae) from Oman
FIGURE 10. Pseudapis lisetae sp. nov., female. A, dorsal view; B, lateral view.
FIGURE 2 in Two new species of Pseudapis Kirby, 1900 (Hymenoptera: Halictidae: Nomiinae) from Oman
FIGURE 2. Pseudapis kuhlmanni, sp. nov., male.
FIGURE 8 in Two new species of Pseudapis Kirby, 1900 (Hymenoptera: Halictidae: Nomiinae) from Oman
FIGURE 8. Pseudapis lisetae sp. nov., male. A, dorsal view; B, hind leg; C, last sterna.
FIGURE 7 in Two new species of Pseudapis Kirby, 1900 (Hymenoptera: Halictidae: Nomiinae) from Oman
FIGURE 7. Pseudapis lisetae sp. nov., male.
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