We have developed an efficient program, the Perfect Phylogeny Haplotyper (PPH) that takes in unphased population genotype data, and determines if that data can be explained by haplotype pairs that could have evolved on a perfect phylogeny.
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Divergence time and environmental similarity predict the strength of morphological convergence in stick and leaf insects.
Proc Natl Acad Sci U S A
January 2025
Division of Biological Sciences, University of Montana, Missoula, MT 59812.
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- Convergent evolution in similar environments supports the idea of natural selection but often shows imperfect similarities due to differing environmental factors and genetic variations.
- The study of 212 species of stick and leaf insects revealed that lineages independently adapted to similar habitats, demonstrating parallel morphological changes, though with variations in magnitude and direction.
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HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X.
bioRxiv
December 2024
Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
In Bayesian phylogenetic and phylodynamic studies it is common to summarise the posterior distribution of trees with a time-calibrated consensus phylogeny. While the maximum clade credibility (MCC) tree is often used for this purpose, we here show that a novel consensus tree method - the highest independent posterior subtree reconstruction, or HIPSTR - contains consistently higher supported clades over MCC. We also provide faster computational routines for estimating both consensus trees in an updated version of TreeAnnotator X, an open-source software program that summarizes the information from a sample of trees and returns many helpful statistics such as individual clade credibilities contained in the consensus tree.
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Key Laboratory for Biodiversity Conservation in Karst Mountain Area of Southwestern China, National Foresty and Grassland Administration, Guiyang 550005, China.
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View Article and Find Full Text PDFThe Bayesian Phylogenetic Bootstrap and its Application to Short Trees and Branches.
Mol Biol Evol
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Institut de Systématique Evolution, Biodiversité (ISYEB UMR7205-CNRS, Muséum National d'Histoire Naturelle, SU, EPHE, UA), Paris 75005, France.
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View Article and Find Full Text PDFAssembly and comparative analysis of the first complete mitochondrial genome of Astragalus membranaceus (Fisch.) Bunge: an invaluable traditional Chinese medicine.
BMC Plant Biol
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College of Agriculture and Life Sciences, Shanxi Datong University, Datong, Shanxi, China.
Background: Astragalus membranaceus (Fisch.) Bunge is one of the most well-known tonic herbs in traditional Chinese medicine, renowned for its remarkable medicinal value in various clinical contexts. The corresponding chloroplast (cp) and nuclear genomes have since been accordingly sequenced, providing valuable information for breeding and phylogeny studies.
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