The Dayhoff Exchange Score: A new metric to quantify entropic site saturation in amino acid datasets prior to phylogenetic analysis [0.03%]
一种新的度量标准——Dayhoff得分：用于表征氨基酸序列数据集中位点的熵值大小及进行系统发生分析之前的数据集饱和度评估方法
James F Fleming,Torsten Hugo Struck
James F Fleming
Entropic site saturation is a persistent problem in phylogenetic analyses, where it can hinder the accuracy of topology reconstruction. It is fundamentally caused by large amounts of independent change along branches, causing the model to b...
Using gene trees with lineage-specific duplicates for phylogenetic inference mitigates the effects of long-branch attraction [0.03%]
利用含有谱系特异性重复基因的基因树进行系统发育推断可减轻长枝吸引效应的影响
Megan L Smith,Matthew W Hahn
Megan L Smith
Traditionally, the inference of species trees has relied on orthologs, or genes related through speciation events, to the exclusion of paralogs, or genes related through duplication events. This has led to a focus on using only gene familie...
Phylotranscriptomic analyses uncover the evolutionary history and asymmetric diversification patterns of the wheat tribe [0.03%]
系 transcriptome 分析揭示小麦族的进化历史及其不对称多样化模式
Li-Na Sha,Hao Yan,Cao Deng et al.
Li-Na Sha et al.
The wheat tribe Triticeae, widely known for its economic importance, is a species-diverse and polyploid-rich group in Poaceae. However, despite decades of intensive efforts, the phylogenetic relationships, genome origins, and diversificatio...
Unravelling complex hybrid and polyploid evolutionary relationships using phylogenetic placement of homologous gene copies from target enrichment data [0.03%]
利用目标富集数据的同源基因拷贝的系统发育定位解开复杂的杂交和多倍体现象间的进化关系
Nora Walden,Christiane Kiefer,Marcus A Koch
Nora Walden
Phylogenomic datasets comprising hundreds of genes have become the standard for plant systematics and phylogenetics. However, large-scale phylogenomic studies often exclude polyploids and hybrids due to the challenges in assessing the origi...
Inferring branch-specific rates of lineage diversification under the birth-death-shift process [0.03%]
基于出生-死亡-转变过程推测分支特异性谱系多样化速率
Sebastian Höhna,William A Freyman,Zachary Nolen et al.
Sebastian Höhna et al.
Inferring how rates of speciation and extinction vary across lineages has proven to be a difficult statistical problem. Here we describe a stochastic-diversification model-called the birth-death-shift (BDS) process-in which diversification ...
Using Phylogenetic Network Methods for Genomic Data Exploration and Hypothesis Generation Fails to Untangle a Confusing History of Hybridization in New Zealand Cicadas [0.03%]
用于基因组数据探索和假设生成的系统发育网络方法无法解开新西兰蝉杂交的混乱历史
Mark Stukel,Chris Simon
Mark Stukel
Rapid species radiations make hybridization among species more likely. Detecting and reconstructing hybridization is therefore critical for understanding species relationships in many cases. We explored the relative performance of two phylo...
Soaring Systematics: an evaluation of biogeography and flight behavior in dragonflies and damselflies (Insecta: Odonata) using phylogenomics [0.03%]
基于系统基因组学的蜻蜓目分类研究：生物地理学与飞行行为评估
Lacie G Newton,John C Abbott,Seth M Bybee et al.
Lacie G Newton et al.
Dragonflies and damselflies (Insecta: Odonata) are descended from what were most likely the first winged animals, which flew ∼320 million years ago (Ma). They comprise ∼6400 extant species distributed across all continents except Antarcti...
Population Genomics of Endangered Lenoks (Brachymystax spp.) in China Reveals the Presence of Cryptic Species [0.03%]
中国东亚盔虾虎鱼（裂腹鱼）的群体基因组学揭示了未被认知物种的存在
Xinmiao Zhang,Judith E Mank,Sunandan Das et al.
Xinmiao Zhang et al.
Lenoks, species within the genus Brachymystax, are freshwater salmonids with a scattered distribution in the rivers of Siberia, Northeast China, Xinjiang, Hebei, and the Qinling Mountains. Owing to long-term population declines, all species...
Laura Kubatko
Laura Kubatko
Nearly all modern studies that address evolutionary questions require consideration of the phylogenetic relationships among species. But what, exactly, is a species tree? And how do we go about estimating such a tree from genomic data? In t...
A Genomic Perspective on Cryptic Species Reveals Complex Evolutionary Dynamics in the Gray Zone of the Speciation Continuum [0.03%]
基因组视角下的隐存物种揭示了 speciation 连续体灰色区域内的复杂进化动态
Kin Onn Chan,Dario N Neokleous,Shahrul Anuar et al.
Kin Onn Chan et al.
The evolutionary dynamics of cryptic species remain poorly understood, and their detection relies primarily on methods that quantify divergence, assuming that gene flow is absent. Here, we examine how gene flow shapes the evolutionary traje...