Link between the Birth-Death process and the Kingman Coalescent - Applications to Phylogenetic Epidemiology [0.03%]
birth-death过程与Kingman coalescent之间的关系及其在系谱流行病学中的应用
Josselin Cornuault,Fabio Pardi,Celine Scornavacca
Josselin Cornuault
The two most popular tree models used in phylogenetics are the birth-death process (BD) and the Kingman coalescent (KC). These two models differ in several respects, notably: (i) the curve of the population size through time is a stochastic...
Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization [0.03%]
通过提前停止以避免过度优化来加速最大似然法的系统发育推断
Anastasis Togkousidis,Alexandros Stamatakis,Olivier Gascuel
Anastasis Togkousidis
Maximum Likelihood (ML) based phylogenetic inference constitutes a challenging optimization problem. Given a set of aligned input sequences, phylogenetic inference tools strive to determine the tree topology, the branch-lengths, and the evo...
Phylogenetic Estimation of Branch-specific Shifts in the Tempo of Origination [0.03%]
分支特异性起源速率变化的谱系地质估计
Bjørn T Kopperud,Sebastian Höhna
Bjørn T Kopperud
Studying rates of species diversification is one of the key themes in macroevolution. In particular, we are interested in if some clades in a phylogeny diversify more rapidly/slowly than others due to branch-specific diversification rates. ...
Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila [0.03%]
基于基因组数据的跨物种基因流推断依赖于方法：果蝇中基因流情况的研究案例
Jiayi Ji,Thomas Roberts,Tomáš Flouri et al.
Jiayi Ji et al.
Analysis of genomic data in the past two decades has highlighted the prevalence of introgression as an important evolutionary force in both plants and animals. The genus Drosophila has received much attention recently, with an analysis of g...
Type genomics: a Framework for integrating Genomic Data into Biodiversity and Taxonomic research [0.03%]
类型组学：一个将基因组数据整合到生物多样性和分类学研究中的框架
Harald Letsch,Carola Greve,Anna K Hundsdoerfer et al.
Harald Letsch et al.
Name-bearing type specimens have a fundamental role in characterising biodiversity, as these objects represent the physical link between a scientific name and the biological organism. Type specimens are usually deposited in natural history ...
Batesian Mimicry Converges Towards Inaccuracy in Myrmecomorphic Spiders [0.03%]
拟态蚂蚁的 spiders 的 Batesian 拟态趋于不准确收敛
Michael B J Kelly,Shahan Derkarabetian,Donald James McLean et al.
Michael B J Kelly et al.
Batesian mimicry is an impressive example of convergent evolution driven by predation. However, the observation that many mimics only superficially resemble their models despite strong selective pressures is an apparent paradox. Here, we te...
Alessio Capobianco,Sebastian Höhna
Alessio Capobianco
Models used in likelihood-based morphological phylogenetics often adapt molecular phylogenetics models to the specificities of morphological data. Such is the case for the widely used Mkv model-which introduces an acquisition bias correctio...
phyddle: software for exploring phylogenetic models with deep learning [0.03%]
基于深度学习的探索发育模型软件PHYDDLE
Michael J Landis,Ammon Thompson
Michael J Landis
Phylogenies contain a wealth of information about the evolutionary history and process that gave rise to the diversity of life. This information can be extracted by fitting phylogenetic models to trees. However, many realistic phylogenetic ...
Unravelling the Effects of Ecology and Evolutionary History in the Phenotypic Convergence of Fishes [0.03%]
解密鱼类表型趋同的生态及进化历史效应
Jennifer R Hodge,Danielle S Adams,Keiffer L Williams et al.
Jennifer R Hodge et al.
Understanding the ecological drivers and limitations of adaptive convergence is a fundamental challenge. Here, we explore how adaptive convergence of planktivorous fishes has been influenced by multiple ecological factors, evolutionary hist...
Phylogenomic and Population Genomic Analyses of Ultraconserved Elements Reveal Deep Coalescence and Introgression Shaped Diversification Patterns in Lamprologine Cichlids of the Congo River [0.03%]
通过超保守元件的系统发育组学和群体基因组分析揭示深共祖现象及基因渐渗对刚果河拉姆布罗格汀丽鱼亚科多样性的塑造作用
Fernando Alda,S Elizabeth Alter,Naoko P Kurata et al.
Fernando Alda et al.
Understanding the drivers of diversification is a central goal in evolutionary biology but can be challenging when lineages radiate quickly and/or hybridize frequently. Cichlids in the tribe Lamprologini, an exceptionally diverse clade foun...