torchtree: flexible phylogenetic model development and inference using PyTorch [0.03%]
TorchTree：使用PyTorch灵活的生成模型开发和推理
Mathieu Fourment,Matthew Macaulay,Christiaan J Swanepoel et al.
Mathieu Fourment et al.
Bayesian inference has predominantly relied on the Markov chain Monte Carlo (MCMC) algorithm for many years. However, MCMC is computationally laborious, especially for complex phylogenetic models of time trees. This bottleneck has led to th...
Ana Serra Silva,Karen Siu-Ting,Christopher J Creevey et al.
Ana Serra Silva et al.
Missing data is a long standing issue in phylogenetic inference, which often results in high levels of taxonomic instability, obscuring otherwise well supported relationships. Multiple approaches have been developed to deal with the negativ...
The explosive radiation of the Neotropical Tillandsia subgenus Tillandsia (Bromeliaceae) has been accompanied by pervasive hybridization [0.03%]
辐射构造革叶铁兰亚属（凤梨科）的爆发伴随着广泛的杂交现象
Gil Yardeni,Michael H J Barfuss,Walter Till et al.
Gil Yardeni et al.
The recent rapid radiation of Tillandsia subgenus Tillandsia (Bromeliaceae) provides an attractive system to study the drivers and constraints of species diversification. This species-rich Neotropical monocot clade includes predominantly ep...
Lara M Ko Sters,Kevin Karbstein,Martin Hofmann et al.
Lara M Ko Sters et al.
DNA analyses have revolutionized species identification and taxonomic work. Yet, persistent challenges arise from little differentiation among and considerable variation within species, particularly among closely related groups. While image...
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...