On the utility of Deep Learning for model classification and parameter estimation on complex diversification scenarios [0.03%]
Pablo Gutiérrez de la Peña,Guillermo Iglesias,Edgar Talavera et al.
Pablo Gutiérrez de la Peña et al.
Birth-Death models applied to dated phylogenies are useful tools to study past diversification dynamics. Parameters in these stochastic models are typically inferred using likelihood-based methods; however, these approaches can exhibit comp...
Qian Cong,Jing Zhang,Nick V Grishin
Qian Cong
The classification of organisms into species is fundamental to the study of life. Contrary to popular belief, simple and quantitative standards for species delineation are often lacking, and debates about species boundaries create obstacles...
Sean W McHugh,Michael J Donoghue,Michael J Landis
Sean W McHugh
Where each species actually lives is distinct from where it could potentially survive and persist. This suggests it is important to distinguish established biome affinities (where species live) from enabled affinities (where species could l...
Bayesian test of gene flow between sister lineages using genomic data [0.03%]
基于基因组数据的姊妹谱系间基因流的贝叶斯检验
Ziheng Yang,Xiyun Jiao,Sirui Cheng et al.
Ziheng Yang et al.
Inference of interspecific gene flow using genomic data is important to reliable reconstruction of species phylogenies and to our understanding of the speciation process. Gene flow is harder to detect if it involves sister lineages than non...
Shayesteh Arasti,Puoya Tabaghi,Yasamin Tabatabaee et al.
Shayesteh Arasti et al.
The abundant discordance between evolutionary relationships across the genome has rekindled interest in methods for comparing and averaging trees on a shared leaf set. However, compared to tree topology, where much progress has been made, h...
Integrating Secondary Structure Information Enhances Phylogenetic Signal in Mitochondrial Protein Coding Genes [0.03%]
二级结构信息的整合增强了线粒体蛋白编码基因的系统发育信号
Claudio Cucini,Francesco Nardi,Joan Pons
Claudio Cucini
Accurate phylogenetic inference requires models that account for heterogeneity in molecular evolution. Mitochondrial protein-coding genes, which encode membrane-bound proteins composed of multiple transmembrane α-helices, exhibit considera...
Improving the Robustness of Phylogenetic Independent Contrasts: Addressing Abrupt Evolutionary Shifts with Outlier- and Distribution-Guided Correlation [0.03%]
利用异常值和分布引导相关性应对突发性进化转变以提高系统发生独立对比的鲁棒性
Zheng-Lin Chen,Rui Huang,Hong-Ji Guo et al.
Zheng-Lin Chen et al.
Traditional phylogenetically aware correlation methods perform well under gradual evolutionary processes. However, abrupt evolutionary shifts-or macroevolutionary jumps, characteristic of punctuated evolution-can produce extreme phylogeneti...
Tensor cores unlock efficient and lower-energy massive parallelization on phylogenetic trees [0.03%]
tensor cores解锁高效且低能耗的系统发育树大规模并行化
Karthik Gangavarapu,Xiang Ji,Yucai Shao et al.
Karthik Gangavarapu et al.
Massively parallel algorithms leveraging graphics processing units (GPUs) have significantly accelerated inference in statistical phylogenetics, with applications in understanding pathogen evolution, population dynamics, natural selection, ...
The impact of incomplete taxon sampling on inference of gene flow by Bayesian and summary methods using genomic sequence data [0.03%]
不完全取样对基于基因组序列数据的贝叶斯和汇总法推断基因流的影响研究
Sirui Cheng,Thomas Flouri,Tianqi Zhu et al.
Sirui Cheng et al.
Interspecific gene flow is commonly inferred using genomic data under the multispecies coalescent (MSC) model. Incomplete taxon sampling can impact inference of gene flow in multiple ways. First unsampled ghost lineages that are sources of ...