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 ...
Phylogenomics and a New Fossil Synthesis Illuminate the Early Evolution of Palms (Arecaceae) [0.03%]
磷脂基因组和新化石合成阐明了榈树（槟榔科）的早期进化
Sidonie Bellot,Fabien L Condamine,Kelly K S Matsunaga et al.
Sidonie Bellot et al.
Tropical rainforests are home to almost half of plant diversity, yet a shortfall in phylogenetic hypotheses for tropical plants hinders our understanding of how rainforests have formed and adapted to past global changes. Phylogenetic and hi...
Michael Lind Severinsen,Morten Akhøj,Rasmus Nielsen et al.
Michael Lind Severinsen et al.
Ancestral state reconstruction is a fundamental challenge in evolutionary biology, requiring methods that can capture complex morphological changes while accounting for phylogenetic relationships. Current approaches are based on linear assu...
Dietary specialization drives adaptation, convergence, and integration across the cranial and appendicular skeleton in Waterfowl (Anseriformes) [0.03%]
饮食专性化驱动雁形目鸟类头骨和附肢骨骼的适应、趋同及整合
Ray Chatterji,Tracy A Heath,Helen F James et al.
Ray Chatterji et al.
Convergence provides strong evidence for adaptation, reflecting similar responses to recurring selection pressures. Waterfowl (order Anseriformes) have repeatedly evolved morphotypes putatively correlated with foraging ecology (e.g., dabble...
James D Boyko
James D Boyko
Modeling discrete character evolution in a Markovian framework has become common practice in phylogenetic comparative methods. The increasing size and complexity of these models reflects a trend of analyses to include more taxa and more dis...