Article
Biochemistry & Molecular Biology
Tomas Flouri, Jun Huang, Xiyun Jiao, Paschalia Kapli, Bruce Rannala, Ziheng Yang
Summary: The multispecies coalescent model provides a natural framework for phylogenetic analysis of genomic data, allowing estimation of species divergence times and ancestral population sizes. Clock violation should be considered, and the relaxed-clock models can extract valuable phylogenetic information from gene-tree branch lengths.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Ecology
Siavash Mirarab, Luay Nakhleh, Tandy Warnow
Summary: Species tree estimation is crucial for biological research, but it faces challenges due to various complex factors. Over the past decade, there has been significant progress in methods and mathematical theory for species tree estimation, although limitations still exist.
ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 52, 2021
(2021)
Article
Biochemical Research Methods
Elizabeth S. Allman, Hector Banos, John A. Rhodes
Summary: As more genomic-scale datasets are being used for species tree inference, simulators of the multispecies coalescent (MSC) process are necessary to test and evaluate new inference methods. However, the simulators themselves need to be tested to ensure their validity. This study develops methods to check if a collection of gene trees aligns with the MSC model on a given species tree. The tests conducted on well-known simulators reveal flaws in some of the samples, and are implemented in the freely available R package MSCsimtester for easy application by developers and users.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biology
A. Richards, L. Kubatko
Summary: The first step in statistical inference of the evolutionary histories of species is to develop a probability model that accurately describes the mutation process. This paper generalizes previous work to a relaxed clock model, enabling better phylogenetic inference in cases where the molecular clock does not hold.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Evolutionary Biology
Zhi Yan, Megan L. Smith, Peng Du, Matthew W. Hahn, Luay Nakhleh
Summary: Recent phylogenetic methods have focused on accurately inferring species trees in the presence of gene tree discordance due to incomplete lineage sorting (ILS). Most of these methods assume that data for each locus consist of orthologous, single-copy sequences, excluding loci with more than one copy in any of the studied genomes. This study examines the consequences of running such methods on data with paralogs, with or without ILS. Through simulations and analysis of biological data sets, the researchers demonstrate that these methods can still provide accurate results when paralogs are present. The findings have significant implications for expanding the data available for phylogenetic inference.
SYSTEMATIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Xavier Didelot, David Helekal, Michelle Kendall, Paolo Ribeca
Summary: The ability to distinguish imported cases from locally acquired cases is important for selecting public health control strategies. This study proposes an alternative approach using genomic data from a specific location to detect imported cases by comparing them with previous cases from the same location.
Article
Evolutionary Biology
Bo He, Youjie Zhao, Chengyong Su, Gonghua Lin, Yunliang Wang, Luyan Li, Junye Ma, Qun Yang, Jiasheng Hao
Summary: This study resolves the phylogenetic relationships among subgenera in the alpine butterfly Parnassius using nuclear and mitochondrial genome datasets. It identifies gene-tree/species-tree conflicts and considerable phylogenetic discordance due to incomplete lineage sorting (ILS). The study also compares different approaches and explores sources of phylogenomic conflict, providing insights for future evolutionary studies of the genus.
SYSTEMATIC ENTOMOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Xinxin Tan, Jiwei Qi, Zhijin Liu, Pengfei Fan, Gaoming Liu, Liye Zhang, Ying Shen, Jing Li, Christian Roos, Xuming Zhou, Ming Li
Summary: In this study, a phylogenomic analysis was conducted on Macaca genus to investigate the intrageneric phylogenetic relationships among species. Strong evidence was found supporting the division of this genus into 7 species groups. Incomplete lineage sorting and hybridization events were identified as the main factors contributing to the discordance observed among gene trees. These findings provide insights into the rapid speciation occurring in nonhuman primates.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Liliya Doronina, Olga Reising, Hiram Clawson, Gennady Churakov, Juergen Schmitz
Summary: This study investigates the phylogenetics of Euarchontoglires using whole-genome analysis and a marker system with minimal homoplasy. By analyzing presence/absence patterns of transposed elements, diagnostic insertions were identified and provided support for current resolutions of Primatomorpha and Euarchonta, as well as alternative phylogenetic scenarios.
Article
Plant Sciences
Jianling You, Stephen C. Lougheed, Yao Zhao, Guojie Zhang, Wensheng Liu, Fan Lu, Yuguo Wang, Wenju Zhang, Ji Yang, La Qiong, Zhiping Song
Summary: Introgressive hybridization and incomplete lineage sorting play important roles in the phylogeography of plant species that experienced rapid diversification in the Qinghai-Tibetan Plateau and the Hengduan Mountains.
Article
Genetics & Heredity
Jennifer M. Korstian, Nicole S. Paulat, Roy N. Platt, Richard D. Stevens, David A. Ray
Summary: Using presence/absence data from over 10,000 Ves SINE insertions, the researchers reconstructed a phylogeny for 11 Myotis species. They found that phylogenetic conflict was rampant in this genus, with almost one-third of individual gene trees being discordant with the overall species tree. The study suggests that incomplete lineage sorting (ILS) is a major contributor to the discordance. The researchers also observed signs of introgression between Old and New World taxa, as well as within the New World Myotis species. The findings highlight the role of hybridization in the evolutionary history of Myotis.
Article
Evolutionary Biology
Qiuyi Li, Celine Scornavacca, Nicolas Galtier, Yao-Ban Chan
Summary: Incomplete lineage sorting and gene duplication/transfers/loss can lead to incongruences between gene trees and species trees. The interaction between these processes can result in patterns typically interpreted as gene loss, and the rate of gene duplication, transfer, and loss becomes nonhomogeneous over time when considering incomplete lineage sorting. The introduction of the multilocus multispecies coalescent model provides a versatile and powerful framework for simulation and inference of gene family evolution.
SYSTEMATIC BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Anna A. Nagel, Bruce Rannala
Summary: HIV evolves rapidly within individuals, allowing phylogenetic studies to infer histories of viral lineages. Latent HIV sequences are an exception to this rapid evolution. A Bayesian phylogenetic method is developed to infer integration times of latent HIV sequences. Accurate estimates of latent integration dates are crucial in relating integration times to key events during HIV infection.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Biochemical Research Methods
Jing Peng, David L. Swofford, Laura Kubatko
Summary: In this paper, we propose a method for estimating the timing of speciation events within a phylogeny based on the multispecies coalescent model. We demonstrate the statistical consistency and asymptotic normality of the proposed method, and provide a computationally efficient estimator for its asymptotic variance. We evaluate the performance of our method using simulation and an empirical dataset for gibbons.
Article
Biochemistry & Molecular Biology
Wenpan Dong, Yanlei Liu, Enze Li, Chao Xu, Jiahui Sun, Wenying Li, Shiliang Zhou, Zhixiang Zhang, Zhili Suo
Summary: This study reconstructed the phylogenetic relationships within Catalpa using a large genomic dataset, revealing that Catalpa is monophyletic with two main clades. Biogeographic analysis suggested three main dispersal events in the evolutionary history of Catalpa, highlighting the impact of incomplete lineage sorting.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
