Article
Evolutionary Biology
Mathieu Brevet, Nicolas Lartillot
Summary: The study introduces an integrative framework for reconstructing the phylogenetic history of Ne, allowing for testing the nearly neutral theory and estimating the evolution of genetic variation patterns. The results show that both Ne and u play important roles in modulating patterns of genetic variation, with opposing trends observed in their variations.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Ornithology
Bing-Run Zhu, Yvonne I. Verkuil, Jesse R. Conklin, Ailin Yang, Weipan Lei, Jose A. Alves, Chris J. Hassell, Dmitry Dorofeev, Zhengwang Zhang, Theunis Piersma
Summary: Comparing the morphometrics and genetic population structuring of Black-tailed Godwits in northern Bohai Bay, China, with the known subspecies, it was found that Bohai Godwits are significantly larger than melanuroides and may belong to a distinct new subspecies.
Article
Genetics & Heredity
Tullia Di Corcia, Giuseppina Scano, Cristina Martinez-Labarga, Stefania Sarno, Sara De Fanti, Donata Luiselli, Olga Rickards
Summary: The study reconstructed the genetic maternal and paternal inheritance of the Tsachilas, suggesting a possible common origin between them, the Chachi, and other Barbacoan people, as well as an interesting ancient linkage to the Inca invaders in Yumbo country. Contrasting patterns of genetic diversity were found for different genetic markers, indicating complex relationships with surrounding populations in northwestern South America.
Article
Zoology
Pavel Just, Frantisek Stahlavsky, Frantisek Kovarik, Jana Stundlova
Summary: In this study, we used an integrative approach combining cytogenetic data and sequence-based phylogeny to investigate the mechanisms of karyotype differentiation in scorpions of the genus Gint. Our results revealed significant karyotype diversity and chromosome heterozygosity in Gint species. We also found that interspecific differences in chromosome counts corresponded with genetic divergence. Furthermore, the study indicated ongoing structural changes in the genome architecture of some Gint species.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Biodiversity Conservation
Jinqiang Quan, Yongqing Li, Yonghui Yang, Tianliang Yang, Yuzhu Sha, Yuan Cai, Ting Jiao, Jianping Wu, Shengguo Zhao
Summary: The study analyzed the mtDNA D-loop sequences of 1163 Chinese indigenous cattle to determine their maternal origin and population genetic structure, prioritizing conservation evaluations based on a population genetic model. Three maternal origins or domestication events were identified among Chinese indigenous cattle, with various levels of genetic diversity and contributions to the richness of genetic resources. The research provides a scientific basis and effective evaluation methods for the protection of genetic resources of indigenous livestock varieties.
GLOBAL ECOLOGY AND CONSERVATION
(2021)
Article
Ecology
Robin Leppitt, Alea Rose, Wayne A. Houston, Peter M. Kyne, Sam C. Banks, John C. Z. Woinarski, Stephen T. Garnett
Summary: The delineation of subspecies is important in biodiversity evaluation and protection, but inconsistent criteria and lack of agreement cause challenges. By using mitochondrial DNA, the study evaluated the genetic variation of the endemic Yellow Chat in Australia and found low levels of genetic variation, indicating vulnerability to environmental change.
ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Adrianna D. Musial, Katarzyna Ropka-Molik, Monika Stefaniuk-Szmukier, Grzegorz Mycka, Agnieszka Bieniek, Nataliya Yasynetska
Summary: Przewalski horses are the last population of wild horses, descended from herds domesticated by the Botai culture 5000 years ago. This study aimed to determine the maternal variation of Przewalski horses in Askania-Nova Reserve through analysis of mitochondrial DNA and Y chromosome markers, as well as coat color genes. The results showed distinct haplotypes in the mtDNA analysis, unique Y chromosome polymorphisms, and confirmation of native, wild genotypes through coat color analysis.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Genetics & Heredity
Ruoyi Cai, Brian L. Browning, Sharon R. Browning
Summary: The effective size of a population (N-e) can be estimated through analysis of identity-by-descent (IBD) segments, and this study proposes a method to estimate the X chromosome effective population size from X chromosome IBD segments. The accuracy of the estimation is demonstrated using simulated data, and it is found that short-term differences in sex-specific N-e may not reliably indicate true sex-specific differences. The study also analyzes the effective size of UK White British and UK Indian populations using sequenced samples from the UK Biobank.
G3-GENES GENOMES GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Xing-Yan Yang, Allah Rakha, Wei Chen, Juzhi Hou, Xue-Bin Qi, Quan-Kuan Shen, Shan-Shan Dai, Xierzhatijiang Sulaiman, Najmudinov Tojiddin Abdulloevich, Manilova Elena Afanasevna, Khudoidodov Behruz Ibrohimovich, Xi Chen, Wei-Kang Yang, Atif Adnan, Ruo-Han Zhao, Yong-Gang Yao, Bing Su, Min-Sheng Peng, Ya-Ping Zhang
Summary: The genetic impact of Tibetans on Balti people in Baltistan, Pakistan was explored through genome sequencing, showing that they possess 22.6-26% Tibetan ancestry. Analysis indicated that both ancient Tibetan males and females were involved in dispersal, suggesting a dominant cultural impact of the Tibetan Empire on Baltistan.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Ecology
Krystyna Nadachowska-Brzyska, Mateusz Konczal, Wieslaw Babik
Summary: Effective population size (Ne) is a key evolutionary parameter that determines genetic variation levels and selection efficacy. Ne estimation and interpretation are essential in evolutionary and conservation biology, with diverse applications and methods available. Recent advancements in estimating temporal Ne trends provide a comprehensive understanding of the evolutionary continuum.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Xu Wang, Hao Zhang, Ian Kitching, Zhen-Bang Xu, Yi-Xin Huang
Summary: This study analyzed the mitochondrial genomes of Sphingidae to investigate the phylogenetic relationships and genomic differences among different subfamilies within this moth family. The results supported the monophyly of all four recognized subfamilies and suggested a revised placement of Langiinae within the family.
Article
Biochemistry & Molecular Biology
Nils Ryman, Linda Laikre, Ola Hossjer
Summary: Measurement of allele frequency shifts between temporally spaced samples has been used to estimate effective population size (N-e), also known as variance effective size (N-eV). Our study reveals that N-eV of a local population within a sub-structured population is influenced by genetic drift, migration rate (m), and census size (N-c). The relationship between N-e and N-c determines whether the realized N-eV of a local population increases or decreases with increasing m. The effect of N-c on N-eV is most significant at higher migration rates.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biology
Nicola Zadra, Annapaola Rizzoli, Omar Rota-Stabelli
Summary: The study reveals a strong incongruence between nuclear and mitochondrial markers in the phylogeny of Aedini mosquitoes, suggesting potential evolutionary events or hybridization history as explanations. The findings may guide future research in phylogenomic studies of Aedini mosquitoes.
Article
Genetics & Heredity
Olga Koshkina, Tatiana Deniskova, Arsen Dotsev, Elisabeth Kunz, Marina Selionova, Ivica Medugorac, Natalia Zinovieva
Summary: Russia has a rich variety of local sheep breeds, but their genetic diversity and maternal origin have not been thoroughly investigated. This study analyzes the mitochondrial genomes of Russian sheep breeds from different regions, revealing their diversity and phylogeny.
Article
Biochemistry & Molecular Biology
Thibault Latrille, Vincent Lanore, Nicolas Lartillot
Summary: Mutation-selection phylogenetic codon models are a principled approach for studying the interplay between mutation, selection, and drift, but their assumption of constant genetic drift is unrealistic. By introducing variation in effective population size and mutation rate between lineages, the model can better account for the joint evolutionary process of these lineage-specific variables. The model, tested on simulated and empirical data, suggests reasonable reconstructions of evolutionary trends, although potential issues with assumptions about epistatic interactions between sites remain.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)