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Fan Z, Zhang R, Zhou A, Hey J, Song Y, Osada N, Hamada Y, Yue B, Xing J, Li J. Genomic Evidence for the Complex Evolutionary History of Macaques (Genus Macaca). J Mol Evol 2024; 92:286-299. [PMID: 38634872 DOI: 10.1007/s00239-024-10166-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/20/2024] [Indexed: 04/19/2024]
Abstract
The genus Macaca is widely distributed, occupies a variety of habitats, shows diverse phenotypic characteristics, and is one of the best-studied genera of nonhuman primates. Here, we reported five re-sequencing Macaca genomes, including one M. cyclopis, one M. fuscata, one M. thibetana, one M. silenus, and one M. sylvanus. Together with published genomes of other macaque species, we combined 20 genome sequences of 10 macaque species to investigate the gene introgression and genetic differences among the species. The network analysis of the SNV-fragment trees indicates a reticular phylogeny of macaque species. Combining the results from various analytical methods, we identified extensive ancient introgression events among macaque species. The multiple introgression signals between different species groups were also observed, such as between fascicularis group species and silenus group species. However, gene flow signals between fascicularis and sinica group were not as strong as those between fascicularis group and silenus group. On the other hand, the unidirect gene flow in M. arctoides probably occurred between the progenitor of M. arctoides and the common ancestor of fascicularis group. Our study also shows that the genetic backgrounds and genetic diversity of different macaques vary dramatically among species, even among populations of the same species. In conclusion, using whole genome sequences and multiple methods, we have studied the evolutionary history of the genus Macaca and provided evidence for extensive introgression among the species.
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Affiliation(s)
- Zhenxin Fan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Rusong Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Anbo Zhou
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Jody Hey
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
| | - Yang Song
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido, 060-0814, Japan
| | - Yuzuru Hamada
- National Primate Research Center of Thailand, Chulalongkorn University, Bangkok, Thailand
| | - Bisong Yue
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Jinchuan Xing
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Jing Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.
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2
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Chung Y. Assessing the impact of recombination on the estimation of isolation-with-migration models using genomic data: a simulation study. Genomics Inform 2023; 21:e27. [PMID: 37415456 PMCID: PMC10326538 DOI: 10.5808/gi.23016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 07/08/2023] Open
Abstract
Recombination events complicate the evolutionary history of populations and species and have a significant impact on the inference of isolation-with-migration (IM) models. However, several existing methods have been developed, assuming no recombination within a locus and free recombination between loci. In this study, we investigated the effect of recombination on the estimation of IM models using genomic data. We conducted a simulation study to evaluate the consistency of the parameter estimators with up to 1,000 loci and analyze true gene trees to examine the sources of errors in estimating the IM model parameters. The results showed that the presence of recombination led to biased estimates of the IM model parameters, with population sizes being more overestimated and migration rates being more underestimated as the number of loci increased. The magnitude of the biases tended to increase with the recombination rates when using 100 or more loci. On the other hand, the estimation of splitting times remained consistent as the number of loci increased. In the absence of recombination, the estimators of the IM model parameters remained consistent.
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Affiliation(s)
- Yujin Chung
- Department of Applied Statistics, Kyonggi University, Suwon 16227, Korea
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3
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Molo MS, White JB, Cornish V, Gell RM, Baars O, Singh R, Carbone MA, Isakeit T, Wise KA, Woloshuk CP, Bluhm BH, Horn BW, Heiniger RW, Carbone I. Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control. PLoS One 2022; 17:e0276556. [PMID: 36301851 PMCID: PMC9620740 DOI: 10.1371/journal.pone.0276556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/08/2022] [Indexed: 11/23/2022] Open
Abstract
Aspergillus flavus is an agriculturally important fungus that causes ear rot of maize and produces aflatoxins, of which B1 is the most carcinogenic naturally-produced compound. In the US, the management of aflatoxins includes the deployment of biological control agents that comprise two nonaflatoxigenic A. flavus strains, either Afla-Guard (member of lineage IB) or AF36 (lineage IC). We used genotyping-by-sequencing to examine the influence of both biocontrol agents on native populations of A. flavus in cornfields in Texas, North Carolina, Arkansas, and Indiana. This study examined up to 27,529 single-nucleotide polymorphisms (SNPs) in a total of 815 A. flavus isolates, and 353 genome-wide haplotypes sampled before biocontrol application, three months after biocontrol application, and up to three years after initial application. Here, we report that the two distinct A. flavus evolutionary lineages IB and IC differ significantly in their frequency distributions across states. We provide evidence of increased unidirectional gene flow from lineage IB into IC, inferred to be due to the applied Afla-Guard biocontrol strain. Genetic exchange and recombination of biocontrol strains with native strains was detected in as little as three months after biocontrol application and up to one and three years later. There was limited inter-lineage migration in the untreated fields. These findings suggest that biocontrol products that include strains from lineage IB offer the greatest potential for sustained reductions in aflatoxin levels over several years. This knowledge has important implications for developing new biocontrol strategies.
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Affiliation(s)
- Megan S. Molo
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
| | - James B. White
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
| | - Vicki Cornish
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
| | - Richard M. Gell
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
- Program of Genetics, North Carolina State University, Raleigh, North
Carolina, United States of America
| | - Oliver Baars
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
| | - Rakhi Singh
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
| | - Mary Anna Carbone
- Center for Integrated Fungal Research and Department of Plant and
Microbial Biology, North Carolina State University, Raleigh, NC, United States
of America
| | - Thomas Isakeit
- Department of Plant Pathology and Microbiology, Texas AgriLife Extension
Service, Texas A&M University, College Station, TX, United States of
America
| | - Kiersten A. Wise
- Department of Plant Pathology, University of Kentucky, Princeton, KY,
United States of America
| | - Charles P. Woloshuk
- Department of Plant Pathology and Botany, Purdue University, West
Lafayette, IN, United States of America
| | - Burton H. Bluhm
- University of Arkansas Division of Agriculture, Department of Entomology
and Plant Pathology, Fayetteville, AR, United States of
America
| | - Bruce W. Horn
- United States Department of Agriculture, Agriculture Research Service,
Dawson, GA, United States of America
| | - Ron W. Heiniger
- Department of Crop and Soil Sciences, North Carolina State University,
Raleigh, NC, United States of America
| | - Ignazio Carbone
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
- Program of Genetics, North Carolina State University, Raleigh, North
Carolina, United States of America
- * E-mail:
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Balmori-de la Puente A, Ventura J, Miñarro M, Somoano A, Hey J, Castresana J. Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola. Sci Rep 2022; 12:4065. [PMID: 35260719 PMCID: PMC8904462 DOI: 10.1038/s41598-022-07877-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/21/2022] [Indexed: 01/18/2023] Open
Abstract
Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus Arvicola, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of A. scherman present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, A. amphibius, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.
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Affiliation(s)
- Alfonso Balmori-de la Puente
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain.,Àrea de Recerca en Petits Mamífers, Granollers Museum of Natural Sciences, Palaudàries, 102, 08402, Granollers, Barcelona, Spain
| | - Marcos Miñarro
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra AS-267, PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Aitor Somoano
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra AS-267, PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Jody Hey
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain.
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Webb A, Knoblauch J, Sabankar N, Kallur AS, Hey J, Sethuraman A. The Pop-Gen Pipeline Platform: A Software Platform for Population Genomic Analyses. Mol Biol Evol 2021; 38:3478-3485. [PMID: 33950197 PMCID: PMC8321520 DOI: 10.1093/molbev/msab113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The Pop-Gen Pipeline Platform (PPP) is a software platform for population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including input preparation, file format conversion, various population genomic analyses, and output generation. The platform has also been developed with reproducibility and extensibility of analyses in mind. The PPP is an open-source package that is available for download and use at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html.
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Affiliation(s)
- Andrew Webb
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
| | - Jared Knoblauch
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
| | - Nitesh Sabankar
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA, USA
| | - Apeksha Sukesh Kallur
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA, USA
| | - Jody Hey
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
| | - Arun Sethuraman
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA.,Department of Biological Sciences, California State University San Marcos, San Marcos, CA, USA
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Phifer-Rixey M, Harr B, Hey J. Further resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories. BMC Evol Biol 2020; 20:120. [PMID: 32933487 PMCID: PMC7493149 DOI: 10.1186/s12862-020-01666-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/27/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The three main subspecies of house mice, Mus musculus castaneus, Mus musculus domesticus, and Mus musculus musculus, are estimated to have diverged ~ 350-500KYA. Resolution of the details of their evolutionary history is complicated by their relatively recent divergence, ongoing gene flow among the subspecies, and complex demographic histories. Previous studies have been limited to some extent by the number of loci surveyed and/or by the scope of the method used. Here, we apply a method (IMa3) that provides an estimate of a population phylogeny while allowing for complex histories of gene exchange. RESULTS Results strongly support a topology with M. m. domesticus as sister to M. m. castaneus and M. m. musculus. In addition, we find evidence of gene flow between all pairs of subspecies, but that gene flow is most restricted from M. m. musculus into M. m. domesticus. Estimates of other key parameters are dependent on assumptions regarding generation time and mutation rate in house mice. Nevertheless, our results support previous findings that the effective population size, Ne, of M. m. castaneus is larger than that of the other two subspecies, that the three subspecies began diverging ~ 130 - 420KYA, and that the time between divergence events was short. CONCLUSIONS Joint demographic and phylogenetic analyses of genomic data provide a clearer picture of the history of divergence in house mice.
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Affiliation(s)
| | - Bettina Harr
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - Jody Hey
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
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