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Xiong H, Wang D, Shao C, Yang X, Yang J, Ma T, Davis CC, Liu L, Xi Z. Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication. Syst Biol 2022; 71:1348-1361. [PMID: 35689633 PMCID: PMC9558847 DOI: 10.1093/sysbio/syac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 12/02/2022] Open
Abstract
Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of eukaryotes and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD; however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs–paralogous genes mistakenly identified as orthologs because they are present in single copies within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as a result of gene extinction (or incomplete laboratory sampling) are only recently gaining empirical attention in the phylogenomics community. Moreover, few studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and differential gene loss scenarios following WGD. When gene loss occurs along the terminal branches of the species tree, alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the degree of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of genes increases. Additionally, pseudoorthologs can greatly mislead species tree inference when gene loss occurs along the internal branches of the species tree. Here, both coalescent and concatenation methods yield inconsistent results. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era. [Coalescent method; concatenation method; incomplete lineage sorting; pseudoorthologs; single-copy gene; whole-genome duplication.]
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Affiliation(s)
- Haifeng Xiong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Danying Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Chen Shao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xuchen Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jialin Yang
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
| | - Liang Liu
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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Liang J, Liu X, Tsui CKM, Ma Z, Luo Y. Genetic Structure and Asymmetric Migration of Wheat Stripe Rust Pathogen in Western Epidemic Areas of China. Phytopathology 2021; 111:1252-1260. [PMID: 33210988 DOI: 10.1094/phyto-06-20-0236-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Puccinia striiformis f. sp. tritici causes severe global epidemics of wheat stripe rust primarily by airborne urediniospores. Understanding long-distance migration patterns of P. striiformis f. sp. tritici is critical for disease forecasting and management. Although the western epidemic areas in China have been considered as the source of inoculum spread eastward across the country, migration pathways among different populations within the western epidemic areas are poorly understood. In this study, we investigated the population genetics of 200 P. striiformis f. sp. tritici isolates from western epidemic areas using amplified fragment length polymorphism and simple sequence repeat markers. A coalescent approach was also used to calculate the migration rates among populations. Data analyses with both marker systems indicated high genetic diversity in each regional population. The Mantel test revealed significant positive correlation between genetic and geographic distances. Both discriminant analysis of principal components and STRUCTURE analysis supported moderate population structure shaped by seasonality and geography. The calculated migration rates indicated the presence of asymmetric migration between major populations in western epidemic areas, with greater migration rates from high elevation, oversummering areas to low elevation, overwintering areas. Sichuan Basin, one of the low elevation, overwintering areas, sampled in both fall and spring, was inferred as a recipient in fall but a donor in spring. Migration among P. striiformis f. sp. tritici populations may be partly attributable to terrace farming and prevailing wind direction in different seasons. Our study provides a better understanding of fine-scale population structure and the interregional migration pattern of P. striiformis f. sp. tritici in northwestern China and will inform future rust management.
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Affiliation(s)
- Junmin Liang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiufeng Liu
- Tianjin Key Laboratory of Crop Genetics and Breeding, Institute of Crop Sciences, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Clement K M Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zhanhong Ma
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Yong Luo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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