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Authors Xu, SH; He, ZW; Guo, ZX; Zhang, Z; Wyckoff, GJ; Greenberg, A; Wu, CI; Shi, SH
Author Full Name Xu, Shaohua; He, Ziwen; Guo, Zixiao; Zhang, Zhang; Wyckoff, Gerald J.; Greenberg, Anthony; Wu, Chung-I.; Shi, Suhua
Title Genome-Wide Convergence during Evolution of Mangroves from Woody Plants
Source MOLECULAR BIOLOGY AND EVOLUTION
Language English
Document Type Article
Author Keywords mangroves; convergent evolution; adaptive evolution; marginal environments; genomes
Keywords Plus PHYLOGENETIC ANALYSIS; PARALLEL EVOLUTION; PROTEIN EVOLUTION; ARABIDOPSIS; GENES; IDENTIFICATION; SUBSTITUTIONS; GLUTATHIONE; ORIGINS; MODEL
Abstract When living organisms independently invade a new environment, the evolution of similar phenotypic traits is often observed. An interesting but contentious issue is whether the underlying molecular biology also converges in the new habitat. Independent invasions of tropical intertidal zones by woody plants, collectively referred to as mangrove trees, represent some dramatic examples. The high salinity, hypoxia, and other stressors in the new habitatmight have affected both genomic features and protein structures. Here, we developed a new method for detecting convergence at conservative Sites (CCS) and applied it to the genomic sequences of mangroves. In simulations, the CCS method drastically reduces random convergence at rapidly evolving sites as well as falsely inferred convergence caused by the misinferences of the ancestral character. In mangrove genomes, we estimated similar to 400 genes that have experienced convergence over the background level of convergence in the nonmangrove relatives. The convergent genes are enriched in pathways related to stress response and embryo development, which could be important for mangroves' adaptation to the new habitat.
Author Address [Xu, Shaohua; He, Ziwen; Guo, Zixiao; Zhang, Zhang; Wu, Chung-I.; Shi, Suhua] Sun Yat Sen Univ, Sch Life Sci, Key Lab Biodivers Dynam & Conservat Guangdong Hig, Guangdong Prov Key Lab Plant Resources,State Key, Guangzhou, Guangdong, Peoples R China; [Wyckoff, Gerald J.] Univ Missouri, Mol Biol & Biochem, Kansas City, MO 64110 USA; [Greenberg, Anthony] Bayesic Res, Ithaca, NY USA; [Wu, Chung-I.] Univ Chicago, Dept Ecol & Evolut, 940 E 57th St, Chicago, IL 60637 USA
Reprint Address Wu, CI; Shi, SH (corresponding author), Sun Yat Sen Univ, Sch Life Sci, Key Lab Biodivers Dynam & Conservat Guangdong Hig, Guangdong Prov Key Lab Plant Resources,State Key, Guangzhou, Guangdong, Peoples R China.; Wu, CI (corresponding author), Univ Chicago, Dept Ecol & Evolut, 940 E 57th St, Chicago, IL 60637 USA.
E-mail Address ciwu@uchicago.edu; lssssh@mail.sysu.edu.cn
ORCID Number Guo, Zixiao/0000-0003-4820-4056; Wyckoff, Gerald/0000-0003-2604-2666
Funding Agency and Grant Number National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [41130208, 91331202, 31600182]; 985 ProjectJilin UniversityXiamen University [33000-31131105]; Science Foundation of State Key Laboratory of Biocontrol [SKLBC16A35, SKLBC16A37]; Fundamental Research Funds for the Central UniversitiesFundamental Research Funds for the Central Universities [16lgjc39]; China Postdoctoral Science FoundationChina Postdoctoral Science Foundation [2014M552264, 2015T80931]; Chang Hungta Science Foundation of Sun Yat-Sen University
Funding Text We thank Y.X. Fu and K. Zeng for suggestions and discussions. This work was supported by the National Natural Science Foundation of China (grant numbers 41130208, 91331202, and 31600182), the 985 Project (grant number 33000-31131105), the Science Foundation of State Key Laboratory of Biocontrol (grant number SKLBC16A35 and SKLBC16A37), the Fundamental Research Funds for the Central Universities (grant number 16lgjc39), the China Postdoctoral Science Foundation (grant numbers 2014M552264 and 2015T80931), and the Chang Hungta Science Foundation of Sun Yat-Sen University.
Times Cited 25
Total Times Cited Count (WoS, BCI, and CSCD) 27
Publisher OXFORD UNIV PRESS
Publisher City OXFORD
Publisher Address GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND
ISSN 0737-4038
29-Character Source Abbreviation MOL BIOL EVOL
ISO Source Abbreviation Mol. Biol. Evol.
Publication Date APR
Year Published 2017
Volume 34
Issue 4
Beginning Page 1008
Ending Page 1015
Digital Object Identifier (DOI) 10.1093/molbev/msw277
Page Count 8
Web of Science Category Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & Heredity
Subject Category Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & Heredity
Document Delivery Number EO5VY
Unique Article Identifier WOS:000396762200018
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