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Prof. Suhua Shi’s group at School of Life Sciences made important achievements in the field of convergent evolution

Last updated :2020-07-25

Source: School of Life Sciences
Written by: School of Life Sciences
Edited by: Tan Rongyu, Wang Dongmei

The independent emergence of similar traits between species, known as convergent evolution, is proposed as compelling evidence of adaption. Utilizing genomic data to study the molecular mechanism of convergent evolution has become a hot spot in evolutionary genomics. The research group led by Prof. Suhua Shi at School of Life Sciences in Sun Yat-sen University summarized the studies on genomic convergence published in recent years, and found that the false positives had led researchers to overestimate the convergent evolution at genomic level. The research group developed a method to accurately estimate the molecular convergence. Utilizing a variety of mangrove plants, they clarified the mechanisms of convergent evolution at the mangrove genomes. Their findings were published back to back in the latest issue of National Science Review in the form of perspective and original research article, and were displayed as the cover story.

 
The cover of National Science Review Issue 6, 2020 (The cover depicts a delicate sapling of Rhizophora living in the intertidal zone with the pneumatophores of Sonneratia in the background.)

Convergent evolution is one of the central topics in evolutionary genetics. In recent years, with the burst of genomic data, more and more studies have tried to detect convergent amino acid substitutions on the whole genome. However, there are large number of neutral convergence at the large genomes in addition to the adaptive ones. Therefore, the setting of control groups to estimate the level of neutral convergence is necessary for detecting adaptive convergence. This perspective summarized the currently published researches on the detection of convergent evolution at the whole genome level. Although these studies have detected convergence on whole genomes, it’s unclear whether these convergence are adaptive or neutral because of the lack of empirical controls. The researchers re-analyzed the convergence of 13 mammalian genomes by setting inland mammals as control groups. When the background noises are reduced to the minimum, the marine mammals showed a lower signal of genome convergence than the inland relatives. The perspective therefore highlighted the importance of the choice of taxa from identical environments and the setting of empirical controls in detecting genomic convergence.

Mangrove plants that independently adapted to the intertidal environments from inland ancestors are ideal models to explore adaptive convergence. Researchers selected 16 representative mangrove species from three major mangrove clades, performed whole genome and transcriptome sequencing and assembly, and tested convergent evolution at the whole genomic levels. Through phylogenetic analysis, researchers found that the origins of the three mangrove clades were in the same time interval. They have jointly experienced the historical sea level fluctuations and gradually adapted to the intertidal environment. The study further improved the CCS (Convergence at Conservative Site) method for accurately estimating the molecular convergence. Using terrestrial plants as control groups, the study successfully collected more than 70 genes that have experienced convergent amino acid substitutions in mangroves. Importantly, convergence is more often manifested at a higher level such as AA usage and AA substitution patterns. This convergent evolution of amino acid composition helps mangroves adapt to the high-salinity, fluctuating and nutrient-poor coastal intertidal environment. By selecting suitable taxa, large number of genomes and, in particular, the setting of empirical control, this large study of mangroves is the first successful attempt at detecting genome-wide site convergence.

Professor Suhua Shi is the corresponding author of this work. Associate Professor Ziwen He and Postdoctoral Researchers Shaohua Xu and Zhang Zhang are the co-first authors. The academic affiliation of the first and corresponding author is School of Life Sciences, Sun Yat-sen University. This work was supported by the National Natural Science Foundation of China, the National Key Research and Development Plan, the Guangdong Basic and Applied Basic Research Foundation and the China Postdoctoral Science Foundation.

Link to the paper:
1. He Ziwen, Xu Shaohua, Shi Suhua. Adaptive convergence at the genomic level—prevalent, uncommon or very rare? Natl Sci Rev. 2020, 7(6):947–951.
https://academic.oup.com/nsr/article/7/6/947/5824675

2. He Ziwen, Xu Shaohua, Zhang Zhang, et al., Shi Suhua. Convergent adaptation of the genomes of woody plants at the land–sea interface. Natl Sci Rev. 2020, 7(6):978–993.
https://academic.oup.com/nsr/article/7/6/978/5741706