Suhua Shi

Suhua Shi
Sun Yat-Sen University | SYSU

About

288
Publications
63,907
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6,335
Citations
Citations since 2016
117 Research Items
3553 Citations
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20162017201820192020202120220100200300400500600
20162017201820192020202120220100200300400500600
Introduction
My research focuses on adaptive evolution and speciation in mangroves. The aim of her research is to understand the molecular basis of adaptation and phenotypic variation by using genomic techniques. We are particularly interested in the evolutionary convergence among independently evolved species in the same biological community, as well as geographical mechanisms of speciation revealed by mangroves.

Publications

Publications (288)
Article
Adaptation to new environments is a key evolutionary process which presumably involves complex genomic changes. Mangroves, a collection of ~80 woody plants that have independently invaded intertidal zones >20 times, are ideal for studying this process. We assembled near‐chromosome‐scale genomes of three Xylocarpus species as well as an outgroup spe...
Article
Full-text available
Genomic studies are now poised to explore whole communities of species. The ~70 species of woody plants that anchor the coastal ecosystems of the tropics, collectively referred to as mangroves, are particularly suited to this exploration. In this study, we de novo sequenced the whole genomes of 32 mangroves, which we combined with other sequences o...
Article
How plants adapt and diverge in extreme environments is a key question of plant evolution and ecology. Mangrove invasion of intertidal environments is facilitated by adaptive phenotypes such as aerial roots, salt‐secreting leaf, and viviparity, and genomic mechanisms including whole genome duplication and transposable element number reduction. Howe...
Article
Full-text available
Background Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering ‘blue carbon’. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring nat...
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There is a large literature in the last two decades affirming adaptive DNA sequences evolution between species. The main lines of evidence are from i) the McDonald-Kreitman (MK) test, which compares divergence and polymorphism data, and ii) the PAML test, which analyzes multi-species divergence data. Here, we apply these two tests concurrently on t...
Article
Full-text available
Whole‐genome duplication (WGD) is believed to increase the chance of adaptation to a new environment. This conjecture may apply particularly well to new environments that are not only different, but also more variable than ancestral habitats. One such prominent environment is the interface between land and sea, which has been invaded by woody plant...
Article
Historic climate changes drive geographical populations of coastal plants to contract and recover dynamically, even die out completely. Species suffering from such bottlenecks usually lose intraspecific genetic diversity, but how do these events influence population subdivision patterns of coastal plants? We investigated this question in the typica...
Preprint
Full-text available
There is a large literature in the last two decades affirming adaptive DNA sequences evolution between species. The main lines of evidence are from i) the McDonald-Kreitman (MK) test, which compares divergence and polymorphism data, and ii) the PAML test, which analyzes multi-species divergence data. Here, we apply these two tests concurrently on t...
Preprint
Historic climate changes had always driven geographical populations of coastal plants to contract and recover dynamically, even die out completely. Species suffering from such bottlenecks usually lose intraspecific genetic diversity, but how do these events influence population subdivision patterns of coastal plants? We investigated this question i...
Article
Full-text available
Mangroves have colonized extreme intertidal environments characterized by high salinity, hypoxia, and other abiotic stresses. Aegiceras corniculatum, a pioneer mangrove species that evolved two specialized adaptive traits (salt secretion and crypto‐vivipary), is an attractive ecological model to investigate molecular mechanisms underlying adaptatio...
Article
Full-text available
Biodiversity science in China has seen rapid growth over recent decades, ranging from baseline biodiversity studies to understanding the processes behind evolution across dynamic regions such as the Qinghai-Tibetan Plateau. We review research, including species catalogues, biodiversity monitoring, the origins, distributions, maintenance, and threat...
Article
Full-text available
Biodiversity science in China has seen rapid growth over recent decades, ranging from baseline biodiversity studies to understanding the processes behind evolution across dynamic regions such as the Qinghai-Tibetan Plateau. We review research, including species catalogues; biodiversity monitoring; the origins, distributions, maintenance and threats...
Preprint
Full-text available
Mangroves have colonized extreme intertidal environments characterized by high salinity, hypoxia, and other abiotic stresses. During millions of years of evolution, mangroves have adapted to these habitats, evolving a series of highly specialized traits. Aegiceras corniculatum , a pioneer mangrove species that evolved salt secretion and crypto-vivi...
Article
Subspecies is used to designate taxa below species but above geographical populations. What patterns of genomic variation is expected if taxa are designated as subspecies? In this study, we carry out such a survey on the mangrove tree Avicennia marina of the Indo‐West Pacific coasts. This species has three subspecies, distinguished by morphological...
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Full-text available
Convergent evolution is especially common in plants that have independently adapted to the same extreme environments (i.e., extremophile plants). The recent burst of omics data has alleviated many limitations that have hampered molecular convergence studies of non-model extremophile plants. In this review, we summarize cases of genomic convergence...
Preprint
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The biological species concept (BSC) is the prevailing definition of species whereby genes cannot be exchanged during or after speciation. In contrast, since only genes that contribute to the adaptive divergence between species should be non-exchangeable, BSC appears to bear little relationship to the genetic process of speciation. The rejection of...
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Sequencing multiple species that share the same ecological niche may be a new frontier for genomic studies. While such studies should shed light on molecular convergence, genomic-level analyses have been unsuccessful, due mainly to the absence of empirical controls. Woody plant species that colonized the global tropical coasts, collectively referre...
Preprint
Full-text available
Evidence for biological adaptation is often obtained by studying DNA sequence evolution. Since the analyses are affected by both positive and negative selection, studies usually assume constant negative selection in the time span of interest. For this reason, hundreds of studies that conclude adaptive evolution might have reported false signals cau...
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Full-text available
Background: Mangroves have adapted to intertidal zones - the interface between terrestrial and marine ecosystems. Various studies have shown adaptive evolution in mangroves at physiological, ecological, and genomic levels. However, these studies paid little attention to gene regulation of salt adaptation by transcriptome profiles. Results: We se...
Article
Full-text available
The biological species concept (BSC) is the cornerstone of the neo-Darwinian thinking. In BSC, species do not exchange genes either during or after speciation. However, since a substantial literature has increasingly reported gene flow during speciation, it seems time to reassess the revered but often doubted BSC. Contrary to the common perception,...
Article
Hybridization between introduced and native species is highly likely as human introduction removes spatial barriers. The mangrove species Sonneratia apetala has been introduced to South China from Bangladesh and frequently planted as part of reforestation efforts over the previous three decades. Sonneratia apetala has been shown to suppress the gro...
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Intertidal mangrove forests are a dynamic ecosystem experiencing rapid changes in extent and habitat quality over geological history, today and into the future. Climate and sea level have drastically altered mangrove distribution since their appearance in the geological record ∼75 million years ago (Mya), through to the Holocene. In contrast, conte...
Preprint
Full-text available
In the genic view of speciation, two species are distinct as long as genes that delineate morphological, ecological and reproductive differences remain distinct. The rest of the genomes can be interchanged freely. The extent of such genomic sharing is informative about speciation. In a survey of two closely related mangrove species (Rhizophora mucr...
Article
Full-text available
Allopatric speciation requiring an unbroken period of geographical isolation has been the standard model of neo-Darwinism. While doubts have been repeatedly raised, strict allopatry without any gene flow remains a plausible mechanism in most cases. To rigorously reject strict allopatry, genomic sequences superimposed on the geological records of a...
Article
Full-text available
Insect diversity is an indicator of environmental conditions. Frequent outbreaks of mangrove pests have threatened the fragile mangrove ecosystem in China and the sustainable utilization of mangrove resources. The understanding of mangrove pests, as well as a fundamental knowledge of insect diversity, in mangrove forests in China has been hindered...
Preprint
Full-text available
Measuring positive selection on DNA sequences between species is key to testing the neutral theory of molecular evolution. Here, we compare the two most commonly used tests that rely on very different assumptions. The MK test compares divergence and polymorphism data, while the PAML test analyzes multi-species divergence. The two tests are now forc...
Article
The prevalence of de novo coding genes is controversial due to length and coding constraints. Noncoding genes, especially small ones, are freer to evolve de novo by comparison. The best examples are microRNAs (miRNAs), a large class of regulatory molecules ∼22 nt in length. Here, we study six de novo miRNAs in Drosophila, which, like most new genes...
Article
The prevalence of de novo coding genes is controversial due to the length and coding constraints. Non-coding genes, especially small ones, are freer to evolve de novo by comparison. The best examples are microRNAs (miRNAs), a large class of regulatory molecules ~22 nt in length. Here, we study 6 de novo miRNAs in Drosophila which, like most new gen...
Data
Supplementary files of Prevalence of cryptic species in morphologically uniform taxa - Fast speciation and evolutionary radiation in Asian frogs
Article
Diversity and distributions of cryptic species have long been a vexing issue. Identification of species boundaries is made difficult by the lack of obvious morphological differences. Here, we investigate the cryptic diversity and evolutionary history of an underappreciated group of Asian frog species (Megophrys) to explore the pattern and dynamic o...
Preprint
Full-text available
Allopatric speciation requiring an unbroken period of geographical isolation has been the standard model of neo-Darwinism. While doubts have been repeatedly raised, strict allopatry without any gene flow remains a plausible mechanism in most cases. To rigorously reject strict allopatry, genomic sequences superimposed on the geological records of a...
Article
Full-text available
The projected increases in sea levels are expected to affect coastal ecosystems. Tropical communities, anchored by mangrove trees and having experienced frequent past sea level changes, appear to be vibrant at present. However, any optimism about the resilience of these ecosystems is premature because the impact of past climate events may not be re...
Article
Full-text available
Alternative splicing (AS), which produces multiple mRNA transcripts from a single gene, plays crucial roles in plant growth, development and environmental stress responses. Functional significances of conserved AS events among congeneric species have not been well characterized. In this study, we performed transcriptome sequencing to characterize A...
Article
Full-text available
The genus Xylocarpus contains two mangrove species, X. granatum and X. moluccensis, and a rare non-mangrove, X. rumphii. The two mangrove species are ideal models to study the biogeography of coastal plants with a unique dispersal ability, that is via buoyant propagules. We constructed the phylogeny of Xylocarpus and its relatives and determined th...
Article
Full-text available
Several clades of mangrove trees independently invade the interface between land and sea at the margin of woody plant distribution. As phenotypic convergence among mangroves is common, the possibility of convergent adaptation in their genomes is quite intriguing. To study this molecular convergence, we sequenced multiple mangrove genomes. In this s...
Article
Each microRNA (miRNA) represses a web of target genes and, through them, controls multiple phenotypes. The difficulties inherent in such controls cast doubt on how effective miRNAs are in driving phenotypic changes. A "simple regulation" model posits "one target-one phenotype" control under which most targeting is nonfunctional. In an alternative "...
Article
In order to reconstruct the environmental conditions of marine isotope stage (MIS) 5 in the coastal area of northern South China Sea, a sediment core was collected from the south coast of Hainan Island (18°16'57″N, 109°42'38″E), from which a thick marine mud unit (39 m) is found to be the deposit of MIS 5. According to the high abundance of alkenon...
Article
Full-text available
Mangroves invade some very marginal habitats for woody plants—at the interface between land and sea. Since mangroves anchor tropical coastal communities globally, their origin, diversification and adaptation are of scientific significance, particularly at a time of global climate change. In this study, a combination of single-molecule long reads an...
Article
Full-text available
Mangroves invade some very marginal habitats for woody plants-at the interface between land and sea. Since mangroves anchor tropical coastal communities globally, their origin, diversification and adaptation are of scientific significance, particularly at a time of global climate change. In this study, a combination of single-molecule long reads an...