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Xu H, Huang L, Chen T, Wang C, Wu Z, Cheng Y, Su Q, Kang B, Yan Y, Zhang X. Phylogeography and population structure of Lagocephalus spadiceus (Richardson, 1845) (Tetraodontiformes, Tetraodontidae) in the South China Sea. Ecol Evol 2024; 14:e11320. [PMID: 38681184 PMCID: PMC11045559 DOI: 10.1002/ece3.11320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 05/01/2024] Open
Abstract
The climate fluctuations during the Late Pleistocene significantly influenced the phylogeographic structure and historical dynamics of marine fishes in the marginal seas of the western Pacific Ocean. The puffer fish, Lagocephalus spadiceus, holds substantial nutritional and economic value in the South China Sea. To investigate the demographic history and population structure of the L. spadiceus, the mitochondrial DNA COI and Cyt b gene datasets from 300 individuals across eight populations in the South China Sea were sequenced. Our findings revealed high haplotype diversity (0.874 ± 0.013) and low nucleotide diversity (0.00075 ± 0.00058). The phylogenetic tree and haplotype networks revealed no significant genetic differentiation along the northern coast of South China Sea. Neutrality tests, mismatch distribution analyses, and Bayesian skyline plots suggested that L. spadiceus underwent population expansion during the Late Pleistocene. Both ocean currents and climate change significantly influenced the geographical distribution and genetic population structure of L. spadiceus.
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Affiliation(s)
- Hao Xu
- College of Environmental Science and EngineeringGuilin University of TechnologyGuilinChina
- Guangxi Key Laboratory of Theory and Technology for Environmental Pollution ControlGuilinChina
| | - Liangliang Huang
- College of Environmental Science and EngineeringGuilin University of TechnologyGuilinChina
- Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst AreasGuilinChina
| | - Tao Chen
- College of Basic MedicineGuilin Medical UniversityGuilinChina
| | - Caiguang Wang
- College of Environmental Science and EngineeringGuilin University of TechnologyGuilinChina
- Guangxi Key Laboratory of Theory and Technology for Environmental Pollution ControlGuilinChina
| | - Zhiqiang Wu
- College of Environmental Science and EngineeringGuilin University of TechnologyGuilinChina
- Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst AreasGuilinChina
| | - Yanan Cheng
- College of Environmental Science and EngineeringGuilin University of TechnologyGuilinChina
- Guangxi Key Laboratory of Theory and Technology for Environmental Pollution ControlGuilinChina
| | - Qiongyuan Su
- College of Environmental Science and EngineeringGuilin University of TechnologyGuilinChina
- Guangxi Key Laboratory of Theory and Technology for Environmental Pollution ControlGuilinChina
| | - Bin Kang
- Fisheries CollegeOcean University of ChinaQingdaoChina
| | - Yunrong Yan
- Fisheries CollegeGuangdong Ocean UniversityZhanjiangChina
| | - Xiuguo Zhang
- Guangxi Jinggong Marine Science and Technology LtdBeihaiChina
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Mitochondrial genomes reveal mid-Pleistocene population divergence, and post-glacial expansion, in Australasian snapper (Chrysophrys auratus). Heredity (Edinb) 2023; 130:30-39. [PMID: 36463371 DOI: 10.1038/s41437-022-00579-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Glacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern (n = 350) and ancient (n = 26) mitochondrial genomes from Australasian snapper (Chrysophrys auratus) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years (p = 0.343), with no detectable loss of diversity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that diverged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.
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Gu S, Yan YR, Yi MR, Luo ZS, Wen H, Jiang CP, Lin HD, He XB. Genetic pattern and demographic history of cutlassfish (Trichiurus nanhaiensis) in South China Sea by the influence of Pleistocene climatic oscillations. Sci Rep 2022; 12:14716. [PMID: 36042258 PMCID: PMC9427976 DOI: 10.1038/s41598-022-18861-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 08/22/2022] [Indexed: 11/09/2022] Open
Abstract
Trichiurus nanhaiensis is one of the most important commercial fish species in the South China Sea. This study aimed to investigate the level of genetic variation and population genetic structure of T. nanhaiensis in the South China Sea for the first time, using 281 individuals collected from seven locations along the coast of mainland China, Taiwan, and Hainan Island. A high level of haplotype diversity and low nucleotide diversity were detected in the mitochondrial DNA cyt b gene and nuDNA RYR 3 gene. The overall expected heterozygosity (He = 0.693) among the seven populations ranged from 0.681 to 0.706 in microsatellite DNA data, which revealed high levels of genetic diversity. Significant genetic differentiation was found in Taidong populations in Taiwan, revealing the prevention of gene flow caused by the Kuroshio Current. Two major lineages based on the cyt b gene suggested that the Taiwan Strait acted as a geographic barrier for T. nanhaiensis during the glacier periods in the late Pleistocene. The Bayesian skyline plot also revealed that population demographic expansion of T. nanhaiensis was estimated to have occurred in 0.1 Mya. Our results indicated that all populations of T. nanhaiensis had experienced a recent genetic bottleneck following recent expansion based on ABC analysis.
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Affiliation(s)
- Sui Gu
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China
| | - Yun-Rong Yan
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524000, China.,Guangdong Provincial Engineering and Technology Research Center of Far Sea Fisheries Management and Fishing of South China Sea, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Mu-Rong Yi
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524000, China
| | - Zhi-Sen Luo
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China
| | - Hui Wen
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China
| | - Chang-Ping Jiang
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, No. 1, Sec. 1, Mintzu Rd., Tainan, 701, Taiwan.
| | - Xiong-Bo He
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China. .,Guangdong Provincial Engineering and Technology Research Center of Far Sea Fisheries Management and Fishing of South China Sea, Guangdong Ocean University, Zhanjiang, 524088, China.
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Demographic history and population genetic structure of Anisakis pegreffii in the cutlassfish Trichiurus japonicus along the coast of mainland China and Taiwan. Parasitol Res 2022; 121:2803-2816. [PMID: 35918454 DOI: 10.1007/s00436-022-07611-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 07/25/2022] [Indexed: 10/16/2022]
Abstract
Studying the genetic diversity of nematode parasite populations is crucial to gaining insight into parasite infection dynamics and informing parasite phylogeography. Anisakiasis is a zoonotic disease caused by the consumption of infectious third-stage larvae (L3) of Anisakis spp. carried by marine fish. In the present study, a total of 206 mitochondrial DNA sequences (cytochrome c oxidase 2, cox2) were used to study the genetic diversity, genetic structure, and historical demography of twelve A. pegreffii populations from Trichiurus japonicas along the coast of mainland China and Taiwan. Two distinct evolutionary lineages of A. pegreffii and no significant genealogical structures corresponding to sampling localities suggested that isolation in the marginal seas shaped their patterns of phylogeographic distribution along the coast of mainland China and Taiwan during glaciation with lower sea levels. Furthermore, pairwise FST values and AMOVA did not indicate any significant genetic differentiation among groups with no relation to the geographic area, which might be attributed to fewer barriers to gene flow as well as large population sizes. The results of the neutrality test, mismatch distribution, and Bayesian skyline plot analyses showed that entire population underwent population expansion during the late Pleistocene. Analysis of the demographic history revealed that A. pegreffii underwent historical lineage diversification and admixture due to secondary contact based on ABC analysis. The present research represents the first definitive population structure and demographic history across sampling locations of A. pegreffii along the coast of mainland China and Taiwan.
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Wu H, Wang H, Ding S. Reproductive biology and annual reproductive cycles of two sympatric lineages of Bostrychus sinensis with a natural habitat on southeastern coast of China. Anim Reprod Sci 2021; 232:106821. [PMID: 34388359 DOI: 10.1016/j.anireprosci.2021.106821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 02/02/2023]
Abstract
The two phylogeographic lineages [South China Sea (SCS) lineage and East China Sea (ESC) lineage] of the four-eyed sleeper (Bostrychus sinensis) occur sympatrically along the southeastern coast of China, where there is a small percentage of hybrids in a natural habitat. To assess the mechanism responsible for the incomplete reproductive isolation between the SCS and ECS lineages of four-eyed sleeper, there was sampling of individuals from the Yueqing Bay from November 2018 to November 2019 to determine whether there are differences in characteristics of the reproductive cycles and reproductive biology. The two lineages varied in reproductive seasonality, body size and shape, and egg number. The SCS lineage spawned annually between May and August, with the absolute fecundity (AF) of the SCS lineage being 9960 to 39,517 eggs per female, and there was positive allometric growth of this species. The ECS lineage spawned annually between June and July, with females producing 4064 to 10,370 eggs per fish and individuals having an isometric growth pattern. Preliminary results indicated that there was partial overlap in the spawning season between the two lineages in the sympatric region, which may not be a primary factor in the incomplete reproductive isolation. Furthermore, the lineage differences in fecundity and body shape and size may lead to variation in mate choice and reproductive strategy. The results from this study provide insight into the biology, reproductive strategies, and speciation of the four-eyed sleepers.
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Affiliation(s)
- Haohao Wu
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361005, China
| | - Hangjun Wang
- Wenzhou Marine Environmental Monitoring Center Station, State Oceanic Administration, Wenzhou, 325013, China
| | - Shaoxiong Ding
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361005, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China.
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Liu Q, Mishra M, Saxena AS, Wu H, Qiu Y, Zhang X, You X, Ding S, Miyamoto MM. Balancing selection maintains ancient polymorphisms at conserved enhancers for the olfactory receptor genes of a Chinese marine fish. Mol Ecol 2021; 30:4023-4038. [PMID: 34107131 DOI: 10.1111/mec.16016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 05/10/2021] [Accepted: 06/01/2021] [Indexed: 12/22/2022]
Abstract
The study of balancing selection, as a selective force maintaining adaptive genetic variation in gene pools longer than expected by drift, is currently experiencing renewed interest due to the increased availability of new data, methods of analysis, and case studies. In this investigation, evidence of balancing selection operating on conserved enhancers of the olfactory receptor (OR) genes is presented for the Chinese sleeper (Bostrychus sinensis), a coastal marine fish that is emerging as a model species for evolutionary studies in the Northwest Pacific marginal seas. Coupled with tests for Gene Ontology enrichment and transcription factor binding, population genomic data allow for the identification of an OR cluster in the sleeper with a downstream flanking region containing three enhancers that are conserved with human and other fish species. Phylogenetic and population genetic analyses indicate that the enhancers are under balancing selection as evidenced by their translineage polymorphisms, excess common alleles, and increased within-group diversities. Age comparisons between the translineage polymorphisms and most recent common ancestors of neutral genealogies substantiate that the former are old, and thus, due to ancient balancing selection. The survival and reproduction of vertebrates depend on their sense of smell, and thereby, on their ORs. In addition to locus duplication and allelic variation of structural genes, this study highlights a third mechanism by which receptor diversity can be achieved for detecting and responding to the huge variety of environmental odorants (i.e., by balancing selection acting on OR gene expression through their enhancer variability).
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Affiliation(s)
- Qiaohong Liu
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Mrinal Mishra
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Ayush S Saxena
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Haohao Wu
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Qiu
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Sciences, BGI Marine, Shenzhen, China
| | - Xinhui Zhang
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Sciences, BGI Marine, Shenzhen, China
| | - Xinxin You
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Sciences, BGI Marine, Shenzhen, China
| | - Shaoxiong Ding
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Cheng J, Zhang N, Sha Z. Nuclear microsatellites reveal population genetic structuring and fine-scale pattern of hybridization in the Japanese mantis shrimp Oratosquilla oratoria. PeerJ 2020; 8:e10270. [PMID: 33194430 PMCID: PMC7649012 DOI: 10.7717/peerj.10270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/08/2020] [Indexed: 11/27/2022] Open
Abstract
The interplay between historical and contemporary processes can produce complex patterns of genetic differentiation in the marine realm. Recent mitochondrial and nuclear sequence analyses revealed cryptic speciation in the Japanese mantis shrimp Oratosquilla oratoria. Herein, we applied nuclear microsatellite markers to examine patterns and causes of genetic differentiation in this morphotaxon. Population structure analyses revealed two genetically divergent and geographically structured clades in O. oratoria, one dominating the temperate zone of the Northwestern (NW) Pacific and the other occurring in the subtropical and tropical waters where are influenced by the Kuroshio Current. Two sympatric zones, one around the Changjiang Estuary in China coast and the other in the northern Japan Sea, were demonstrated to be hybrid zones where introgressive hybridization occurred asymmetrically. The interaction between historical climate shifts and contemporary factors (e.g., freshwater discharge, temperature gradient and isolation by distance) may contribute to the present-day genetic architecture in the Japanese mantis shrimp. Range shift induced by climate changes and oceanographic factors may promote hybridization and gene flow between the O. oratoria complex. Our results provide insights into the interacting mechanisms that give rise to diversification and speciation of coastal species in the NW Pacific.
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Affiliation(s)
- Jiao Cheng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Nan Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhongli Sha
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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8
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Johannesson K, Le Moan A, Perini S, André C. A Darwinian Laboratory of Multiple Contact Zones. Trends Ecol Evol 2020; 35:1021-1036. [DOI: 10.1016/j.tree.2020.07.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
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Wang P, Chen B, Zheng J, Cheng W, Zhang H, Wang J, Su Y, Xu P, Mao Y. Fine-Scale Population Genetic Structure and Parapatric Cryptic Species of Kuruma Shrimp ( Marsupenaeus japonicus), Along the Northwestern Pacific Coast of China. Front Genet 2020; 11:118. [PMID: 32161618 PMCID: PMC7052491 DOI: 10.3389/fgene.2020.00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/31/2020] [Indexed: 11/13/2022] Open
Abstract
The kuruma shrimp (Marsupenaeus japonicus) includes two cryptic species, which are distributed mostly allopatrically but co-occur in the northern South China Sea (from Huilai to Beihai). To obtain a better understanding of the fine-scale genetic structure and parapatric diversification of these two varieties in the northwestern Pacific region, we used a genotyping-by-sequencing (GBS) and comparative transcriptomics approach to establish their phylogenetic relationships. Using the GBS technique, we genotyped 28891 SNPs in 160 individuals in the Northwest Pacific. The results supported two highly diverged evolutionary lineages of kuruma shrimp (var. I and II). The ND and XM populations showed complex genetic patterns, which might be affected by the complex environment of the Taiwan Strait. In addition, the migration rates and inbreeding coefficients of XM and BH were much lower than those of the other populations, which might be related to the land-sea changes and complex ocean currents in the Taiwan Strait and Qiongzhou Strait. Based on the synonymous substitution rates (ds) of 2,491 candidate orthologs, we estimated that the divergence time between the two varieties was 0.26~0.69 Mya. Choice and no-choice interbreeding experiments provided support for the biological species concept, by showing the existence of reproductive isolation or incompatibility. In view of these differences between the two Marsupenaeus species, we believe that it is essential and urgent to establish a genetic database for each and reevaluate their ecological suitable conditions in order to improve species-specific culturing techniques. Moreover, this research can serve as a case study for future research on speciation and hybridization.
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Affiliation(s)
- Panpan Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| | - Baohua Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| | - Jinbin Zheng
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wenzhi Cheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| | - Heqian Zhang
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Jun Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yongquan Su
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| | - Yong Mao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
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Wang P, Xing C, Wang J, Su Y, Mao Y. Evolutionary adaptation analysis of immune defense and hypoxia tolerance in two closely related Marsupenaeus species based on comparative transcriptomics. FISH & SHELLFISH IMMUNOLOGY 2019; 92:861-870. [PMID: 31276791 DOI: 10.1016/j.fsi.2019.06.055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/22/2019] [Accepted: 06/29/2019] [Indexed: 06/09/2023]
Abstract
Kuruma shrimp, a major farmed shrimp species in the world, includes two cryptic or sibling species, Form I (Marsupenaeus japonicus) and Form II (Marsupenaeus pulchricaudatus). Due to the lack of genomic resources, little is known about the molecular mechanisms associated with immune defense and hypoxia tolerance. Here, we sequenced the transcriptomes of two closely related Marsupenaeus species and compared genomic divergence. This study obtained 77049 and 84561 unigenes with N50 values of 1281bp and 1244bp for M. japonicus and M. pulchricaudatus, respectively, and 5036 pairs of putative orthologs were identified between two Marsupenaeus species. Estimation of Ka/Ks ratios indicated that 165 orthologous genes may be under positive selection (Ka/Ks > 0.5), including 49 pairs with a Ka/Ks ratio >1. According to the peak of synonymous rates, the divergence time between M. japonicus and M. pulchricaudatus was about 0.26-0.69 Mya. These positively selected orthologous genes related to the immune process mainly comprised single VWC domain protein, legumain, ras-related C3 botulinum, caspase, C-type lectin and were enriched in functions related to immune (Toll-like receptor and PI3K-Akt signaling) and hypoxia signaling (HIF-1 signaling and VEGF signaling). In this study, dozens of caspase-like unigenes were screened from two Marsupenaeus transcriptomes. Among these, the PjCaspase orthologous gene was subjected to positive selection (Ka/Ks = 1.22), which had different secondary and three-dimensional structure prediction. Based on the single copy caspase gene, eight populations of Marsupenaeus species were divided into two phylogeographic lineages from the East and South China. We characterized the transcriptomes of the two Marsupenaeus species and obtained several key orthologs associated with immune defense and hypoxia tolerance, which provides new insights into the immunity and genetic divergence of the two varieties. Moreover, this study will facilitate further comparative genomic studies of the two varieties.
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Affiliation(s)
- Panpan Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Chaofan Xing
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jun Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yongquan Su
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yong Mao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
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Wang X, Que P, Heckel G, Hu J, Zhang X, Chiang CY, Zhang N, Huang Q, Liu S, Martinez J, Pagani-Núñez E, Dingle C, Leung YY, Székely T, Zhang Z, Liu Y. Genetic, phenotypic and ecological differentiation suggests incipient speciation in two Charadrius plovers along the Chinese coast. BMC Evol Biol 2019; 19:135. [PMID: 31248363 PMCID: PMC6598359 DOI: 10.1186/s12862-019-1449-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 05/29/2019] [Indexed: 02/01/2023] Open
Abstract
Background Speciation with gene flow is an alternative to the nascence of new taxa in strict allopatric separation. Indeed, many taxa have parapatric distributions at present. It is often unclear if these are secondary contacts, e.g. caused by past glaciation cycles or the manifestation of speciation with gene flow, which hampers our understanding of how different forces drive diversification. Here we studied genetic, phenotypic and ecological aspects of divergence in a pair of incipient shorebird species, the Kentish (Charadrius alexandrinus) and the White-faced Plovers (C. dealbatus), shorebirds with parapatric breeding ranges along the Chinese coast. We assessed divergence based on molecular markers with different modes of inheritance and quantified phenotypic and ecological divergence in aspects of morphometric, dietary and climatic niches. Results Our integrative analyses revealed small to moderate levels of genetic and phenotypic distinctiveness with symmetric gene flow across the contact area at the Chinese coast. The two species diverged approximately half a million years ago in dynamic isolation with secondary contact occurring due to cycling sea level changes between the Eastern and Southern China Sea in the mid-late Pleistocene. We found evidence of character displacement and ecological niche differentiation between the two species, invoking the role of selection in facilitating divergence despite gene flow. Conclusion These findings imply that ecology can indeed counter gene flow through divergent selection and thus contributes to incipient speciation in these plovers. Furthermore, our study highlights the importance of using integrative datasets to reveal the evolutionary history and assist the inference of mechanisms of speciation. Electronic supplementary material The online version of this article (10.1186/s12862-019-1449-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xuejing Wang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.,Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Pinjia Que
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, Genopode, 1015, Lausanne, Switzerland
| | - Junhua Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xuecong Zhang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chung-Yu Chiang
- Department of Environmental Science, Tunhai University, Taichun, Taiwan
| | - Nan Zhang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qin Huang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Simin Liu
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | | | - Emilio Pagani-Núñez
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Caroline Dingle
- School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Yu Yan Leung
- School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Tamás Székely
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.,Milner Center for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA1 7AY, UK
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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