

FOLLOWUS
1.Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266500, China
2.University of Chinese Academy of Sciences, Beijing 100049, China
3.School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266237, China
licui@qdio.ac.cn
haiyanwang@qdio.ac.cn
Received:15 January 2025,
Accepted:27 March 2025,
Online First:14 April 2025,
Published:01 January 2026
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TANG Zeyu,LI Cui,ZANG Guochen,et al.Molecular phylogeography and population history of Saccostrea mordax based on mitochondrial DNA[J].Journal of Oceanology and Limnology,2026,44(01):357-371.
TANG Zeyu,LI Cui,ZANG Guochen,et al.Molecular phylogeography and population history of Saccostrea mordax based on mitochondrial DNA[J].Journal of Oceanology and Limnology,2026,44(01):357-371. DOI: 10.1007/s00343-025-5014-3.
The
Saccostrea
mordax
Gould
1850 is a typical intertidal species
whose genetic differentiation is influenced by various factors
including geological and climatic changes. To explore the genetic structure and historical population characteristics of
Saccostrea
mordax
we sequenced the mitochondrial cytochrome c oxidase subunit I (COI) gene from 58 specimens sampled from four locations in the western Pacific. Additionally
103 individuals from the Persian Gulf and western Pacific (from databases) were included for phylogenetic analysis. The Bayesian Inference tree showed that all specimens were divided into two clades
i.e.
the Persian Gulf population and the western Pacific population. Spatial molecular variance analysis indicated significant genetic differentiation between the two populations
and isolation by distance analysis revealed a positive correlation between genetic differentiation and geographic distance. Neutrality tests and Bayesian Skyline Plot suggested that both populations underwent expansions during the late Pleistocene. This study revealed the population history of
Saccostrea
mordax
and described a new lineage
Saccostrea
mordax
lineage D
providing a foundation for understanding oyster biodiversity formation and genetic resource conservation.
Cavalcante G H , Feary D A , Burt J A . 2016 . The influence of extreme winds on coastal oceanography and its implications for coral population connectivity in the southern Arabian Gulf . Marine Pollution Bulletin , 105 ( 2 ): 489 - 497 , https://doi.org/10.1016/j.marpolbul.2015.10.031 https://doi.org/10.1016/j.marpolbul.2015.10.031 .
Chao S Y , Kao T W , Al-Hajri K R . 1992 . A numerical investigation of circulation in the Arabian Gulf . Journal of Geophysical Research: Oceans , 97 ( C7 ): 11219 - 11236 , https://doi.org/10.1029/92JC00841 https://doi.org/10.1029/92JC00841 .
Clement M , Posada D , Crandall K A . 2000 . TCS: a computer program to estimate gene genealogies . Molecular Ecology , 9 ( 10 ): 1657 - 1659 , https://doi.org/10.1046/j.1365-294x.2000.01020.x https://doi.org/10.1046/j.1365-294x.2000.01020.x .
Conover D O , Clarke L M , Munch S B et al . 2006 . Spatial and temporal scales of adaptive divergence in marine fishes and the implications for conservation . Journal of Fish Biology , 69 (sc): 21 - 47 , https://doi.org/10.1111/j.1095-8649.2006.01274.x https://doi.org/10.1111/j.1095-8649.2006.01274.x .
Cui Z M , Hu L S , Li C et al . 2021 . Identification of Saccostrea mordax and a new species Saccostrea mordoides sp. nov. (Bivalvia: Ostreidae) from China . Journal of Shellfish Research , 40 ( 1 ): 63 - 75 , https://doi.org/10.2983/035.040.0107 https://doi.org/10.2983/035.040.0107 .
David P , Berthou P , Noel P et al . 1997 . Patchy recruitment patterns in marine invertebrates: a spatial test of the density-dependent hypothesis in the bivalve Spisula ovalis . Oecologia , 111 ( 3 ): 331 - 340 , https://doi.org/10.1007/s004420050243 https://doi.org/10.1007/s004420050243 .
Drummond A J , Rambaut A . 2007 . BEAST: Bayesian evolutionary analysis by sampling trees . BMC Evolutionary Biology , 7 ( 1 ): 214 , https://doi.org/10.1186/1471-2148-7-214 https://doi.org/10.1186/1471-2148-7-214 .
Dupanloup I , Schneider S , Excoffier L . 2002 . A simulated annealing approach to define the genetic structure of populations . Molecular Ecology , 11 ( 12 ): 2571 - 2581 , https://doi.org/10.1046/j.1365-294X.2002.01650.x https://doi.org/10.1046/j.1365-294X.2002.01650.x .
Elmy F I , Gaspare L , Mfilinge P L et al . 2024 . Genetic structure and demographic history of Anguilla bicolor from Tanzania based on mitochondrial cytochrome oxidase I sequence: implications for effective management and conservation strategies . Aquatic Conservation: Marine and Freshwater Ecosystems , 34 ( 7 ): e 4225 , https://doi.org/10.1002/aqc.4225 https://doi.org/10.1002/aqc.4225 .
Evanno G , Regnaut S , Goudet J . 2005 . Detecting the number of clusters of individuals using the software structure : a simulation study . Molecular Ecology , 14 ( 8 ): 2611 - 2620 , https://doi.org/10.1111/j.1365-294X.2005.02553.x https://doi.org/10.1111/j.1365-294X.2005.02553.x .
Excoffier L , Lischer H E L . 2010 . Arlequin suite Ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows . Molecular Ecology Resources , 10 ( 3 ): 564 - 567 , https://doi.org/10.1111/j.1755-0998.2010.02847.x https://doi.org/10.1111/j.1755-0998.2010.02847.x .
Excoffier L , Smouse P E , Quattro J M . 1992 . Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data . Genetics , 131 ( 2 ): 479 - 491 , https://doi.org/10.1093/genetics/131.2.479 https://doi.org/10.1093/genetics/131.2.479 .
Folmer O , Black M , Hoeh W et al . 1994 . DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates . Molecular Marine Biology and Biotechnology , 3 ( 5 ): 294 - 299 . https://do 10.4028/www.scientific.net/DDF.7.460 http://dx.doi.org/10.4028/www.scientific.net/DDF.7.460
Fu Y X . 1997 . Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection . Genetics , 147 ( 2 ): 915 - 925 , https://doi.org/10.1093/genetics/147.2.915 https://doi.org/10.1093/genetics/147.2.915 .
Ghaffari H , Ahmadzadeh F , Saberi-Pirooz R et al . 2022 . A molecular phylogeny of the Persian Gulf and the Gulf of Oman oyster species . Biological Journal of the Linnean Society , 137 ( 4 ): 626 - 641 , https://doi.org/10.1093/biolinnean/blac112 https://doi.org/10.1093/biolinnean/blac112 .
Grant W A S , Bowen B W . 1998 . Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation . Journal of Heredity , 89 ( 5 ): 415 - 426 , https://doi.org/10.1093/jhered/89.5.415 https://doi.org/10.1093/jhered/89.5.415 .
Guo S M , Li J , Yang X G et al . 2024 . Resistance of an intertidal oyster ( Saccostrea mordax ) to marine heatwaves and the implication for reef building. Science of the Total Environment , 928 : 172474 , https://doi.org/10.1016/j.scitotenv.2024.172474 https://doi.org/10.1016/j.scitotenv.2024.172474 .
Guo X M , Li C , Wang H Y et al . 2018 . Diversity and evolution of living oysters . Journal of Shellfish Research , 37 ( 4 ): 755 - 771 , https://doi.org/10.2983/035.037.0407 https://doi.org/10.2983/035.037.0407 .
Hamrick J L , Godt M J W . 1990 . Allozyme diversity in plant species . In: Brown A H D ed . Plant Population Genetics, Breeding and Genetic Resources. Sinauer Associates Inc., Sunderland, Massachusetts , p. 43 - 63 .
Hu L S , Zhang Z , Wang H Y et al . 2018 . Molecular phylogeography and population history of Crassostrea sikamea (Amemiya, 1928) based on mitochondrial DNA . Journal of Experimental Marine Biology and Ecology , 503 : 23 - 30 , https://doi.org/10.1016/j.jembe.2017.11.004 https://doi.org/10.1016/j.jembe.2017.11.004 .
Kämpf J , Sadrinasab M . 2006 . The circulation of the Persian Gulf: a numerical study . Ocean Science , 2 ( 1 ): 27 - 41 , https://doi.org/10.5194/os-2-27-2006 https://doi.org/10.5194/os-2-27-2006 .
Kimura M . 1980 . A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences . Journal of Molecular Evolution , 16 ( 2 ): 111 - 120 , https://doi.org/10.1007/BF01731581 https://doi.org/10.1007/BF01731581 .
Kinlan B P , Gaines S D . 2003 . Propagule dispersal in marine and terrestrial environments: a community perspective . Ecology , 84 ( 8 ): 2007 - 2020 , https://doi.org/10.1890/01-0622 https://doi.org/10.1890/01-0622 .
Lam K , Morton B . 2006 . Morphological and mitochondrial-DNA analysis of the Indo-West Pacific rock oysters (Ostreidae: Saccostrea species) . Journal of Molluscan Studies , 72 ( 3 ): 235 - 245 , https://doi.org/10.1093/mollus/eyl002 https://doi.org/10.1093/mollus/eyl002 .
Launey S , Ledu C , Boudry P et al . 2002 . Geographic structure in the European Flat Oyster ( Ostrea edulis L.) as revealed by microsatellite polymorphism . Journal of Heredity , 93 ( 5 ): 331 - 351 , https://doi.org/10.1093/jhered/93.5.331 https://doi.org/10.1093/jhered/93.5.331 .
Lee H J , Boulding E G . 2009 . Spatial and temporal population genetic structure of four northeastern Pacific littorinid gastropods: the effect of mode of larval development on variation at one mitochondrial and two nuclear DNA markers . Molecular Ecology , 18 ( 10 ): 2165 - 2184 , https://doi.org/10.1111/j.1365-294X.2009.04169.x https://doi.org/10.1111/j.1365-294X.2009.04169.x .
Leigh J W , Bryant D . 2015 . popart : full‐feature software for haplotype network construction . Methods in Ecology and Evolution , 6 ( 9 ): 1110 - 1116 , https://doi.org/10.1111/2041-210X.12410 https://doi.org/10.1111/2041-210X.12410 .
Li C , Kou Q , Zhang Z et al . 2021a . Reconstruction of the evolutionary biogeography reveal the origins and diversification of oysters (Bivalvia: Ostreidae). Molecular Phylogenetics and Evolution , 164 : 107268 , https://doi.org/10.1016/j.ympev.2021.107268 https://doi.org/10.1016/j.ympev.2021.107268 .
Li C , Kou Q , Zhang Z et al . 2021b . Re construction of the evolutionary biogeography reveal the origins and diversification of oysters (Bivalvia: Ostreidae). Molecular Phylogenetics and Evolution , 164 : 107268 , https://doi.org/10.1016/j.ympev.2021.107268 https://doi.org/10.1016/j.ympev.2021.107268 .
Li Y L , Liu J X . 2018 . S tructureSelector: a web-based software to select and visualize the optimal number of clusters using multiple methods . Molecular Ecology Resources , 18 ( 1 ): 176 - 177 , https://doi.org/10.1111/1755-0998.12719 https://doi.org/10.1111/1755-0998.12719 .
Librado P , Rozas J . 2009 . DnaSP v5: a software for comprehensive analysis of DNA polymorphism data . Bioinformatics , 25 ( 11 ): 1451 - 1452 , https://doi.org/10.1093/bioinformatics/btp187 https://doi.org/10.1093/bioinformatics/btp187 .
Liu J Y . 2013 . Status of marine biodiversity of the China seas . PLoS One , 8 ( 1 ): e 50719 , https://doi.org/10.1371/journal.pone.0050719 https://doi.org/10.1371/journal.pone.0050719 .
Michael Reynolds R . 1993 . Physical oceanography of the Gulf, Strait of Hormuz, and the Gulf of Oman—results from the Mt Mitchell expedition . Marine Pollution Bulletin , 27 : 35 - 59 , https://doi.org/10.1016/0025-326X(93)90007-7 https://doi.org/10.1016/0025-326X(93)90007-7 .
Ni G , Li Q , Kong L F et al . 2014 . Comparative phylogeography in marginal seas of the northwestern Pacific . Molecular Ecology , 23 ( 3 ): 534 - 548 , https://doi.org/10.1111/mec.12620 https://doi.org/10.1111/mec.12620 .
Nowland S J , Silva C N S , Southgate P C et al . 2019 . Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster ( Saccostrea echinata ) reveals population subdivision and informs sustainable aquaculture development . BMC Genomics , 20 ( 1 ): 711 , https://doi.org/10.1186/s12864-019-6052-z https://doi.org/10.1186/s12864-019-6052-z .
Palumbi S R . 2024 . Genetic divergence, reproductive isolation, and marine speciation . Annual Review of Ecology, Evolution, and Systematics , 25 ( 1994 ): 547 - 572 , https://doi.org/10.1146/annurev.es.25.110194.002555 https://doi.org/10.1146/annurev.es.25.110194.002555 .
Peakall R , Smouse P E . 2006 . genalex 6: genetic analysis in Excel. population genetic software for teaching and research . Molecular Ecology Notes , 6 ( 1 ): 288 - 295 , https://doi.org/10.1111/j.1471-8286.2005.01155.x https://doi.org/10.1111/j.1471-8286.2005.01155.x .
Petraglia M D , Rose J I . 2010 . The Evolution of Human Populations in Arabia . Springer, Dordrecht , https://doi.org/10.1007/978-90-481-2719-1 https://doi.org/10.1007/978-90-481-2719-1 .
Posada D , Buckley T R . 2004 . Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests . Systematic Biology , 53 ( 5 ): 793 - 808 , https://doi.org/10.1080/10635150490522304 https://doi.org/10.1080/10635150490522304 .
Posada D , Crandall K A . 2001 . Intraspecific gene genealogies: trees grafting into networks . Trends in Ecology & Evolution , 16 ( 1 ): 37 - 45 , https://doi.org/10.1016/S0169-5347(00)02026-7 https://doi.org/10.1016/S0169-5347(00)02026-7 .
Pritchard J K , Stephens M , Donnelly P . 2000 . Inference of population structure using multilocus genotype data . Genetics , 155 ( 2 ): 945 - 959 , https://doi.org/10.1093/genetics/155.2.945 https://doi.org/10.1093/genetics/155.2.945 .
Ramadhaniaty M , Setyobudiandi I , Madduppa H H . 2018 . Morphogenetic and population structure of two species marine bivalve (Ostreidae: Saccostrea cucullata and Crassostrea iredalei ) in Aceh, Indonesia . Biodiversitas Journal of Biological Diversity , 19 ( 3 ): 978 - 988 , https://doi.org/10.13057/biodiv/d190329 https://doi.org/10.13057/biodiv/d190329 .
Rambaut A , Drummond A J , Xie D et al . 2018 . Posterior summarization in Bayesian phylogenetics using Tracer 1.7 . Systematic Biology , 67 ( 5 ): 901 - 904 , https://doi.org/10.1093/sysbio/syy032 https://doi.org/10.1093/sysbio/syy032 .
Rogers A R , Harpending H . 1992 . Population growth makes waves in the distribution of pairwise genetic differences . Molecular Biology and Evolution , 9 ( 3 ): 552 - 569 . https://doi.org/10.1093/oxfordjournals.molbev.a040727 https://doi.org/10.1093/oxfordjournals.molbev.a040727 .
Ronquist F , Teslenko M , Van Der Mark P et al . 2012 . MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space . Systematic Biology , 61 ( 3 ): 539 - 542 , https://doi.org/10.1093/sysbio/sys029 https://doi.org/10.1093/sysbio/sys029 .
Sekino M , Yamashita H . 2013 . Mitochondrial DNA barcoding for Okinawan oysters: a cryptic population of the Portuguese oyster Crassostrea angulata in Japanese waters . Fisheries Science , 79 ( 1 ): 61 - 76 , https://doi.org/10.1007/s12562-012-0577-2 https://doi.org/10.1007/s12562-012-0577-2 .
Sekino M , Yamashita H . 2016 . Mitochondrial and nuclear DNA analyses of Saccostrea oysters in Japan highlight the confused taxonomy of the genus . Journal of Molluscan Studies , 82 ( 4 ): 492 - 506 , https://doi.org/10.1093/mollus/eyw022 https://doi.org/10.1093/mollus/eyw022 .
Selkoe K A , Toonen R J . 2011 . Marine connectivity: a new look at pelagic larval duration and genetic metrics of dispersal . Marine Ecology Progress Series , 436 : 291 - 305 , https://doi.org/10.3354/meps09238 https://doi.org/10.3354/meps09238 .
Swift S A , Bower A S . 2003 . Formation and circulation of dense water in the Persian/Arabian Gulf . Journal of Geophysical Research: Oceans , 108 ( C1 ): 3004 , https://doi.org/10.1029/2002JC001360 https://doi.org/10.1029/2002JC001360 .
Tajima F . 1989a . Statistical method for testing the neutral mutation hypothesis by DNA polymorphism . Genetics , 123 ( 3 ): 585 - 595 , https://doi.org/10.1093/genetics/123.3.585 https://doi.org/10.1093/genetics/123.3.585 .
Tajima F . 1989b . The effect of change in population size on DNA polymorphism . Genetics , 123 ( 3 ): 597 - 601 , https://doi.org/10.1093/genetics/123.3.597 https://doi.org/10.1093/genetics/123.3.597 .
Thompson J , Gibson T J , Plewniak F et al . 1997 . The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools . Nucleic Acids Research , 25 ( 24 ): 4876 - 4882 , https://doi.org/10.1093/nar/25.24.4876 https://doi.org/10.1093/nar/25.24.4876 .
Wang H Y , Qian L M , Liu X et al . 2010 . Classification of a common cupped oyster from southern China . Journal of Shellfish Research , 29 ( 4 ): 857 - 866 , https://doi.org/10.2983/035.029.0420 https://doi.org/10.2983/035.029.0420 .
Yao F C , Johns W E . 2010 . A HYCOM modeling study of the Persian Gulf: 1. model configurations and surface circulation . Journal of Geophysical Research: Oceans , 115 ( C11 ): 2009 JC 005781 , https://doi.org/10.1029/2009JC005781 https://doi.org/10.1029/2009JC005781 .
Zhang X , Lou Z . 1956 . Oyster research in China. Acta Zool . Sin. , 8 : 65 - 94 . (in Chinese)
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