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Schmid S, Bachmann Salvy M, Garcia Jimenez A, Bertrand JAM, Cortesi F, Heim S, Huyghe F, Litsios G, Marcionetti A, O'Donnell JL, Riginos C, Tettamanti V, Salamin N. Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish. Mol Ecol 2024; 33:e17436. [PMID: 38872589 DOI: 10.1111/mec.17436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/12/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on Amphiprion clarkii (Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sedentary adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of A. clarkii has been under debate. We used whole-genome resequencing data of 67 A. clarkii specimens spread across the Indian and Pacific Oceans to characterize the species' population structure, demographic history and colour polymorphism. We found that A. clarkii spread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Interestingly, colour patterns differed noticeably among the Indonesian populations and the two populations at the extreme of the sampling distribution (i.e. Maldives and New Caledonia), which exhibited more comparable colour patterns despite their geographic and genetic distances. Our study emphasizes how whole-genome studies can uncover the intricate evolutionary past of wide-ranging species with diverse phenotypes, shedding light on the complex nature of the species concept paradigm.
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Affiliation(s)
- Sarah Schmid
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Joris A M Bertrand
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Fabio Cortesi
- Queensland Brain Institute, the University of Queensland, Brisbane, Queensland, Australia
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
| | - Sara Heim
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Filip Huyghe
- Marine Biology Laboratory, Department of Ecology and Biodiversity, Vrije Universiteit Brussel, Brussel, Belgium
| | - Glenn Litsios
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Anna Marcionetti
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - James L O'Donnell
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, USA
| | - Cynthia Riginos
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
| | - Valerio Tettamanti
- Queensland Brain Institute, the University of Queensland, Brisbane, Queensland, Australia
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
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Semenova AV, Stroganov AN, Rubtsova GA, Rybakov MO. Genetic Structure of the Pacific Herring Clupea pallasii Valenciennes, 1847 on a Macrogeographic Scale. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421060090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Xu S, Wang Z, Zhang Y, Gao T, Zou J, Zhang X. Evidence for intra-mitochondrial variation in population genetic structure of Platycephalus sp.1 In the Northwestern Pacific. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:281-288. [PMID: 30196742 DOI: 10.1080/24701394.2018.1484119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Understanding evolutionary dynamics of population structure and genetic diversity of marine fish species is of great importance for fishery management and resource conservation. Platycephalus sp.1 is a commercially important marine fish in the Northwestern Pacific. Yet, current understanding of population genetic patterns of Platycephalus sp.1 remains limited. In this study, the Platycephalus sp.1 individuals from four populations in the Northwestern Pacific, which cover large geographic distances and latitudinal gradients, were sampled to examine genetic diversity and population structure by investigating the mitochondrial sequences of Cytochrome b (CYTB, 1141 bp) and control region (CR, 458 bp), and then to assess intra-mitochondrial genetic variability by using a combination of population- and individual-based analytical approaches. Moderate to low levels of genetic diversity were observed in sampled populations by investigating both CR and CYTB datasets. In CR dataset, weak genetic differentiation among populations were observed and population Tokyo Bay was significantly differentiated with other sampled populations. In CYTB dataset, lower genetic differentiations were observed and population Beihai (BH) was significantly differentiated. A non-synonymous substitution was predominantly detected in population BH, and such substitution was tested as a significantly positive selective site in natural selection tests. Based on these findings, we propose that local adaptation influenced by natural selection contributes largely to the intra-mitochondrial variation in Platycephalus sp.1 populations. The present study provides new perspectives on the population genetic structure of Platycephalus sp.1, which could have important implications for the sound management and conservation of this fishery species.
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Affiliation(s)
- Shengyong Xu
- a National Engineering Research Center For Marine Aquaculture , Zhejiang Ocean University , Zhoushan , P.R. China
| | - Zhiyang Wang
- b School of Ocean , Yantai University , Yantai , P.R. China
| | - Yan Zhang
- c Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences , Qingdao , P.R. China
| | - Tianxiang Gao
- a National Engineering Research Center For Marine Aquaculture , Zhejiang Ocean University , Zhoushan , P.R. China
| | - Jianwei Zou
- d Beihai Fisheries Technical Extension station , Beihai , P.R. China
| | - Xiumei Zhang
- a National Engineering Research Center For Marine Aquaculture , Zhejiang Ocean University , Zhoushan , P.R. China
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Gao TX, Yang TY, Yanagimoto T, Xiao YS. Levels and patterns of genetic variation in Japanese whiting (Sillago japonica) based on mitochondrial DNA control region. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:172-183. [DOI: 10.1080/24701394.2018.1467411] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Tian-Xiang Gao
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhejiang, China
| | - Tian-Yan Yang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhejiang, China
| | - Takashi Yanagimoto
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Japan
| | - Yong-Shuang Xiao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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5
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Abstract
Understanding how geography, oceanography, and climate have ultimately shaped marine biodiversity requires aligning the distributions of genetic diversity across multiple taxa. Here, we examine phylogeographic partitions in the sea against a backdrop of biogeographic provinces defined by taxonomy, endemism, and species composition. The taxonomic identities used to define biogeographic provinces are routinely accompanied by diagnostic genetic differences between sister species, indicating interspecific concordance between biogeography and phylogeography. In cases where individual species are distributed across two or more biogeographic provinces, shifts in genotype frequencies often align with biogeographic boundaries, providing intraspecific concordance between biogeography and phylogeography. Here, we provide examples of comparative phylogeography from (i) tropical seas that host the highest marine biodiversity, (ii) temperate seas with high productivity but volatile coastlines, (iii) migratory marine fauna, and (iv) plankton that are the most abundant eukaryotes on earth. Tropical and temperate zones both show impacts of glacial cycles, the former primarily through changing sea levels, and the latter through coastal habitat disruption. The general concordance between biogeography and phylogeography indicates that the population-level genetic divergences observed between provinces are a starting point for macroevolutionary divergences between species. However, isolation between provinces does not account for all marine biodiversity; the remainder arises through alternative pathways, such as ecological speciation and parapatric (semiisolated) divergences within provinces and biodiversity hotspots.
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Lescak EA, Wund MA, Bassham S, Catchen J, Prince DJ, Lucas R, Dominguez G, von Hippel FA, Cresko WA. Ancient three-spined stickleback (Gasterosteus aculeatus) mtDNA lineages are not associated with phenotypic or nuclear genetic variation. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Song N, Liu M, Yanagimoto T, Sakurai Y, Han ZQ, Gao TX. Restricted Gene Flow for Gadus macrocephalus from Yellow Sea Based on Microsatellite Markers: Geographic Block of Tsushima Current. Int J Mol Sci 2016; 17:467. [PMID: 27043534 PMCID: PMC4848923 DOI: 10.3390/ijms17040467] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 11/27/2022] Open
Abstract
The Pacific cod Gadus macrocephalus is a demersal, economically important fish in the family Gadidae. Population genetic differentiation of Pacific cod was examined across its northwestern Pacific range by screening variation of eight microsatellite loci in the present study. All four populations exhibited high genetic diversity. Pairwise fixation index (Fst) suggested a moderate to high level of genetic differentiation among populations. Population of the Yellow Sea (YS) showed higher genetic difference compared to the other three populations based on the results of pairwise Fst, three-dimensional factorial correspondence analysis (3D-FCA) and STRUCTURE, which implied restricted gene flow among them. Wilcoxon signed rank tests suggested no significant heterozygosity excess and no recent genetic bottleneck events were detected. Microsatellite DNA is an effective molecular marker for detecting the phylogeographic pattern of Pacific cod, and these Pacific cod populations should be three management units.
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Affiliation(s)
- Na Song
- Fisheries College, Ocean University of China, Qingdao 266003, China.
| | - Ming Liu
- Fisheries College, Ocean University of China, Qingdao 266003, China.
| | - Takashi Yanagimoto
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama 220-6115, Japan.
| | - Yasunori Sakurai
- Graduate School of Fisheries Sciences, Hokkaido University, Hokkaido 041-8611, Japan.
| | - Zhi-Qiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China.
| | - Tian-Xiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China.
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Otolith variation in Pacific herring (Clupea pallasii) reflects mitogenomic variation rather than the subspecies classification. Polar Biol 2016. [DOI: 10.1007/s00300-015-1882-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Bani L, Pisa G, Luppi M, Spilotros G, Fabbri E, Randi E, Orioli V. Ecological connectivity assessment in a strongly structured fire salamander (Salamandra salamandra) population. Ecol Evol 2015; 5:3472-85. [PMID: 26380679 PMCID: PMC4569041 DOI: 10.1002/ece3.1617] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 11/08/2022] Open
Abstract
Small populations are more prone to extinction if the dispersal among them is not adequately maintained by ecological connections. The degree of isolation between populations could be evaluated measuring their genetic distance, which depends on the respective geographic (isolation by distance, IBD) and/or ecological (isolation by resistance, IBR) distances. The aim of this study was to assess the ecological connectivity of fire salamander Salamandra salamandra populations by means of a landscape genetic approach. The species lives in broad-leaved forest ecosystems and is particularly affected by fragmentation due to its habitat selectivity and low dispersal capability. We analyzed 477 biological samples collected in 47 sampling locations (SLs) in the mainly continuous populations of the Prealpine and Eastern foothill lowland (PEF) and 10 SLs in the fragmented populations of the Western foothill (WF) lowland of Lombardy (northern Italy). Pairwise genetic distances (Chord distance, DC) were estimated from allele frequencies of 16 microsatellites loci. Ecological distances were calculated using one of the most promising methodology in landscape genetics studies, the circuit theory, applied to habitat suitability maps. We realized two habitat suitability models: one without barriers (EcoD) and a second one accounting for the possible barrier effect of main roads (EcoDb). Mantel tests between distance matrices highlighted how the Log-DC in PEF populations was related to log-transformed geographic distance (confirming a prevalence of IBD), while it was explained by the Log-EcoD, and particularly by the Log-EcoDb, in WF populations, even when accounting for the confounding effect of geographic distance (highlighting a prevalence of IBR). Moreover, we also demonstrated how considering the overall population, the effect of Euclidean or ecological distances on genetic distances acting at the level of a single group (PEF or WF populations) could not be detected, when population are strongly structured.
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Affiliation(s)
- Luciano Bani
- Department of Earth and Environmental Sciences, University of Milano-Bicocca Piazza della Scienza 1, I-20126, Milano, Italy
| | - Giulia Pisa
- Department of Earth and Environmental Sciences, University of Milano-Bicocca Piazza della Scienza 1, I-20126, Milano, Italy
| | - Massimiliano Luppi
- Department of Earth and Environmental Sciences, University of Milano-Bicocca Piazza della Scienza 1, I-20126, Milano, Italy
| | - Giulia Spilotros
- Department of Biology, University of Milano via Celoria 26, I-20133, Milano, Italy
| | - Elena Fabbri
- Laboratory of Genetics, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA) I-40064, Ozzano Emilia, Bologna, Italy
| | - Ettore Randi
- Laboratory of Genetics, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA) I-40064, Ozzano Emilia, Bologna, Italy ; Section of Biology and Environmental Science, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University Sohngaardsholmsvej 57, DK-9000, Aalborg, Denmark
| | - Valerio Orioli
- Department of Earth and Environmental Sciences, University of Milano-Bicocca Piazza della Scienza 1, I-20126, Milano, Italy
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Population structure and variability of Pacific herring (Clupea pallasii) in the White Sea, Barents and Kara Seas revealed by microsatellite DNA analyses. Polar Biol 2015. [DOI: 10.1007/s00300-015-1653-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Population genetic structure of chub mackerel Scomber japonicus in the Northwestern Pacific inferred from microsatellite analysis. Mol Biol Rep 2014; 42:373-82. [PMID: 25366174 DOI: 10.1007/s11033-014-3777-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 09/22/2014] [Indexed: 10/24/2022]
Abstract
Marine pelagic fishes are usually characterized by subtle but complex patterns of genetic differentiation, which are influenced by both historical process and contemporary gene flow. Genetic population differentiation of chub mackerel, Scomber japonicus, was examined across most of its range in the Northwestern Pacific by screening variation of eight microsatellite loci. Our genetic analysis detected a weak but significant genetic structure of chub mackerel, which was characterized by areas of gene flow and isolation by distance. Consistent with previous estimates of stock structure, we found genetic discontinuity between Japan and China samples. Local-scale pattern of genetic differentiation was observed between samples from the Bohai Sea and North Yellow Sea and those from the East China Sea, which we ascribed to differences in spawning time and migratory behavior. Furthermore, the observed homogeneity among collections of chub mackerel from the East and South China Seas could be the result of an interaction between biological characteristics and marine currents. The present study underlies the importance of understanding the biological significance of genetic differentiation to establish management strategies for exploited fish populations.
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Semenova AV, Stroganov AN, Smirnov AA, Afanas’ev KI, Rubtsova GA. Genetic variations in Clupea pallasii herring from Sea of Okhotsk based on microsatellite markers. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795413120107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Li Y, Han Z, Song N, Gao TX. New evidence to genetic analysis of small yellow croaker (Larimichthys polyactis) with continuous distribution in China. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Xiao Y, Ren G, Song N, Li J, Gao T. Genetic diversity and population structure of largehead hairtail, Trichiurus japonicus, based on mtDNA control region. ACTA ACUST UNITED AC 2013; 25:473-81. [PMID: 23859051 DOI: 10.3109/19401736.2013.809427] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Largehead hairtail, Trichiurus japonicus, is a valuable commercially exploited demersal species. We gathered mtDNA control region sequences (3' mtDNA CR) of T. japonicus to investigate its genetic diversity and population genetic structure. Fifty-four specimens were collected from the nearshore localities along the coastline of China. A total of 42 polymorphic sites were found, which defined 40 haplotypes. A pattern with high level of haplotype diversity (h = 0.98 ± 0.01) and very low level of nucleotide diversity (π = 0.008 ± 0.005) were detected in the examined range. Comparing π with other fish species shows that T. japonicus has remarkable low genetic diversity values compared with other Pacific Ocean marine fishes. AMOVA and conventional Fst values revealed no significant genetic structure throughout the examined range, which is inconsistent with the previous findings based on the morphological and ecological studies. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimateic and physiographic evidence, we infer that the genetic make-up of extant populations of T. japonicus was shaped by Pleistocene environmental impacts on the historical demography of this species. Coalescent analyses (Neutrality tests, Mismatch distribution analysis, Bayesian skyline analyses) showed that the species along the coastline of China has experienced population expansions originated in its most recent history at about 153-216 kyr.
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Affiliation(s)
- Yongshuang Xiao
- Institute of Evolution & Marine Biodiversity, Ocean University of China , Qingdao , China
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