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Kundu S, Kang HE, Kim AR, Lee SR, Kim EB, Amin MHF, Andriyono S, Kim HW, Kang K. Mitogenomic Characterization and Phylogenetic Placement of African Hind, Cephalopholis taeniops: Shedding Light on the Evolution of Groupers (Serranidae: Epinephelinae). Int J Mol Sci 2024; 25:1822. [PMID: 38339100 PMCID: PMC10855530 DOI: 10.3390/ijms25031822] [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: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The generated mitogenome spans 16,572 base pairs and exhibits a gene order analogous to that of the ancestral teleost's, featuring 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. The mitogenome of C. taeniops displays an AT bias (54.99%), aligning with related species. The majority of PCGs in the mitogenome initiate with the start codon ATG, with the exceptions being COI (GTG) and atp6 (TTG). The relative synonymous codon usage analysis revealed the maximum abundance of leucine, proline, serine, and threonine. The nonsynonymous/synonymous ratios were <1, which indicates a strong negative selection among all PCGs of the Cephalopholis species. In C. taeniops, the prevalent transfer RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), which lacks a dihydrouracil (DHU) stem. A comparative examination of conserved domains and sequence blocks across various Cephalopholis species indicates noteworthy variations in length and nucleotide diversity. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic analyses, employing the concatenated PCGs and a combination of PCGs + rRNAs, distinctly separate all Cephalopholis species, including C. taeniops. Overall, these findings deepen our understanding of evolutionary relationships among serranid groupers, emphasizing the significance of structural considerations in mitogenomic analyses.
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Affiliation(s)
- Shantanu Kundu
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea;
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea;
| | - Ah Ran Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Soo Rin Lee
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Eun-Bi Kim
- Ocean Georesources Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea;
| | - Muhammad Hilman Fu’adil Amin
- Advance Tropical Biodiversity, Genomics, and Conservation Research Group, Department of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia;
| | - Sapto Andriyono
- Department of Marine, Faculty of Fisheries and Marine, Airlangga University, Surabaya 60115, Indonesia
| | - Hyun-Woo Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Kyoungmi Kang
- International Graduate Program of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
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Vimono IB, Borsa P, Hocdé R, Pouyaud L. Phylogeography of Long-spined Sea Urchin Diadema setosum Across the Indo-Malay Archipelago. Zool Stud 2023; 62:e39. [PMID: 37772168 PMCID: PMC10522617 DOI: 10.6620/zs.2023.62-39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 05/26/2023] [Indexed: 09/30/2023]
Abstract
Widely distributed, broadcast-spawning Diadema sea urchins have been used as model invertebrate species for studying the zoogeography of the tropical Indo-Pacific. So far, the Indo-Malay archipelago, a wide and geographically complex maritime region extending from the eastern Indian Ocean to the western Pacific Ocean, has been under-sampled. This study aims to fill this sampling gap and uncover the phylogeographic structure of the long-spined sea-urchin D. setosum in the central Indo-West pacific region. D. setosum samples (total N = 718) were collected in 13 sites throughout the Indo-Malay archipelago. We sequenced over 1157 bp of COI gene. The Phylogeographic structure was derived from pairwise ФST estimates using multidimensional scaling and hierarchical clustering analysis; biogeographic hypotheses were tested by AMOVA; genetic relationships between haplotypes were summarised in the form of a minimum-spanning network; and pairwise mismatch distributions were compared to the expectations from demographic and spatial expansion models. All samples from the Indo-West Pacific were of the previously uncovered D. setosum-a lineage. Phylogeographic structure was evident: the Andaman Sea population and the northern New Guinea population were genetically distinct. Subtler but significant haplotype-frequency differences distinguished two populations within the Indonesian seas, distributed in a parapatric-like fashion. The phylogeographic partition observed was insufficiently explained by previous biogeographic hypotheses. The haplotype network showed a series of closely related star-shaped haplogroups with a high proportion of singletons. Nucleotide-pairwise mismatch patterns in the two populations from the Indonesian seas were consistent with both demographic and spatial expansion models. While geographic barriers to gene flow were inferred at the western and eastern extremities of the Indo-Malay archipelago, the subtler parapatric pattern observed within the Indonesian seas indicated restriction in gene flow, in a fashion that can hardly be explained by geographic isolation given the dynamic current systems that cross this region. Our results thus raise the hypothesis of subtle reproductive isolation between ecologically incompatible populations. While the coalescence pattern of the Andaman-Sea population suggested demographic stability over evolutionary timescales, that of the two populations from the Indonesian seas indicated recent population expansion, possibly linked to the rapid changes in available D. setosum habitat caused by sea-level oscillations in the late Pleistocene. The phylogeographic patterns observed in this study point to likely allopatric differentiation in the central Indo-West Pacific region. Genetic differences between populations were likely reinforced during interglacials by some form of reproductive isolation.
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Affiliation(s)
- Indra Bayu Vimono
- National Research and Innovation Agency Republic of Indonesia (BRIN), Research Center for Oceanography (RCO), Jakarta, Indonesia. E-mail: (Vimono)
- Université de Montpellier, Ecole doctorale Gaia, Montpellier, France
- Institut de recherche pour le développement (IRD), UMR 226 ISEM, Montpellier, France. E-mail: (Pouyaud)
| | - Philippe Borsa
- IRD, UMR 250 Entropi, Montpellier, France. E-mail: (Borsa)
| | - Régis Hocdé
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France. E-mail: (Hocdé)
| | - Laurent Pouyaud
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France. E-mail: (Hocdé)
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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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Payet SD, Pratchett MS, Saenz‐Agudelo P, Berumen ML, DiBattista JD, Harrison HB. Demographic histories shape population genomics of the common coral grouper (
Plectropomus leopardus
). Evol Appl 2022; 15:1221-1235. [PMID: 36051464 PMCID: PMC9423088 DOI: 10.1111/eva.13450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/02/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022] Open
Abstract
Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology since they reveal how diversity is generated and how it may respond to future environmental change. Here, we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50% smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~10–120 kya) and may be vulnerable to localized disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of the Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.
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Affiliation(s)
- S. D. Payet
- Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville Australia
| | - M. S. Pratchett
- Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville Australia
| | - P. Saenz‐Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile Valdivia Chile
| | - M. L. Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology
| | - J. D. DiBattista
- Australian Museum Research Institute Australian Museum, 1 William St Sydney NSW Australia
| | - H. B. Harrison
- Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville Australia
- Australian Institute of Marine Science Townsville Australia
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Xie Z, Wang D, Jiang S, Peng C, Wang Q, Huang C, Li S, Lin H, Zhang Y. Chromosome-Level Genome Assembly and Transcriptome Comparison Analysis of Cephalopholis sonnerati and Its Related Grouper Species. BIOLOGY 2022; 11:biology11071053. [PMID: 36101431 PMCID: PMC9312885 DOI: 10.3390/biology11071053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022]
Abstract
The tomato hind, Cephalopholis sonnerati, is a bottom-dwelling coral reef fish, which is widely distributed in the Indo-Pacific and Red Sea. C. sonnerati also features complex social structures and behaviour mechanisms. Here, we present a high-quality, chromosome-level genome assembly for C. sonnerati that was derived using PacBio sequencing and Hi-C technologies. A 1043.66 Mb genome with an N50 length of 2.49 Mb was assembled, produced containing 795 contigs assembled into 24 chromosomes. Overall, 97.2% of the complete BUSCOs were identified in the genome. A total of 26,130 protein-coding genes were predicted, of which 94.26% were functionally annotated. Evolutionary analysis revealed that C. sonnerati diverged from its common ancestor with E. lanceolatus and E. akaara approximately 41.7 million years ago. In addition, comparative genome analyses indicated that the expanded gene families were highly enriched in the sensory system. Finally, we found the tissue-specific expression of 8108 genes. We found that these tissue-specific genes were highly enriched in the brain. In brief, the high-quality, chromosome-level reference genome will provide a valuable genome resource for studies of the genetic conservation, resistance breeding, and evolution of C. sonnerati.
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Affiliation(s)
- Zhenzhen Xie
- College of Basic Medicine, Nanchang University, Nanchang 330031, China;
| | - Dengdong Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (D.W.); (S.J.); (S.L.); (H.L.)
| | - Shoujia Jiang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (D.W.); (S.J.); (S.L.); (H.L.)
| | - Cheng Peng
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China;
| | - Qing Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China;
| | - Chunren Huang
- Hainan Chenhai Aquatic Products Co., Ltd., Sanya 572000, China;
| | - Shuisheng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (D.W.); (S.J.); (S.L.); (H.L.)
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (D.W.); (S.J.); (S.L.); (H.L.)
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (D.W.); (S.J.); (S.L.); (H.L.)
- Correspondence:
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Banerjee AK, Feng H, Guo W, Harms NE, Xie H, Liang X, Xing F, Lin Y, Shao H, Guo Z, Ng WL, Huang Y. Glacial vicariance and oceanic circulation shape population structure of the coastal legume Derris trifoliata in the Indo-West Pacific. AMERICAN JOURNAL OF BOTANY 2022; 109:1016-1034. [PMID: 35419829 DOI: 10.1002/ajb2.1851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
PREMISE The phylogeography of coastal plant species is shaped by contemporary and historical biogeographic processes. In this study, we aim to decipher the phylogeography of Derris trifoliata, a woody legume of relatively recent origin and wide distribution, in coastal areas in the Indo-West Pacific (IWP) region. METHODS Genetic diversity and population structure were assessed by analyzing six nuclear and three chloroplast DNA sequences from 30 populations across the species' range. Phylogeography was inferred by estimating gene flow, divergence time, historical population size changes, and historical habitat suitability using paleoclimatic niche modeling. RESULTS High genetic diversity was observed at the species level. The populations of three oceanic regions included in this study (i.e., Indian Ocean, South China Sea, and Pacific Ocean) formed distinct clades and likely diverged during the late Pleistocene. Potential barriers to gene flow were identified, including the Sunda and Sahul shelves, geographic distance, and current patterns of oceanic circulation. Analysis of changes in population size supported the bottleneck model, which was strengthened by estimates of habitat suitability across paleoclimatic conditions. CONCLUSIONS The once widespread distribution of D. trifoliata was fragmented by changes in climatic suitability and biogeographic barriers that arose following sea-level changes during the Pleistocene. In addition, contemporary patterns of oceanic circulation and geographic distance between populations appear to maintain genetic differentiation across its distribution in the IWP.
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Affiliation(s)
- Achyut Kumar Banerjee
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Hui Feng
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Wuxia Guo
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
- Department of Bioengineering, Zunyi Medical University, Zhuhai, 519041 Guangdong, China
| | - Nathan E Harms
- US Army Engineer Research and Development Center, Lewisville, TX 75057, USA
| | - Hongxian Xie
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Xinru Liang
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Fen Xing
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Yuting Lin
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Huiyu Shao
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Zixiao Guo
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University, Malaysia, 43900 Sepang, Selangor, Malaysia
| | - Yelin Huang
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
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The population genomic structure of green turtles (Chelonia mydas) suggests a warm-water corridor for tropical marine fauna between the Atlantic and Indian oceans during the last interglacial. Heredity (Edinb) 2021; 127:510-521. [PMID: 34635850 PMCID: PMC8626443 DOI: 10.1038/s41437-021-00475-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 01/01/2023] Open
Abstract
The occasional westward transport of warm water of the Agulhas Current, "Agulhas leakage", around southern Africa has been suggested to facilitate tropical marine connectivity between the Atlantic and Indian oceans, but the "Agulhas leakage" hypothesis does not explain the signatures of eastward gene flow observed in many tropical marine fauna. We investigated an alternative hypothesis: the establishment of a warm-water corridor during comparatively warm interglacial periods. The "warm-water corridor" hypothesis was investigated by studying the population genomic structure of Atlantic and Southwest Indian Ocean green turtles (N = 27) using 12,035 genome-wide single nucleotide polymorphisms (SNPs) obtained via ddRAD sequencing. Model-based and multivariate clustering suggested a hierarchical population structure with two main Atlantic and Southwest Indian Ocean clusters, and a Caribbean and East Atlantic sub-cluster nested within the Atlantic cluster. Coalescent-based model selection supported a model where Southwest Indian Ocean and Caribbean populations diverged from the East Atlantic population during the transition from the last interglacial period (130-115 thousand years ago; kya) to the last glacial period (115-90 kya). The onset of the last glaciation appeared to isolate Atlantic and Southwest Indian Ocean green turtles into three refugia, which subsequently came into secondary contact in the Caribbean and Southwest Indian Ocean when global temperatures increased after the Last Glacial Maximum. Our findings support the establishment of a warm-water corridor facilitating tropical marine connectivity between the Atlantic and Southwest Indian Ocean during warm interglacials.
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Genetic diversity, population structure and historical demography of the two-spined yellowtail stargazer (Uranoscopus cognatus). Sci Rep 2021; 11:13357. [PMID: 34172804 PMCID: PMC8233350 DOI: 10.1038/s41598-021-92905-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
Benthic species, though ecologically important, are vulnerable to genetic loss and population size reduction due to impacts from fishing trawls. An assessment of genetic diversity and population structure is therefore needed to assist in a resource management program. To address this issue, the two-spined yellowtail stargazer (Uranoscopus cognatus) was collected within selected locations in the Indo-West Pacific (IWP). The partial mitochondrial DNA cytochrome c oxidase subunit 1 and the nuclear DNA recombination activating gene 1 were sequenced. Genetic diversity analyses revealed that the populations were moderately to highly diversified (haplotype diversity, H = 0.490-0.900, nucleotide diversity, π = 0.0010-0.0034) except sampling station (ST) 1 and 14. The low diversity level, however was apparent only in the matrilineal marker (H = 0.118-0.216; π = 0.0004-0.0008), possibly due to stochastic factors or anthropogenic stressors. Population structure analyses revealed a retention of ancestral polymorphism that was likely due to incomplete lineage sorting in U. cognatus, and prolonged vicariance by the Indo-Pacific Barrier has partitioned them into separate stock units. Population segregation was also shown by the phenotypic divergence in allopatric populations, regarding the premaxillary protrusion, which is possibly associated with the mechanism for upper jaw movement in biomechanical feeding approaches. The moderate genetic diversity estimated for each region, in addition to past population expansion events, indicated that U. cognatus within the IWP was still healthy and abundant (except in ST1 and 14), and two stock units were identified to be subjected to a specific resource management program.
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Genetic diversity and population structure of wild and domesticated black tiger shrimp (Penaeus monodon) broodstocks in the Indo-Pacific regions using consolidated mtDNA and microsatellite markers. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Williams CT, McIvor AJ, Wallace EM, Lin YJ, Berumen ML. Genetic diversity and life-history traits of bonefish Albula spp. from the Red Sea. JOURNAL OF FISH BIOLOGY 2021; 98:855-864. [PMID: 33258479 DOI: 10.1111/jfb.14638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
The management of bonefishes Albula spp. has been hindered by unresolved species distributions and a general lack of life-history information. This study provides the first genetic species identifications of Albula spp. from the northern Indian Ocean. The roundjaw bonefish Albula glossodonta was documented in the Red Sea, and the smallscale bonefish A. oligolepis was identified in the Gulf of Aden with no evidence supporting sympatry. Estimates of genetic differentiation indicate three closely related lineages of A. glossodonta in the Red Sea, Indian Ocean and Pacific Ocean (Red Sea-Pacific Ocean, Fst = 0.295; Red Sea-Seychelles, Fst = 0.193; Pacific Ocean-Seychelles, Fst = 0.141). In addition, the authors provide the first life-history information of Albula spp. in the Indian Ocean. Age-based growth models of A. glossodonta from the Red Sea demonstrated statistically significant differences compared to previously published data from the Pacific Ocean. Spawning activity during winter months was derived from gonado-somatic index values of A. glossodonta from the Red Sea and corresponded with spawning seasonality previously documented for the species in the Pacific Ocean. The results of this study aid in refining biogeographical uncertainties of Albula spp. and illustrate the importance of collecting regional growth information for subsequent management of A. glossodonta.
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Affiliation(s)
- Collin T Williams
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ashlie J McIvor
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Elizabeth M Wallace
- Florida Fish & Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. Petersburg, Florida, USA
| | - Yu-Jia Lin
- Center for Environment and Water, King Fahd University of Petroleum and Minerals, Dhahran, Kingdom of Saudi Arabia
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
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Klanten OS, Gaither MR, Greaves S, Mills K, O’Keeffe K, Turnbull J, McKinnon R, Booth DJ. Genomic and morphological evidence of distinct populations in the endemic common (weedy) seadragon Phyllopteryx taeniolatus (Syngnathidae) along the east coast of Australia. PLoS One 2020; 15:e0243446. [PMID: 33362197 PMCID: PMC7757807 DOI: 10.1371/journal.pone.0243446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/22/2020] [Indexed: 11/30/2022] Open
Abstract
The common or weedy seadragon, Phyllopteryx taeniolatus, is an iconic and endemic fish found across temperate reefs of southern Australia. Despite its charismatic nature, few studies have been published, and the extent of population sub-structuring remains poorly resolved. Here we used 7462 single nucleotide polymorphisms (SNPs) to identify the extent of population structure in the weedy seadragon along the temperate southeast coast of Australia. We identified four populations, with strong genetic structure (FST = 0.562) between them. Both Discriminant Analysis of Principle Components (DAPC) and Bayesian clustering analyses support four distinct genetic clusters (north to south: central New South Wales, southern NSW, Victoria and Tasmania). In addition to these genetic differences, geographical variation in external morphology was recorded, with individuals from New South Wales shaped differently for a few measurements to those from the Mornington Peninsula (Victoria). We posit that these genetic and morphological differences suggest that the Victorian population of P. taeniolatus was historically isolated by the Bassian Isthmus during the last glacial maximum and should now be considered at least a distinct population. We also recorded high levels of genetic structure among the other locations. Based on the genomic and to a degree morphological evidence presented in this study, we recommend that the Victorian population be managed separately from the eastern populations (New South Wales and Tasmania).
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Affiliation(s)
- O. Selma Klanten
- Fish Ecology Lab, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
- * E-mail:
| | - Michelle R. Gaither
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, United States of America
| | - Samuel Greaves
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, United States of America
| | - Kade Mills
- Victorian National Parks Association, Carlton Melbourne, VIC, Australia
| | | | - John Turnbull
- Underwater Research Group (URG), Sydney, NSW, Australia
- Centre for Marine Biodiversity and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Rob McKinnon
- New South Wales National Parks and Wildlife Service, Merimbula, NSW, Australia
| | - David J. Booth
- Fish Ecology Lab, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
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12
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Wepfer PH, Nakajima Y, Sutthacheep M, Radice VZ, Richards Z, Ang P, Terraneo T, Sudek M, Fujimura A, Toonen RJ, Mikheyev AS, Economo EP, Mitarai S. Evolutionary biogeography of the reef-building coral genus Galaxea across the Indo-Pacific ocean. Mol Phylogenet Evol 2020; 151:106905. [DOI: 10.1016/j.ympev.2020.106905] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 11/16/2022]
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13
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El-Hossary EM, Abdel-Halim M, Ibrahim ES, Pimentel-Elardo SM, Nodwell JR, Handoussa H, Abdelwahab MF, Holzgrabe U, Abdelmohsen UR. Natural Products Repertoire of the Red Sea. Mar Drugs 2020; 18:md18090457. [PMID: 32899763 PMCID: PMC7551641 DOI: 10.3390/md18090457] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
Marine natural products have achieved great success as an important source of new lead compounds for drug discovery. The Red Sea provides enormous diversity on the biological scale in all domains of life including micro- and macro-organisms. In this review, which covers the literature to the end of 2019, we summarize the diversity of bioactive secondary metabolites derived from Red Sea micro- and macro-organisms, and discuss their biological potential whenever applicable. Moreover, the diversity of the Red Sea organisms is highlighted as well as their genomic potential. This review is a comprehensive study that compares the natural products recovered from the Red Sea in terms of ecological role and pharmacological activities.
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Affiliation(s)
- Ebaa M. El-Hossary
- National Centre for Radiation Research & Technology, Egyptian Atomic Energy Authority, Ahmed El-Zomor St. 3, El-Zohoor Dist., Nasr City, Cairo 11765, Egypt;
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
| | - Eslam S. Ibrahim
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt;
- Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/Bau D15, 97080 Würzburg, Germany
| | - Sheila Marie Pimentel-Elardo
- Department of Biochemistry, University of Toronto, MaRS Centre West, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (S.M.P.-E.); (J.R.N.)
| | - Justin R. Nodwell
- Department of Biochemistry, University of Toronto, MaRS Centre West, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (S.M.P.-E.); (J.R.N.)
| | - Heba Handoussa
- Department of Pharmaceutical Biology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
| | - Miada F. Abdelwahab
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt;
| | - Ulrike Holzgrabe
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- Correspondence: (U.H.); (U.R.A.)
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt;
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, P.O. Box 61111 New Minia City, Minia 61519, Egypt
- Correspondence: (U.H.); (U.R.A.)
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14
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Menchaca A, Arteaga MC, Medellin RA, Jones G. Conservation units and historical matrilineal structure in the tequila bat (Leptonycteris yerbabuenae). Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01164] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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15
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Palmerín‐Serrano PN, Tavera J, Espinoza E, Angulo A, Martínez‐Gómez JE, González‐Acosta AF, Domínguez‐Domínguez O. Evolutionary history of the reef fish
Anisotremus interruptus
(Perciformes: Haemulidae) throughout the Tropical Eastern Pacific. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Paola Nallely Palmerín‐Serrano
- Programa Institucional de Maestría en Ciencias Biológicas Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
- Laboratorio de Biología Acuática Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
| | - Jose Tavera
- Laboratorio de Ictiología Departamento de Biología Universidad del Valle Cali Colombia
| | - Eduardo Espinoza
- Investigación Marina Aplicada Parque Nacional Galápagos “Charles Darwin” Puerto Ayora Isla Santa Cruz Ecuador
| | - Arturo Angulo
- Museo de Zoología y Centro de Investigación en Ciencias del Mar y Limnología Universidad de Costa Rica San Pedro de Montes de Oca San José Costa Rica
- Laboratorio de Ictiología Departamento de Zoología e Botánica Universidad Estadual Paulista “Julio de MesquitaFilho” São José do Rio Preto São Paul Brazil
| | - Juan E. Martínez‐Gómez
- Instituto de Ecología A. C. (INECOL)Red de Interacciones Multitróficas Xalapa Veracruz México
| | - Adrián F. González‐Acosta
- Instituto Politécnico NacionalCentro Interdisciplinario de Ciencias Marinas (CICIMAR)Pesquerías y Biología Marina La Paz México
| | - Omar Domínguez‐Domínguez
- Laboratorio de Biología Acuática Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
- Laboratorio Nacional de Análisis y Síntesis Ecológica para la Conservación de Recursos Genéticos de México Escuela Nacional de Estudios SuperioresUniversidad Nacional Autónoma de México Morelia Michoacán México
- Instituto Nacional de BiodiversidadColección de Peces Quito Ecuador
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16
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Banerjee AK, Guo W, Qiao S, Li W, Xing F, Lin Y, Hou Z, Li S, Liu Y, Huang Y. Land masses and oceanic currents drive population structure of Heritiera littoralis, a widespread mangrove in the Indo-West Pacific. Ecol Evol 2020; 10:7349-7363. [PMID: 32760533 PMCID: PMC7391321 DOI: 10.1002/ece3.6460] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/24/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022] Open
Abstract
Phylogeographic forces driving evolution of sea-dispersed plants are often influenced by regional and species characteristics, although not yet deciphered at a large spatial scale for many taxa like the mangrove species Heritiera littoralis. This study aimed to assess geographic distribution of genetic variation of this widespread mangrove in the Indo-West Pacific region and identify the phylogeographic factors influencing its present-day distribution. Analysis of five chloroplast DNA fragments' sequences from 37 populations revealed low genetic diversity at the population level and strong genetic structure of H. littoralis in this region. The estimated divergence times between the major genetic lineages indicated that glacial level changes during the Pleistocene epoch induced strong genetic differentiation across the Indian and Pacific Oceans. In comparison to the strong genetic break imposed by the Sunda Shelf toward splitting the lineages of the Indian and Pacific Oceans, the genetic differentiation between Indo-Malesia and Australasia was not so prominent. Long-distance dispersal ability of H. littoralis propagules helped the species to attain transoceanic distribution not only across South East Asia and Australia, but also across the Indian Ocean to East Africa. However, oceanic circulation pattern in the South China Sea was found to act as a barrier creating further intraoceanic genetic differentiation. Overall, phylogeographic analysis in this study revealed that glacial vicariance had profound influence on population differentiation in H. littoralis and caused low genetic diversity except for the refugia populations near the equator which might have persisted through glacial maxima. With increasing loss of suitable habitats due to anthropogenic activities, these findings therefore emphasize the urgent need for conservation actions for all populations throughout the distribution range of H. littoralis.
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Affiliation(s)
- Achyut Kumar Banerjee
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Wuxia Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- South China Botanical GardenChinese Academy of SciencesGuangzhouGuangdongChina
| | - Sitan Qiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Weixi Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- Division of Ecology & BiodiversitySchool of Biological SciencesThe University of Hong KongHong KongChina
| | - Fen Xing
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yuting Lin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Zhuangwei Hou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Sen Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yelin Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
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17
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Takeuchi T, Masaoka T, Aoki H, Koyanagi R, Fujie M, Satoh N. Divergent northern and southern populations and demographic history of the pearl oyster in the western Pacific revealed with genomic SNPs. Evol Appl 2020; 13:837-853. [PMID: 32211071 PMCID: PMC7086055 DOI: 10.1111/eva.12905] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 12/26/2022] Open
Abstract
In the open ocean without terrain boundaries, marine invertebrates with pelagic larvae can migrate long distances using ocean currents, suggesting reduced genetic diversification. Contrary to this assumption, however, genetic differentiation is often observed in marine invertebrates. In the present study, we sought to explain how population structure is established in the western Pacific Ocean, where the strong Kuroshio Current maintains high levels of gene flow from south to north, presumably promoting genetic homogeneity. We determined the population structure of the pearl oyster, Pinctada fucata, in the Indo-Pacific Ocean using genome-wide genotyping data from multiple sampling localities. Cluster analysis showed that the western Pacific population is distinct from that of the Indian Ocean, and that it is divided into northern (Japanese mainland) and southern (Nansei Islands, China, and Cambodia) populations. Genetic differentiation of P. fucata can be explained by geographic barriers in the Indian Ocean and a local lagoon, and by environmental gradients of sea surface temperature (SST) and oxygen concentration in the western Pacific. A genome scan showed evidence of adaptive evolution in genomic loci, possibly associated with changes in environmental factors, including SST and oxygen concentration. Furthermore, Bayesian simulation demonstrated that the past population expansion and division are congruent with ocean warming after the last glacial period. It is highly likely that the environmental gradient forms a genetic barrier that diversifies P. fucata populations in the western Pacific. This hypothesis helps to explain genetic differentiation and possible speciation of marine invertebrates.
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Affiliation(s)
- Takeshi Takeuchi
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Tetsuji Masaoka
- Aquaculture Technology DivisionNational Research Institute of Aquaculture, Fisheries Research and Education AgencyTamaki‐choJapan
| | - Hideo Aoki
- Mie Prefecture Fisheries Research InstituteShimaJapan
| | - Ryo Koyanagi
- DNA Sequencing SectionOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Manabu Fujie
- DNA Sequencing SectionOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Noriyuki Satoh
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
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18
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Rodríguez‐Flores PC, Buckley D, Macpherson E, Corbari L, Machordom A. Deep‐sea squat lobster biogeography (Munidopsidae:
Leiogalathea
) unveils Tethyan vicariance and evolutionary patterns shared by shallow‐water relatives. ZOOL SCR 2020. [DOI: 10.1111/zsc.12414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paula C. Rodríguez‐Flores
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
- Centre d'Estudis Avançats de Blanes (CEAB‐CSIC) Blanes Spain
| | - David Buckley
- Departamento de Biología (Genética) Facultad de Biología Universidad Autónoma de Madrid Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM) Facultad de Biología Universidad Autónoma de Madrid Madrid Spain
| | | | - Laure Corbari
- Institut de Systématique Évolution Biodiversité (ISYEB, UMR 7205) Muséum national d'Histoire naturelle CNRS Sorbonne UniversitéEPHE Paris France
| | - Annie Machordom
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
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19
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Simmonds SE, Fritts‐Penniman AL, Cheng SH, Mahardika GN, Barber PH. Genomic signatures of host-associated divergence and adaptation in a coral-eating snail, Coralliophila violacea (Kiener, 1836). Ecol Evol 2020; 10:1817-1837. [PMID: 32128119 PMCID: PMC7042750 DOI: 10.1002/ece3.5977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 12/31/2022] Open
Abstract
The fluid nature of the ocean, combined with planktonic dispersal of marine larvae, lowers physical barriers to gene flow. However, divergence can still occur despite gene flow if strong selection acts on populations occupying different ecological niches. Here, we examined the population genomics of an ectoparasitic snail, Coralliophila violacea (Kiener 1836), that specializes on Porites corals in the Indo-Pacific. Previous genetic analyses revealed two sympatric lineages associated with different coral hosts. In this study, we examined the mechanisms promoting and maintaining the snails' adaptation to their coral hosts. Genome-wide single nucleotide polymorphism (SNP) data from type II restriction site-associated DNA (2b-RAD) sequencing revealed two differentiated clusters of C. violacea that were largely concordant with coral host, consistent with previous genetic results. However, the presence of some admixed genotypes indicates gene flow from one lineage to the other. Combined, these results suggest that differentiation between host-associated lineages of C. violacea is occurring in the face of ongoing gene flow, requiring strong selection. Indeed, 2.7% of all SNP loci were outlier loci (73/2,718), indicative of divergence with gene flow, driven by adaptation of each C. violacea lineage to their specific coral hosts.
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Affiliation(s)
- Sara E. Simmonds
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
| | | | - Samantha H. Cheng
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
- Center for Biodiversity and ConservationAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Gusti Ngurah Mahardika
- Animal Biomedical and Molecular Biology LaboratoryFaculty of Veterinary MedicineUdayana University BaliDenpasarIndonesia
| | - Paul H. Barber
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
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20
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González CE, Goetze E, Escribano R, Ulloa O, Victoriano P. Genetic diversity and novel lineages in the cosmopolitan copepod Pleuromamma abdominalis in the Southeast Pacific. Sci Rep 2020; 10:1115. [PMID: 31980660 PMCID: PMC6981114 DOI: 10.1038/s41598-019-56935-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 12/16/2019] [Indexed: 11/20/2022] Open
Abstract
Across boundary currents, zooplankton are subject to strong oceanographic gradients and hence strong selective pressures. How such gradients interact with the speciation process of pelagic organisms is still poorly understood in the open ocean realm. Here we report on genetic diversity within the pelagic copepod Pleuromamma abdominalis in the poorly known Southeast Pacific region, with samples spanning an ocean gradient from coastal upwelling to the oligotrophic South Pacific Subtropical Gyre. We assessed variation in fragments of the mitochondrial (mt) genes cytochrome c oxidase subunit I (COI) and Cytochrome b as well as in the nuclear internal transcribed spacer (ITS) region and 28 S rRNA. Phylogenetic analyses revealed the presence of 8 divergent lineages occurring across the gradient with genetic distances in the range of 0.036 and 0.44 (mt genes), and GMYC species delimitation methods support their inference as distinct (undescribed) species. Genetic lineages occurring across the zonal gradient showed strong genetic structuring, with the presence of at least two new lineages within the coastal upwelling zone, revealing an unexpectedly high level of endemism within the Humboldt Current System. Multivariate analyses found strong correlation between genetic variation and surface chlorophyll-a and salinity, suggesting an important role for hydrographic gradients in maintaining genetic diversity. However, the presence of cryptic lineages within the upwelling zone cannot be easily accounted for by environmental heterogeneity and poses challenging questions for understanding the speciation process for oceanic zooplankton.
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Affiliation(s)
- Carolina E González
- Graduate Program in Oceanography, Department of Oceanography, University of Concepción, PO Box 160, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile. .,Instituto Milenio de Oceanografía (IMO) and Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, PO Box 160 C, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile.
| | - Erica Goetze
- Department of Oceanography, University of Hawaii at Manoa, 1000 Pope Road, Honolulu, Hawaii, USA
| | - Rubén Escribano
- Instituto Milenio de Oceanografía (IMO) and Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, PO Box 160 C, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile
| | - Osvaldo Ulloa
- Instituto Milenio de Oceanografía (IMO) and Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, PO Box 160 C, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile
| | - Pedro Victoriano
- Department of Zoology, Faculty of Natural and Oceanographic Sciences, University of Concepción, PO Box 160 C, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile
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21
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Yamamoto T, Tsuda Y, Takayama K, Nagashima R, Tateishi Y, Kajita T. The presence of a cryptic barrier in the West Pacific Ocean suggests the effect of glacial climate changes on a widespread sea-dispersed plant, Vigna marina (Fabaceae). Ecol Evol 2019; 9:8429-8440. [PMID: 31410251 PMCID: PMC6686344 DOI: 10.1002/ece3.5099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/12/2018] [Accepted: 09/13/2018] [Indexed: 11/29/2022] Open
Abstract
Ocean currents are an important driver of evolution for sea-dispersed plants, enabling them to maintain reciprocal gene flow via sea-dispersed diaspores and obtain wide distribution ranges. Although geographic barriers are known to be the primary factors shaping present genetic structure of sea-dispersed plants, cryptic barriers which form clear genetic structure within oceanic regions are poorly understood. To test the presence of a cryptic barrier, we conducted a phylogeographic study together with past demographic inference for a widespread sea-dispersed plant, Vigna marina, using 308 individuals collected from the entire Indo-West Pacific (IWP) region. Chloroplast DNA variation showed strong genetic structure that separated populations into three groups: North Pacific (NP), South Pacific (SP) and Indian Ocean (IN) (F'CT among groups = 0.954-1.000). According to the Approximate Bayesian computation inference, splitting time between NP and SP was approximately 20,200 years (95%HPD, 4,530-95,400) before present. Moreover, a signal of recent population expansion was detected in the NP group. This study clearly showed the presence of a cryptic barrier in the West Pacific region of the distributional range of V. marina. The locations of the cryptic barrier observed in V. marina corresponded to the genetic breaks found in other plants, suggesting the presence of a common cryptic barrier for sea-dispersed plants. Demographic inference suggested that genetic structure related to this cryptic barrier has been present since the last glacial maximum and may reflect patterns of past population expansion from refugia.
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Affiliation(s)
- Takashi Yamamoto
- Iriomote Station, Tropical Biosphere Research CenterUniversity of the RyukyusOkinawaJapan
- United Graduate School of Agricultural ScienceKagoshima UniversityKagoshimaJapan
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science CenterUniversity of TsukubaUeda‐shiJapan
| | - Koji Takayama
- Department of Botany, Graduate School of ScienceKyoto UniversityKyotoJapan
- Museum of Natural and Environmental HistoryShizuokaJapan
| | - Reiko Nagashima
- Department of Biology, Graduate School of ScienceChiba UniversityChibaJapan
| | | | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research CenterUniversity of the RyukyusOkinawaJapan
- United Graduate School of Agricultural ScienceKagoshima UniversityKagoshimaJapan
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22
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Liu SYV, Tuanmu MN, Rachmawati R, Mahardika GN, Barber PH. Integrating phylogeographic and ecological niche approaches to delimitating cryptic lineages in the blue-green damselfish ( Chromis viridis). PeerJ 2019; 7:e7384. [PMID: 31392097 PMCID: PMC6677123 DOI: 10.7717/peerj.7384] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 06/30/2019] [Indexed: 12/22/2022] Open
Abstract
Species delimitation is challenging in sibling species/cryptic lineages because of the absence of clear diagnostic traits. However, integration of different approaches such as phylogeography and ecological niche comparison offers one potential approach to tease apart recently diverged lineages. In this study, we estimate the ecological niche divergence among lineages in Chromis viridis in a broad-scale phylogeographic framework to test whether the combination of these two approaches can effectively distinguish recently diverged lineages. Results from Cytb and Rag2 analyses identified two cryptic lineages (C. viridis A and C. viridis B) that diverged ∼3 Myr ago. Estimates of ecological niche divergence with 11 environmental parameters across the broad geographic range of these lineages showed overlapping ecological niches and niche conservatism. However, regardless of the incongruence between genetic and ecological niche divergence, the substantial genetic divergence between the two clades of C. viridis in both mtDNA and nuclear loci strong suggest that they are cryptic taxa.
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Affiliation(s)
- Shang Yin Vanson Liu
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Mao-Ning Tuanmu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Rita Rachmawati
- Center for Fisheries Research, Ministry of Marine Affairs and Fisheries, Jakarta, Indonesia.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | | | - Paul H Barber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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23
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Gajdzik L, Bernardi G, Lepoint G, Frédérich B. Genetic diversity mirrors trophic ecology in coral reef fish feeding guilds. Mol Ecol 2018; 27:5004-5018. [DOI: 10.1111/mec.14936] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 10/16/2018] [Accepted: 10/24/2018] [Indexed: 11/26/2022]
Affiliation(s)
- Laura Gajdzik
- Laboratory of Functional and Evolutionary Morphology FOCUS, University of Liège Liège Belgium
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz California
| | - Gilles Lepoint
- Laboratory of Oceanology FOCUS, University of Liège Liège Belgium
| | - Bruno Frédérich
- Laboratory of Functional and Evolutionary Morphology FOCUS, University of Liège Liège Belgium
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24
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Ma KY, van Herwerden L, Newman SJ, Berumen ML, Choat JH, Chu KH, Sadovy de Mitcheson Y. Contrasting population genetic structure in three aggregating groupers (Percoidei: Epinephelidae) in the Indo-West Pacific: the importance of reproductive mode. BMC Evol Biol 2018; 18:180. [PMID: 30514203 PMCID: PMC6278153 DOI: 10.1186/s12862-018-1284-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/30/2018] [Indexed: 11/10/2022] Open
Abstract
Background Understanding the factors shaping population genetic structure is important for evolutionary considerations as well as for management and conservation. While studies have revealed the importance of palaeogeographic changes in shaping phylogeographic patterns in multiple marine fauna, the role of reproductive behaviour is rarely considered in reef fishes. We investigated the population genetics of three commercially important aggregating grouper species in the Indo-West Pacific, namely the camouflage grouper Epinephelus polyphekadion, the squaretail coral grouper Plectropomus areolatus, and the common coral trout P. leopardus, with similar life histories but distinct spatio-temporal characteristics in their patterns of forming spawning aggregations. Results By examining their mitochondrial control region and 9–11 microsatellite markers, we found an overarching influence of palaeogeographic events in the population structure of all species, with genetic breaks largely coinciding with major biogeographic barriers. The divergence time of major lineages in these species coincide with the Pleistocene glaciations. Higher connectivity is evident in E. polyphekadion and P. areolatus that assemble in larger numbers at fewer spawning aggregations and in distinctive offshore locations than in P. leopardus which has multiple small, shelf platform aggregations. Conclusions While palaeogeographic events played an important role in shaping the population structure of the target species, the disparity in population connectivity detected may be partly attributable to differences in their reproductive behaviour, highlighting the need for more investigations on this characteristic and the need to consider reproductive mode in studies of connectivity and population genetics. Electronic supplementary material The online version of this article (10.1186/s12862-018-1284-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ka Yan Ma
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Lynne van Herwerden
- College of Science and Engineering, James Cook University, Douglas, Townsville, QLD, 4811, Australia
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, PO Box 20, North Beach, WA, 6920, Australia
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - John Howard Choat
- College of Science and Engineering, James Cook University, Douglas, Townsville, QLD, 4811, Australia
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yvonne Sadovy de Mitcheson
- Swire Institute of Marine Science, School of Biological Sciences, University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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Sandoval-Huerta ER, Beltrán-López RG, Pedraza-Marrón CR, Paz-Velásquez MA, Angulo A, Robertson DR, Espinoza E, Domínguez-Domínguez O. The evolutionary history of the goby Elacatinus puncticulatus in the tropical eastern pacific: Effects of habitat discontinuities and local environmental variability. Mol Phylogenet Evol 2018; 130:269-285. [PMID: 30359746 DOI: 10.1016/j.ympev.2018.10.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/05/2018] [Accepted: 10/15/2018] [Indexed: 10/28/2022]
Abstract
Habitat discontinuities, temperature gradients, upwelling systems, and ocean currents, gyres and fronts, can affect distributions of species with narrow environmental tolerance or motility and influence the dispersal of pelagic larvae, with effects ranging from the isolation of adjacent populations to connections between them. The coast of the Tropical Eastern Pacific (TEP) is a highly dynamic environment, with various large gyres and upwelling systems, alternating currents and large rocky-habitat discontinuities, which may greatly influence the genetic connectivity of populations in different parts of the coast. Elacatinus puncticulatus is a cryptic, shallow-living goby that is distributed along the continental shore of virtually the entire TEP, which makes it a good model for testing the influence of these environmental characteristics in the molecular evolution of widespread species in this region. A multilocus phylogeny was used to evaluate the influence of habitat gaps, and oceanographic processes in the evolutionary history of E. puncticulatus throughout its geographical range in the TEP. Two well-supported allopatric clades (one with two allopatric subclades) were recovered, the geographic distribution of which does not correspond to any previously proposed major biogeographic provinces. These populations show strong genetic structure and substantial genetic distances between clades and sub-clades (cytb 0.8-7.3%), with divergence times between them ranging from 0.53 to 4.88 Mya, and recent population expansions dated at 170-130 Kya. The ancestral area of all populations appears to be the Gulf of Panama, while several isolation events have formed the phylogeographic patterns evident in this species. Local and regional oceanographic processes as well as habitat discontinuities have shaped the distribution patterns of the genetic lineages along the continental TEP. Large genetic distances, high genetic differentiation, and the results of species-tree and phylogenetic analyses indicate that E. puncticulatus comprises a complex of three allopatric species with an unusual geographic arrangement.
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Affiliation(s)
- E R Sandoval-Huerta
- Programa Institucional de Maestría en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico; Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico
| | - R G Beltrán-López
- Programa Institucional de Doctorado en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico; Laboratorio de Ictiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Av. Universidad no. 1001, Cuernavaca, Morelos 62209, Mexico.
| | - C R Pedraza-Marrón
- Programa Institucional de Maestría en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico; Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico
| | - M A Paz-Velásquez
- Centro de Estudios del Mar y Acuicultura, Universidad de San Carlos de Guatemala, Guatemala City, Guatemala
| | - A Angulo
- Museo de Zoología y Centro de Investigación en Ciencias del Mar y Limnología, Universidad de Costa Rica. 11501-2060, San Pedro de Montes de Oca, San José, Costa Rica
| | - D R Robertson
- Naos Marine Laboratory, Smithsonian Tropical Research Institute, Balboa, Panama.
| | - E Espinoza
- Dirección del Parque Nacional Galápagos, Puerto Ayora, Islas Galápagos, Ecuador.
| | - O Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico.
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Otwoma LM, Diemel V, Reuter H, Kochzius M, Meyer A. Genetic population structure of the convict surgeonfish Acanthurus triostegus: a phylogeographic reassessment across its range. JOURNAL OF FISH BIOLOGY 2018; 93:597-608. [PMID: 29956317 DOI: 10.1111/jfb.13686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
This study investigates the genetic population structure and connectivity of Acanthurus triostegus in five Indo-Pacific biogeographic regions (western and eastern Indian Ocean, western, central and eastern Pacific Ocean), using a mitochondrial DNA marker spanning the ATPase8 and ATPase6 gene regions. In order to assess the phylogeography and genetic population structure of A. triostegus across its range, 35 individuals were sampled from five localities in the western Indian Ocean and complemented with 227 sequences from two previous studies. Results from the overall analysis of molecular variance (AMOVA) without a priori grouping showed evidence of significant differentiation in the Indo-Pacific, with 25 (8.3%) out of 300 pairwise ΦST comparisons being significant. However, the hierarchical AMOVA grouping of Indian and Pacific Ocean populations failed to support the vicariance hypothesis, showing a lack of a genetic break between the two ocean basins. Instead, the correlation between pairwise ΦST values and geographic distance showed that dispersal of A. triostegus in the Indo-Pacific Ocean follows an isolation-by-distance model. Three haplogroups could be deduced from the haplotype network and phylogenetic tree, with haplogroup 1 and 2 dominating the Indian and the Pacific Ocean, respectively, while haplogroup 3 exclusively occurring in the Hawaiian Archipelago of the central Pacific Ocean.
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Affiliation(s)
- Levy M Otwoma
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Kenya Marine and Fisheries Research Institute (KMFRI), Mombasa, Kenya
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Valeska Diemel
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Hauke Reuter
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | | | - Achim Meyer
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
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Byrne L, Chapleau F, Aris-Brosou S. How the Central American Seaway and an Ancient Northern Passage Affected Flatfish Diversification. Mol Biol Evol 2018; 35:1982-1989. [PMID: 29788493 DOI: 10.1093/molbev/msy104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
While the natural history of flatfish has been debated for decades, the mode of diversification of this biologically and economically important group has never been elucidated. To address this question, we assembled the largest molecular data set to date, covering > 300 species (out of ca. 800 extant), from 13 of the 14 known families over nine genes, and employed relaxed molecular clocks to uncover their patterns of diversification. As the fossil record of flatfish is contentious, we used sister species distributed on both sides of the American continent to calibrate clock models based on the closure of the Central American Seaway (CAS), and on their current species range. We show that flatfish diversified in two bouts, as species that are today distributed around the equator diverged during the closure of CAS, whereas those with a northern range diverged after this, hereby suggesting the existence of a postCAS closure dispersal for these northern species, most likely along a trans-Arctic northern route, a hypothesis fully compatible with paleogeographic reconstructions.
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Affiliation(s)
- Lisa Byrne
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | | | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Mathematics & Statistics, University of Ottawa, Ottawa, ON, Canada
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28
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Mennesson MI, Bonillo C, Feunteun E, Keith P. Phylogeography of Eleotris fusca (Teleostei: Gobioidei: Eleotridae) in the Indo-Pacific area reveals a cryptic species in the Indian Ocean. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1063-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Cryptic lineage differentiation among Indo-Pacific bottlenose dolphins (Tursiops aduncus) in the northwest Indian Ocean. Mol Phylogenet Evol 2018; 122:1-14. [DOI: 10.1016/j.ympev.2017.12.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 12/15/2017] [Accepted: 12/26/2017] [Indexed: 11/19/2022]
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30
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Qu M, Tang W, Liu Q, Wang D, Ding S. Genetic diversity within grouper species and a method for interspecific hybrid identification using DNA barcoding and RYR3 marker. Mol Phylogenet Evol 2017; 121:46-51. [PMID: 29294404 DOI: 10.1016/j.ympev.2017.12.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/27/2017] [Accepted: 12/27/2017] [Indexed: 01/16/2023]
Abstract
Groupers (family Epinephelidae) are an assemblage of coral reef fishes comprising more than 160 species in 16 genera, many of which are both environmentally and economically valuable. Because of their similar morphology, variable color patterns, and tendency for interspecies hybridization, morphological identification of groupers usually leads to taxonomic confusion. To find an effective method for identifying different grouper species and hybrids, evaluate genetic diversity and uncover any synonymous or cryptic species, we sampled a total of 221 specimens representing 57 species in 9 genera in the China Seas. Both mitochondrial (mt) cytochrome oxidase subunit I (COI) and NADH dehydrogenase subunit 2 (ND2) were found to be effective barcoding genes. We also developed an efficient protocol for identifying hybrid groupers using mt markers and the nuclear RYR3 gene and found the first record of wide interspecies hybridization in genus Epinephelus. This barcoding study revealed high genetic divergence in many widespread species and possible synonyms. In addition to providing a molecular method for identifying grouper species, this study offers important resources for the further study of grouper conservation genetics, speciation, hybridization and other evolutionary traits.
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Affiliation(s)
- Meng Qu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian Province, China
| | - Wei Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian Province, China
| | - Qiaohong Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian Province, China
| | - Dexiang Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian Province, China.
| | - Shaoxiong Ding
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian Province, China.
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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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Community assembly of coral reef fishes along the Melanesian biodiversity gradient. PLoS One 2017; 12:e0186123. [PMID: 29069096 PMCID: PMC5656311 DOI: 10.1371/journal.pone.0186123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 09/26/2017] [Indexed: 11/19/2022] Open
Abstract
The Indo-Pacific is home to Earth’s most biodiverse coral reefs. Diversity on these reefs decreases from the Coral Triangle east through the islands of Melanesia. Despite this pattern having been identified during the early 20th century, our knowledge about the interaction between pattern and process remains incomplete. To evaluate the structure of coral reef fish communities across Melanesia, we obtained distributional records for 396 reef fish species in five taxa across seven countries. We used hierarchical clustering, nestedness, and multiple linear regression analyses to evaluate the community structure. We also compiled data on life history traits (pelagic larval duration, body size and schooling behavior) to help elucidate the ecological mechanisms behind community structure. Species richness for these taxa along the gradient was significantly related to longitude but not habitat area. Communities are significantly nested, indicating that species-poor communities are largely composed of subsets of the species found on species rich reefs. These trends are robust across taxonomic groups except for the Pomacentridae, which exhibit an anti-nested pattern, perhaps due to a large number of endemic species. Correlations between life history traits and the number of reefs on which species occurred indicate that dispersal and survival ability contribute to determining community structure. We conclude that distance from the Coral Triangle dominates community structure in reef fish; however, conservation of the most species-rich areas will not be sufficient alone to conserve the vivid splendor of this region.
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Silva RDA, Silva D, Veneza I, Sampaio I, Schneider H, Gomes G. Development of EPIC-PCR Markers for Lutjanus purpureus (Lutjanidae-Perciformes) and their Potential Applicability in Population Analyses. AN ACAD BRAS CIENC 2017; 89:2095-2100. [PMID: 28678957 DOI: 10.1590/0001-3765201720150476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 05/25/2016] [Indexed: 11/21/2022] Open
Abstract
In the present study, a novel set of eight EPIC primers were developed for Lutjanus purpureus and assayed in five other marine teleosts including three lutjanids, one scianid and one anablepid. Most of the genomic regions used in this study presented genetic diversity indexes equal or greater than the intragenic regions commonly used in population genetics studies. Moreover, six out of eight markers showed cross-amplification with other taxa. Thus, the primers described here may be used to elucidate questions at the intraspecific level for a large number of taxa.
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Affiliation(s)
- Raimundo DA Silva
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Danillo Silva
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Ivana Veneza
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Horacio Schneider
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Grazielle Gomes
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
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Stern N, Rinkevich B, Goren M. Integrative approach revises the frequently misidentified species of Sardinella (Clupeidae) of the Indo-West Pacific Ocean. JOURNAL OF FISH BIOLOGY 2016; 89:2282-2305. [PMID: 27616166 DOI: 10.1111/jfb.13114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 07/08/2016] [Indexed: 06/06/2023]
Abstract
To deal with the difficulties of species differentiation and delimitation among the commercially important sardines from the genus Sardinella, an integrative approach was adopted, incorporating traditional taxonomy with four DNA markers (coI, cytb, 16s and nuclear rag2). Combining these methodologies has enabled a thorough re-description of three of the most common species of Sardinella of the Indo-west Pacific Ocean: white sardinella Sardinella albella, fringescale sardinella Sardinella fimbriata and the goldstripe sardinella Sardinella gibbosa, as well as a description of a new species, Gon's sardinella Sardinella goni, from the island of Boracay, Philippines. In addition, extensive widespread sampling of S. gibbosa reveals a significant genetic separation between the populations from the western Indian Ocean and the west Pacific Ocean, despite no supporting morphological differentiation. An updated morphological key of the species of Sardinella of the Indo-west Pacific Ocean is also provided in order to minimize future misidentifications within these economically important taxa. Finally, the genetic and morphological variabilities within and between the investigated species are used to discuss their biogeographical distribution and possible processes of speciation.
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Affiliation(s)
- N Stern
- Department of Zoology and the Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, 69978, Israel.
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, P. O. B. 8030, Haifa, 31080, Israel.
| | - B Rinkevich
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, P. O. B. 8030, Haifa, 31080, Israel
| | - M Goren
- Department of Zoology and the Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, 69978, Israel
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35
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Li X, Duke NC, Yang Y, Huang L, Zhu Y, Zhang Z, Zhou R, Zhong C, Huang Y, Shi S. Re-Evaluation of Phylogenetic Relationships among Species of the Mangrove Genus Avicennia from Indo-West Pacific Based on Multilocus Analyses. PLoS One 2016; 11:e0164453. [PMID: 27716800 PMCID: PMC5055292 DOI: 10.1371/journal.pone.0164453] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/26/2016] [Indexed: 01/31/2023] Open
Abstract
Avicennia L. (Avicenniaceae), one of the most diverse mangrove genera, is distributed widely in tropical and subtropical intertidal zones worldwide. Five species of Avicennia in the Indo-West Pacific region have been previously described. However, their phylogenetic relationships were determined based on morphological and allozyme data. To enhance our understanding of evolutionary patterns in the clade, we carried out a molecular phylogenetic study using wide sampling and multiple loci. Our results support two monophyletic clades across all species worldwide in Avicennia: an Atlantic-East Pacific (AEP) lineage and an Indo-West Pacific (IWP) lineage. This split is in line with biogeographic distribution of the clade. Focusing on the IWP branch, we reconstructed a detailed phylogenetic tree based on sequences from 25 nuclear genes. The results identified three distinct subclades, (1) A. rumphiana and A. alba, (2) A. officinalis and A. integra, and (3) the A. marina complex, with high bootstrap support. The results strongly corresponded to two morphological traits in floral structure: stigma position in relation to the anthers and style length. Using Bayesian dating methods we estimated diversification of the IWP lineage was dated to late Miocene (c. 6.0 million years ago) and may have been driven largely by the fluctuating sea levels since that time.
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Affiliation(s)
- Xinnian Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Norman C. Duke
- Trop WATER, James Cook University, Townsville, Queensland, Australia
| | - Yuchen Yang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lishi Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuxiang Zhu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhang Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature Reserve, Haikou, Hainan, China
| | - Yelin Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (YH); (SS)
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (YH); (SS)
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Reid K, Hoareau TB, Graves JE, Potts WM, Dos Santos SMR, Klopper AW, Bloomer P. Secondary contact and asymmetrical gene flow in a cosmopolitan marine fish across the Benguela upwelling zone. Heredity (Edinb) 2016; 117:307-315. [PMID: 27436525 DOI: 10.1038/hdy.2016.51] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 05/09/2016] [Accepted: 05/12/2016] [Indexed: 12/16/2022] Open
Abstract
The combination of oceanographic barriers and habitat heterogeneity are known to reduce connectivity and leave specific genetic signatures in the demographic history of marine species. However, barriers to gene flow in the marine environment are almost never impermeable which inevitably allows secondary contact to occur. In this study, eight sampling sites (five along the South African coastline, one each in Angola, Senegal and Portugal) were chosen to examine the population genetic structure and phylogeographic history of the cosmopolitan bluefish (Pomatomus saltatrix), distributed across a large South-east Atlantic upwelling zone. Molecular analyses were applied to mtDNA cytochrome b, intron AM2B1 and 15 microsatellite loci. We detected uncharacteristically high genetic differentiation (FST 0.15-0.20; P<0.001) between the fish sampled from South Africa and the other sites, strongly influenced by five outlier microsatellite loci located in conserved intergenic regions. In addition, differentiation among the remaining East Atlantic sites was detected, although mtDNA indicated past isolation with subsequent secondary contact between these East Atlantic populations. We further identified secondary contact, with unidirectional gene flow from South Africa to Angola. The directional contact is likely explained by a combination of the northward flowing offshore current and endogenous incompatibilities restricting integration of certain regions of the genome and limiting gene flow to the south. The results confirm that the dynamic system associated with the Benguela current upwelling zone influences species distributions and population processes in the South-east Atlantic.
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Affiliation(s)
- K Reid
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - T B Hoareau
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - J E Graves
- Department of Fisheries Science, Virginia Institute of Marine Science, College of William & Mary, Williamsburg, VA, USA
| | - W M Potts
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - S M R Dos Santos
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - A W Klopper
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - P Bloomer
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
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Investigating Morphospace Occupation in Multi-Scale Ecological and Evolutionary Data Using Regression Tree: Case Studies and Perspectives. Evol Biol 2016. [DOI: 10.1007/s11692-016-9386-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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38
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Vaughan GO, Burt JA. The changing dynamics of coral reef science in Arabia. MARINE POLLUTION BULLETIN 2016; 105:441-458. [PMID: 26621575 DOI: 10.1016/j.marpolbul.2015.10.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/17/2015] [Accepted: 10/22/2015] [Indexed: 06/05/2023]
Abstract
Six percent of the world's coral reefs occur around the Arabian Peninsula, providing a valuable ecological, economic and scientific resource for the nations bordering its shores. We provide the first region-wide assessment of the current status and historical trends in coral reef research, focusing on research in the Red Sea, Arabian Sea, and Arabian Gulf. In total, 633 regional reef publications have been produced since the 1930s, covering a wide variety of themes and taxa. Our results show a great deal of commonality in regional reef research, but also highlight important differences in research among the various seas as well as knowledge gaps that represent opportunities for future research. A regionally-integrated approach to future research is essential. There is a growing need for large-scale research to guide management of reefs and their stressors, as these operate at much larger scales than the national borders within which most research currently occurs.
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Affiliation(s)
- Grace O Vaughan
- Center for Genomics and Systems Biology, New York University - Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
| | - John A Burt
- Center for Genomics and Systems Biology, New York University - Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
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Coleman RR, Eble JA, DiBattista JD, Rocha LA, Randall JE, Berumen ML, Bowen BW. Regal phylogeography: Range-wide survey of the marine angelfish Pygoplites diacanthus reveals evolutionary partitions between the Red Sea, Indian Ocean, and Pacific Ocean. Mol Phylogenet Evol 2016; 100:243-253. [PMID: 27068838 DOI: 10.1016/j.ympev.2016.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 11/27/2022]
Abstract
The regal angelfish (Pygoplites diacanthus; family Pomacanthidae) occurs on reefs from the Red Sea to the central Pacific, with an Indian Ocean/Rea Sea color morph distinct from a Pacific Ocean morph. To assess population differentiation and evaluate the possibility of cryptic evolutionary partitions in this monotypic genus, we surveyed mtDNA cytochrome b and two nuclear introns (S7 and RAG2) in 547 individuals from 15 locations. Phylogeographic analyses revealed four mtDNA lineages (d=0.006-0.015) corresponding to the Pacific Ocean, the Red Sea, and two admixed lineages in the Indian Ocean, a pattern consistent with known biogeographic barriers. Christmas Island in the eastern Indian Ocean had both Indian and Pacific lineages. Both S7 and RAG2 showed strong population-level differentiation between the Red Sea, Indian Ocean, and Pacific Ocean (ΦST=0.066-0.512). The only consistent population sub-structure within these three regions was at the Society Islands (French Polynesia), where surrounding oceanographic conditions may reinforce isolation. Coalescence analyses indicate the Pacific (1.7Ma) as the oldest extant lineage followed by the Red Sea lineage (1.4Ma). Results from a median-joining network suggest radiations of two lineages from the Red Sea that currently occupy the Indian Ocean (0.7-0.9Ma). Persistence of a Red Sea lineage through Pleistocene glacial cycles suggests a long-term refuge in this region. The affiliation of Pacific and Red Sea populations, apparent in cytochrome b and S7 (but equivocal in RAG2) raises the hypothesis that the Indian Ocean was recolonized from the Red Sea, possibly more than once. Assessing the genetic architecture of this widespread monotypic genus reveals cryptic evolutionary diversity that merits subspecific recognition. We recommend P.d. diacanthus and P.d. flavescens for the Pacific and Indian Ocean/Red Sea forms.
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Affiliation(s)
- Richard R Coleman
- Hawai'i Institute of Marine Biology, University of Hawai'i, PO Box 1346, Kāne'ohe, HI 96744, USA; Department of Biology, University of Hawai'i, Mānoa, 2500 Campus Rd, Honolulu, HI 96822, USA.
| | - Jeffrey A Eble
- University of West Florida, 11000 University Pkwy, Pensacola, FL 32514, USA
| | - Joseph D DiBattista
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia; Department of Environment and Agriculture, Curtin University, PO Box U1987, Perth, WA 6845, Australia
| | - Luiz A Rocha
- Section of Ichthyology, California Academy of Sciences, 55 Music Concourse Dr, San Francisco, CA 94118, USA
| | - John E Randall
- Bernice Pauahi Bishop Museum, 1525 Bernice St, Honolulu, HI 96817, USA
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, PO Box 1346, Kāne'ohe, HI 96744, USA
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Comparative phylogeography of the western Indian Ocean reef fauna. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2016. [DOI: 10.1016/j.actao.2015.10.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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The historical biogeography of groupers: Clade diversification patterns and processes. Mol Phylogenet Evol 2016; 100:21-30. [PMID: 26908372 DOI: 10.1016/j.ympev.2016.02.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 02/12/2016] [Accepted: 02/16/2016] [Indexed: 11/20/2022]
Abstract
Groupers (family Epinephelidae) are a clade of species-rich, biologically diverse reef fishes. Given their ecological variability and widespread distribution across ocean basins, it is important to scrutinize their evolutionary history that underlies present day distributions. This study investigated the patterns and processes by which grouper biodiversity has been generated and what factors have influenced their present day distributions. We reconstructed a robust, time-calibrated molecular phylogeny of Epinephelidae with comprehensive (∼87%) species sampling, whereby diversification rates were estimated and ancestral ranges were reconstructed. Our results indicate that groupers originated in what is now the East Atlantic during the mid-Eocene and diverged successively to form six strongly supported main clades. These clades differ in age (late Oligocene to mid-Miocene), geographic origin (West Atlantic to West Indo-Pacific) and temporal-spatial diversification pattern, ranging from constant rates of diversification to episodes of rapid radiation. Overall, divergence within certain biogeographic regions was most prevalent in groupers, while vicariant divergences were more common in Tropical Atlantic and East Pacific groupers. Our findings reveal that both biological and geographical factors have driven grouper diversification. They also underscore the importance of scrutinizing group-specific patterns to better understand reef fish evolution.
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White KN, Reimer JD, Lorion J. Preliminary analyses reveal strong genetic structure in populations of Leucothoe vulgaris (Crustacea: Amphipoda: Leucothoidae) from Okinawa, Japan. SYST BIODIVERS 2015. [DOI: 10.1080/14772000.2015.1078856] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Biology, Chemistry & Marine Sciences, Faculty of Science & Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, Japan
| | - Julien Lorion
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Biology, Chemistry & Marine Sciences, Faculty of Science & Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, Japan
- Palau International Coral Reef Center, 1M-Dock Road, Koror 96940, Republic of Palau
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43
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Dohna TA, Timm J, Hamid L, Kochzius M. Limited connectivity and a phylogeographic break characterize populations of the pink anemonefish, Amphiprion perideraion, in the Indo-Malay Archipelago: inferences from a mitochondrial and microsatellite loci. Ecol Evol 2015; 5:1717-33. [PMID: 25937914 PMCID: PMC4409419 DOI: 10.1002/ece3.1455] [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: 10/19/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 11/25/2022] Open
Abstract
To enhance the understanding of larval dispersal in marine organisms, species with a sedentary adult stage and a pelagic larval phase of known duration constitute ideal candidates, because inferences can be made about the role of larval dispersal in population connectivity. Members of the immensely diverse marine fauna of the Indo-Malay Archipelago are of particular importance in this respect, as biodiversity conservation is becoming a large concern in this region. In this study, the genetic population structure of the pink anemonefish, Amphiprion perideraion, is analyzed by applying 10 microsatellite loci as well as sequences of the mitochondrial control region to also allow for a direct comparison of marker-derived results. Both marker systems detected a strong overall genetic structure (ΦST = 0.096, P < 0.0001; mean D est = 0.17; F ST = 0.015, P < 0.0001) and best supported regional groupings (ΦCT = 0.199 P < 0.0001; F CT = 0.018, P < 0.001) that suggested a differentiation of the Java Sea population from the rest of the archipelago. Differentiation of a New Guinea group was confirmed by both markers, but disagreed over the affinity of populations from west New Guinea. Mitochondrial data suggest higher connectivity among populations with fewer signals of regional substructure than microsatellite data. Considering the homogenizing effect of only a few migrants per generation on genetic differentiation between populations, marker-specific results have important implications for conservation efforts concerning this and similar species.
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Affiliation(s)
- Tina A Dohna
- Biotechnology and Molecular Genetics, UFT, University of BremenBremen, 28359, Germany
| | - Janne Timm
- Biotechnology and Molecular Genetics, UFT, University of BremenBremen, 28359, Germany
| | - Lemia Hamid
- Biotechnology and Molecular Genetics, UFT, University of BremenBremen, 28359, Germany
| | - Marc Kochzius
- Marine Biology, Vrije Universiteit BrusselBrussel, Belgium
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Toms JA, Compton JS, Smale M, von der Heyden S. Variation in palaeo-shorelines explains contemporary population genetic patterns of rocky shore species. Biol Lett 2015; 10:rsbl.2014.0330. [PMID: 24966206 DOI: 10.1098/rsbl.2014.0330] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Processes driving and maintaining disjunct genetic populations in marine systems are poorly understood, owing to a lack of evidence of hard barriers that could have shaped patterns of extant population structure. Here, we map two genetically divergent lineages of an obligate rocky shore fish, Clinus cottoides, and model sea-level change during the last 110 000 years to provide the first evidence of a vicariant event along the southern coastline of Africa. Results reveal that lowered sea levels during glacial periods drastically reduced rocky intertidal habitat, which may have isolated populations in two refugia for at least 40 000 years. Contemporary coastal dynamics and oceanography explain secondary contact between lineages. This scenario provides an explanation for the origin of population genetic breaks despite a lack of obvious present-day geographical barriers and highlights the need for including palaeo-oceanography in unravelling extant population patterns.
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Affiliation(s)
- Jessica A Toms
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag XI, Matieland 7602, South Africa
| | - John S Compton
- Department of Geological Sciences, University of Cape Town, Rondebosch 7701, South Africa
| | - Malcolm Smale
- Department of Zoology, Nelson Mandela Metropolitan University, PO Box 77000, Port Elizabeth, South Africa
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag XI, Matieland 7602, South Africa
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Tenggardjaja KA, Bowen BW, Bernardi G. Vertical and horizontal genetic connectivity in Chromis verater, an endemic damselfish found on shallow and mesophotic reefs in the Hawaiian Archipelago and adjacent Johnston Atoll. PLoS One 2014; 9:e115493. [PMID: 25517964 PMCID: PMC4269425 DOI: 10.1371/journal.pone.0115493] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/13/2014] [Indexed: 11/18/2022] Open
Abstract
Understanding vertical and horizontal connectivity is a major priority in research on mesophotic coral ecosystems (30-150 m). However, horizontal connectivity has been the focus of few studies, and data on vertical connectivity are limited to sessile benthic mesophotic organisms. Here we present patterns of vertical and horizontal connectivity in the Hawaiian Islands-Johnston Atoll endemic threespot damselfish, Chromis verater, based on 319 shallow specimens and 153 deep specimens. The mtDNA markers cytochrome b and control region were sequenced to analyze genetic structure: 1) between shallow (< 30 m) and mesophotic (30-150 m) populations and 2) across the species' geographic range. Additionally, the nuclear markers rhodopsin and internal transcribed spacer 2 of ribosomal DNA were sequenced to assess connectivity between shallow and mesophotic populations. There was no significant genetic differentiation by depth, indicating high levels of vertical connectivity between shallow and deep aggregates of C. verater. Consequently, shallow and deep samples were combined by location for analyses of horizontal connectivity. We detected low but significant population structure across the Hawaiian Archipelago (overall cytochrome b: ΦST = 0.009, P = 0.020; control region: ΦST = 0.012, P = 0.009) and a larger break between the archipelago and Johnston Atoll (cytochrome b: ΦST = 0.068, P < 0.001; control region: ΦST = 0.116, P < 0.001). The population structure within the archipelago was driven by samples from the island of Hawaii at the southeast end of the chain and Lisianski in the middle of the archipelago. The lack of vertical genetic structure supports the refugia hypothesis that deep reefs may constitute a population reservoir for species depleted in shallow reef habitats. These findings represent the first connectivity study on a mobile organism that spans shallow and mesophotic depths and provide a reference point for future connectivity studies on mesophotic fishes.
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Affiliation(s)
- Kimberly A. Tenggardjaja
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
| | - Brian W. Bowen
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, Hawaii, United States of America
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
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46
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Liu SYV, Chang FT, Borsa P, Chen WJ, Dai CF. Phylogeography of the humbug damselfish,Dascyllus aruanus(Linnaeus, 1758): evidence of Indo-Pacific vicariance and genetic differentiation of peripheral populations. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12378] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shang-Yin Vanson Liu
- Institute of Oceanography; National Taiwan University; 1 Roosevelt Road Sec. 4 Taipei 10617 Taiwan
- Department of Ecology and Evolutionary Biology; University of California; Charles E. Young Drive Los Angeles CA 90095 USA
| | - Feng-Ting Chang
- Institute of Oceanography; National Taiwan University; 1 Roosevelt Road Sec. 4 Taipei 10617 Taiwan
| | - Philippe Borsa
- Institut de recherche pour le développement c/o Indonesian Biodiversity Center; Jl Raya Sesetan Denpasar 80228 Indonesia
| | - Wei-Jen Chen
- Institute of Oceanography; National Taiwan University; 1 Roosevelt Road Sec. 4 Taipei 10617 Taiwan
| | - Chang-Feng Dai
- Institute of Oceanography; National Taiwan University; 1 Roosevelt Road Sec. 4 Taipei 10617 Taiwan
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47
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Ukuwela KDB, de Silva A, Mumpuni, Fry BG, Sanders KL. Multilocus phylogeography of the sea snakeHydrophis curtusreveals historical vicariance and cryptic lineage diversity. ZOOL SCR 2014. [DOI: 10.1111/zsc.12070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kanishka D. B. Ukuwela
- School of Earth and Environmental Sciences; University of Adelaide; Darling Building Adelaide SA 5005 Australia
| | - Anslem de Silva
- Amphibia and Reptile research Organization of Sri Lanka; 15/1, Dolosbage Rd. Gampola Sri Lanka
| | - Mumpuni
- Museum of Zoology Bogor; Puslit Biology-LIPI; Cibinong Indonesia
| | - Bryan G. Fry
- Venom Evolution Laboratory; School of Biological Sciences; University of Queensland; Brisbane QLD 4072 Australia
| | - Kate L. Sanders
- School of Earth and Environmental Sciences; University of Adelaide; Darling Building Adelaide SA 5005 Australia
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48
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Andrews KR, Moriwake VN, Wilcox C, Grau EG, Kelley C, Pyle RL, Bowen BW. Phylogeographic analyses of submesophotic snappers Etelis coruscans and Etelis "marshi" (family Lutjanidae) reveal concordant genetic structure across the Hawaiian Archipelago. PLoS One 2014; 9:e91665. [PMID: 24722193 PMCID: PMC3982960 DOI: 10.1371/journal.pone.0091665] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 02/13/2014] [Indexed: 11/18/2022] Open
Abstract
The Hawaiian Archipelago has become a natural laboratory for understanding genetic connectivity in marine organisms as a result of the large number of population genetics studies that have been conducted across this island chain for a wide taxonomic range of organisms. However, population genetic studies have been conducted for only two species occurring in the mesophotic or submesophotic zones (30+m) in this archipelago. To gain a greater understanding of genetic connectivity in these deepwater habitats, we investigated the genetic structure of two submesophotic fish species (occurring ∼200-360 m) in this archipelago. We surveyed 16 locations across the archipelago for submesophotic snappers Etelis coruscans (N = 787) and E. "marshi" (formerly E. carbunculus; N = 770) with 436-490 bp of mtDNA cytochrome b and 10-11 microsatellite loci. Phylogeographic analyses reveal no geographic structuring of mtDNA lineages and recent coalescence times that are typical of shallow reef fauna. Population genetic analyses reveal no overall structure across most of the archipelago, a pattern also typical of dispersive shallow fishes. However some sites in the mid-archipelago (Raita Bank to French Frigate Shoals) had significant population differentiation. This pattern of no structure between ends of the Hawaiian range, and significant structure in the middle, was previously observed in a submesophotic snapper (Pristipomoides filamentosus) and a submesophotic grouper (Hyporthodus quernus). Three of these four species also have elevated genetic diversity in the mid-archipelago. Biophysical larval dispersal models from previous studies indicate that this elevated diversity may result from larval supplement from Johnston Atoll, ∼800 km southwest of Hawaii. In this case the boundaries of stocks for fishery management cannot be defined simply in terms of geography, and fishery management in Hawaii may need to incorporate external larval supply into management plans.
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Affiliation(s)
- Kimberly R. Andrews
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kane'ohe, Hawaii, United States of America
- School of Biological & Biomedical Sciences, Durham University, South Road, United Kingdom
| | - Virginia N. Moriwake
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kane'ohe, Hawaii, United States of America
- Department of Oceanography, University of Hawai'i, Honolulu, Hawaii, United States of America
| | - Christie Wilcox
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kane'ohe, Hawaii, United States of America
- Cell and Molecular Biology Graduate Program, University of Hawai'i, Honolulu, Hawaii, United States of America
| | - E. Gordon Grau
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kane'ohe, Hawaii, United States of America
| | - Christopher Kelley
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kane'ohe, Hawaii, United States of America
- Hawai'i Undersea Research Lab, University of Hawai'i, Honolulu, Hawaii, United States of America
| | - Richard L. Pyle
- Bernice P. Bishop Museum, Honolulu, Hawaii, United States of America
| | - Brian W. Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kane'ohe, Hawaii, United States of America
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Cowman PF, Bellwood DR. Vicariance across major marine biogeographic barriers: temporal concordance and the relative intensity of hard versus soft barriers. Proc Biol Sci 2013; 280:20131541. [PMID: 23945690 PMCID: PMC3757981 DOI: 10.1098/rspb.2013.1541] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/15/2013] [Indexed: 11/12/2022] Open
Abstract
The marine tropics contain five major biogeographic regions (East Pacific, Atlantic, Indian Ocean, Indo-Australian Archipelago (IAA) and Central Pacific). These regions are separated by both hard and soft barriers. Reconstructing ancestral vicariance, we evaluate the extent of temporal concordance in vicariance events across three major barriers (Terminal Tethyan Event (TTE), Isthmus of Panama (IOP), East Pacific Barrier, EPB) and two incomplete barriers (either side of the IAA) for the Labridae, Pomacentridae and Chaetodontidae. We found a marked lack of temporal congruence within and among the three fish families in vicariance events associated with the EPB, TTE and IOP. Vicariance across hard barriers separating the Atlantic and Indo-Pacific (TTE, IOP) is temporally diffuse, with many vicariance events preceding barrier formation. In marked contrast, soft barriers either side of the IAA hotspot support tightly concordant vicariance events (2.5 Myr on Indian Ocean side; 6 Myr on Central Pacific side). Temporal concordance in vicariance points to large-scale temporally restricted gene flow during the Late Miocene and Pliocene. Despite different and often complex histories, both hard and soft barriers have comparably strong effects on the evolution of coral reef taxa.
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Affiliation(s)
- Peter F Cowman
- School of Marine and Tropical Biology, and Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia.
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50
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Matias AMA, Anticamara JA, Quilang JP. High gene flow in reef fishes and its implications for ad-hoc no-take marine reserves. MITOCHONDRIAL DNA 2013; 24:584-595. [PMID: 23530464 DOI: 10.3109/19401736.2013.772147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Integration of genetic connectivity information in effective marine reserve (MR) design is important in sustaining marine biodiversity. Here, genetic connectivity based on mitochondrial DNA (mtDNA) of three reef fish species, namely Epinephelus merra (n = 67; 32 from Bolinao, 14 from Alaminos, and 21 from Masinloc), Parupeneus multifasciatus (n = 23; 12 from Bolinao and 11 from Masinloc), and Odonus niger (n = 35; 21 from Mabini and 14 from Tingloy), sampled across western Luzon, Philippines, was inferred by assessing their genetic diversity, population genetic structure, and historical demography. The results show high haplotype and nucleotide diversity in the three species. Tests for population structure indicate high gene flow and no spatial genetic structuring for the three species. Mismatch analyses suggest unimodal distribution for E. merra and P. multifasciatus, but bimodal distribution for O. niger. Even with differences in mismatch distributions, all the three species exhibit low raggedness index indicating demographic population expansion. The bimodal distribution of O. niger could be attributed to the mixing of two isolated populations. High gene flow between sampling locations implies genetic exchanges and connectivity between many small MRs and fishing grounds in western Luzon, Philippines, at a scale similar to our study. This research is among the first few to elucidate the high genetic connectivity of reef fish communities across the Philippines (here western Luzon), but it also calls for more support (i.e. government and academia) for genetic research that aims to (1) understand the maintenance of megadiversity of the country and (2) search for effective biodiversity conservation options for the coral reefs.
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Affiliation(s)
- Ambrocio Melvin A Matias
- Natural Sciences Research Institute, University of the Philippines, Diliman , 1101 Quezon City , Philippines
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