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Liang Y, Xian L, Pan J, Zhu K, Guo H, Liu B, Zhang N, Ou-Yang Y, Zhang Q, Zhang D. De Novo Genome Assembly of the Whitespot Parrotfish ( Scarus forsteni): A Valuable Scaridae Genomic Resource. Genes (Basel) 2024; 15:249. [PMID: 38397238 PMCID: PMC10888354 DOI: 10.3390/genes15020249] [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: 12/26/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Scarus forsteni, a whitespot parrotfish from the Scaridae family, is a herbivorous fish inhabiting coral reef ecosystems. The deterioration of coral reefs has highly affected the habitats of the parrotfish. The decline in genetic diversity of parrotfish emphasizes the critical importance of conserving their genetic variability to ensure the resilience and sustainability of marine ecosystems for future generations. In this study, a genome of S. forsteni was assembled de novo through using Illumina and Nanopore sequencing. The 1.71-Gb genome of S. forsteni, was assembled into 544 contigs (assembly level: contig). It exhibited an N50 length of 17.97 Mb and a GC content percentage of 39.32%. Our BUSCO analysis revealed that the complete protein of the S. forsteni genome had 98.10% integrity. Combined with structure annotation data, 34,140 (74.81%) genes were functionally annotated out of 45,638 predicted protein-coding genes. Upon comparing the genome size and TE content of teleost fishes, a roughly linear relationship was observed between these two parameters. However, TE content is not a decisive factor in determining the genome size of S. forsteni. Population history analysis results indicate that S. forsteni experienced two major population expansions, both of which occurred before the last interglacial period. In addition, through a comparative genomic analysis of the evolutionary relationship of other species, it was found that S. forsteni had the closest relationship with Cheilinus undulatus, another member of the Labridae family. Our expansion and contraction analysis of the gene family showed that the expansion genes were mainly associated with immune diseases, organismal systems, and cellular processes. At the same time, cell transcription and translation, sex hormone regulation, and other related pathways were also more prominent in the positive selection genes. The genomic sequence of S. forsteni offers valuable resources for future investigations on the conservation, evolution, and behavior of fish species.
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Affiliation(s)
- Yu Liang
- Guangxi Marine Microbial Resources Industrialization Engineering Technology Research Center, Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, 158 University Road, Nanning 530008, China
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Lin Xian
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Jinmin Pan
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Kecheng Zhu
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Huayang Guo
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Baosuo Liu
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Nan Zhang
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Yan Ou-Yang
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Qin Zhang
- Guangxi Marine Microbial Resources Industrialization Engineering Technology Research Center, Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, 158 University Road, Nanning 530008, China
| | - Dianchang Zhang
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
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Carlon DB, Robertson DR, Barron RL, Choat JH, Anderson DJ, Schwartz SA, Sánchez-Ortiz CA. The origin of the parrotfish species Scarus compressus in the Tropical Eastern Pacific: region-wide hybridization between ancient species pairs. BMC Ecol Evol 2021; 21:7. [PMID: 33514314 PMCID: PMC7853319 DOI: 10.1186/s12862-020-01731-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/07/2020] [Indexed: 12/04/2022] Open
Abstract
Background In the Tropical Eastern Pacific (TEP), four species of parrotfishes with complex phylogeographic histories co-occur in sympatry on rocky reefs from Baja California to Ecuador: Scarus compressus, S. ghobban, S. perrico, and S. rubroviolaceus. The most divergent, S. perrico, separated from a Central Indo-Pacific ancestor in the late Miocene (6.6 Ma). We tested the hypothesis that S. compressus was the result of ongoing hybridization among the other three species by sequencing four nuclear markers and a mitochondrial locus in samples spanning 2/3 of the latitudinal extent of the TEP. Results A Structure model indicated that K = 3 fit the nuclear data and that S. compressus individuals had admixed genomes. Our data could correctly detect and assign pure adults and F1 hybrids with > 0.90 probability, and correct assignment of F2s was also high in some cases. NewHybrids models revealed that 89.8% (n = 59) of the S. compressus samples were F1 hybrids between either S. perrico × S. ghobban or S. perrico × S. rubroviolaceus. Similarly, the most recently diverged S. ghobban and S. rubroviolaceus were hybridizing in small numbers, with half of the admixed individuals assigned to F1 hybrids and the remainder likely > F1 hybrids. We observed strong mito-nuclear discordance in all hybrid pairs. Migrate models favored gene flow between S. perrico and S. ghobban, but not other species pairs. Conclusions Mating between divergent species is giving rise to a region-wide, multispecies hybrid complex, characterized by a high frequency of parental and F1 genotypes but a low frequency of > F1 hybrids. Trimodal structure, and evidence for fertility of both male and female F1 hybrids, suggest that fitness declines sharply in later generation hybrids. In contrast, the hybrid population of the two more recently diverged species had similar frequencies of F1 and > F1 hybrids, suggesting accelerating post-mating incompatibility with time. Mitochondrial genotypes in hybrids suggest that indiscriminate mating by male S. perrico is driving pre-zygotic breakdown, which may reflect isolation of this endemic species for millions of years resulting in weak selection for conspecific mate recognition. Despite overlapping habitat use and high rates of hybridization, species boundaries are maintained by a combination of pre- and post-mating processes in this complex.
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Affiliation(s)
- David B Carlon
- Schiller Coastal Studies Centre and Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME, 04011, USA.
| | | | - Robert L Barron
- Schiller Coastal Studies Centre and Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME, 04011, USA
| | - John Howard Choat
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - David J Anderson
- Schiller Coastal Studies Centre and Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME, 04011, USA
| | - Sonja A Schwartz
- Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, 94720, USA
| | - Carlos A Sánchez-Ortiz
- Departamento de Biología Marina, Universidad Autónoma de Baja California Sur, CP 23081, La Paz, Baja California Sur, México
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Cryptic ecological and geographic diversification in coral-associated nudibranchs. Mol Phylogenet Evol 2019; 144:106698. [PMID: 31812568 DOI: 10.1016/j.ympev.2019.106698] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/03/2019] [Accepted: 11/30/2019] [Indexed: 12/18/2022]
Abstract
Coral reefs are among the most biologically diverse ecosystems of the world, yet little is known about the processes creating and maintaining their diversity. Ecologically, corallivory in nudibranchs resembles phytophagy in insects- a process that for decades has served as a model for ecological speciation via host shifting. This study uses extensive field collections, DNA sequencing, and phylogenetic analyses to reconstruct the evolutionary history of coral-associated nudibranchs and assess the relative roles that host shifting and geography may have played in their diversification. We find that the number of species is three times higher than the number previously known to science, with evidence for both allopatric and ecological divergence through host shifting and host specialization. Results contribute to growing support for the importance of ecological diversification in marine environments and provide evidence for new species in the genus Tenellia.
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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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5
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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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Taylor BM, Pardee C. Growth and maturation of the redlip parrotfish Scarus rubroviolaceus. JOURNAL OF FISH BIOLOGY 2017; 90:2452-2461. [PMID: 28382708 DOI: 10.1111/jfb.13309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/06/2017] [Indexed: 06/07/2023]
Abstract
This study presents age-based life-history information for the red lip parrotfish Scarus rubroviolaceus based on a 5 year sampling programme from the commercial fishery of American Samoa. Females reached sexual maturity at 31·9 cm fork length (LF ) and 2·6 years and sex change occurred at 42·3 cm LF , although not all females change sex through their ontogeny. The maximum observed age was 14 years and c. 65% of the fishery harvest was above the median LF at sex change.
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Affiliation(s)
- B M Taylor
- Joint Institute for Marine and Atmospheric Research, University of Hawai'i, Honolulu, HI, 96822, U.S.A
- NOAA Fisheries, Pacific Islands Fisheries Science Center, Honolulu, HI, 96818, U.S.A
| | - C Pardee
- Joint Institute for Marine and Atmospheric Research, University of Hawai'i, Honolulu, HI, 96822, U.S.A
- NOAA Fisheries, Pacific Islands Fisheries Science Center, Honolulu, HI, 96818, U.S.A
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Kendrick GA, Orth RJ, Statton J, Hovey R, Ruiz Montoya L, Lowe RJ, Krauss SL, Sinclair EA. Demographic and genetic connectivity: the role and consequences of reproduction, dispersal and recruitment in seagrasses. Biol Rev Camb Philos Soc 2016; 92:921-938. [DOI: 10.1111/brv.12261] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 02/12/2016] [Accepted: 02/16/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Gary A. Kendrick
- School of Plant Biology, Faculty of Science; University of Western Australia; Crawley Western Australia 6009 Australia
- UWA Oceans Institute; University of Western Australia; Crawley Western Australia 6009 Australia
| | - Robert J. Orth
- Virginia Institute of Marine Science; College of William and Mary; Gloucester Point VA 23062 U.S.A
| | - John Statton
- School of Plant Biology, Faculty of Science; University of Western Australia; Crawley Western Australia 6009 Australia
- UWA Oceans Institute; University of Western Australia; Crawley Western Australia 6009 Australia
| | - Renae Hovey
- School of Plant Biology, Faculty of Science; University of Western Australia; Crawley Western Australia 6009 Australia
- UWA Oceans Institute; University of Western Australia; Crawley Western Australia 6009 Australia
| | - Leonardo Ruiz Montoya
- School of Plant Biology, Faculty of Science; University of Western Australia; Crawley Western Australia 6009 Australia
- UWA Oceans Institute; University of Western Australia; Crawley Western Australia 6009 Australia
| | - Ryan J. Lowe
- UWA Oceans Institute; University of Western Australia; Crawley Western Australia 6009 Australia
- School of Earth and Environment; University of Western Australia; Crawley Western Australia 6009 Australia
- ARC Centre of Excellence for Coral Reef Studies; James Cook University Townsville; Queensland 4811 Australia
| | - Siegfried L. Krauss
- School of Plant Biology, Faculty of Science; University of Western Australia; Crawley Western Australia 6009 Australia
- Kings Park and Botanic Garden; West Perth Western Australia 6005 Australia
| | - Elizabeth A. Sinclair
- School of Plant Biology, Faculty of Science; University of Western Australia; Crawley Western Australia 6009 Australia
- UWA Oceans Institute; University of Western Australia; Crawley Western Australia 6009 Australia
- Kings Park and Botanic Garden; West Perth Western Australia 6005 Australia
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8
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Dyer RJ. Population Graphs and Landscape Genetics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054150] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rodney J. Dyer
- Department of Biology and Center for Environmental Studies, Virginia Commonwealth University, Richmond, Virginia 23284-2012;
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9
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The application of genomics to inform conservation of a functionally important reef fish (Scarus niger) in the Philippines. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0776-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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10
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Adibah A, Ng W, Tan S. The Malay Peninsula as a barrier to gene flow in an Asian horseshoe crab species, Carcinoscorpius rotundicauda Latreille. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.04.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Puckridge M, Last PR, Andreakis N. The role of peripheral endemism and habitat associations in the evolution of the Indo-West Pacific tuskfishes (Labridae: Choerodon). Mol Phylogenet Evol 2014; 84:64-72. [PMID: 25463751 DOI: 10.1016/j.ympev.2014.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 10/29/2014] [Accepted: 11/10/2014] [Indexed: 11/25/2022]
Abstract
The unrivalled level of biodiversity across the tropical Indo-Australian Archipelago (IAA) has been the subject of wide debate. Attempts to understand its origins have focussed on the timing of speciation, rates of diversification and the directionality of colonisation across geographical and climatic gradients in an array of marine groups. We investigate origins and evolution in the Choerodon tuskfishes, a group of labrids whose centre of diversity coincides with this region. Mitochondrial (COI, 16S) and nuclear (RAG2, Tmo4c4) molecular phylogenies and biogeographic analyses, coupled with molecular clock dating, were inferred from 19 of the 23 valid Choerodon species. Two additional, undescribed Choerodon species were also included, showing reciprocal monophyly in both genomes, confirming their species level status. Choerodon diverged from their ancestral sister group, the Odacines, at the onset of the Miocene, coinciding with the collision of the Australian and Eurasian Plates when extensive areas of shallow-water habitat formed. Despite subsequent evolutionary patterns being partially obscured by overlapping distribution ranges between many species and a lack of clear evidence for climatically driven lineage divergences, our data support an evolutionary scenario of peripheral endemics budding from once widespread populations across this biodiversity hotspot. Interestingly, these peripheral endemics tend to occupy more specialised reef or non-reef habitats whereas widespread groups appear to generally take advantage of both reef and non-reef environments. Our results are discussed in light of the most accredited hypotheses proposed to explain species richness in the IAA, with some support for processes such as centrifugal speciation.
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Affiliation(s)
- Melody Puckridge
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart, TAS 7001, Australia; CSIRO Marine and Atmospheric Research, Wealth from Oceans Flagship, Castray Esplanade, Hobart, TAS 7000, Australia.
| | - Peter R Last
- CSIRO Marine and Atmospheric Research, Wealth from Oceans Flagship, Castray Esplanade, Hobart, TAS 7000, Australia
| | - Nikos Andreakis
- Australian Institute of Marine Science, PMB No. 3, Townsville, QLD 4810, Australia
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12
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Closely related and sympatric but not all the same: genetic variation of Indo-West Pacific Rhizophora mangroves across the Malay Peninsula. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0647-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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13
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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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14
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Weese DA, Fujita Y, Santos SR. Multiple colonizations lead to cryptic biodiversity in an island ecosystem: comparative phylogeography of anchialine shrimp species in the Ryukyu Archipelago, Japan. THE BIOLOGICAL BULLETIN 2013; 225:24-41. [PMID: 24088794 DOI: 10.1086/bblv225n1p24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Archipelagos of the Indo-West Pacific are considered to be among the richest in the world in biodiversity, and phylogeographic studies generally support either the center of origin or the center of accumulation hypothesis to explain this pattern. To differentiate between these competing hypotheses for organisms from the Indo-West Pacific anchialine ecosystem, defined as coastal bodies of mixohaline water fluctuating with the tides but having no direct oceanic connections, we investigated the genetic variation, population structure, and evolutionary history of three caridean shrimp species (Antecaridina lauensis, Halocaridinides trigonophthalma, and Metabetaeus minutus) in the Ryukyu Archipelago, Japan. We used two mitochondrial genes--cytochrome c oxidase subunit I (COI) and large ribosomal subunit (16S-rDNA)--complemented with genetic examination of available specimens from the same or closely related species from the Indian and Pacific Oceans. In the Ryukyus, each species encompassed 2-3 divergent (9.52%-19.2% COI p-distance) lineages, each having significant population structure and varying geographic distributions. Phylogenetically, the A. lauensis and M. minutus lineages in the Ryukyus were more closely related to ones from outside the archipelago than to one another. These results, when interpreted in the context of Pacific oceanographic currents and geologic history of the Ryukyus, imply multiple colonizations of the archipelago by the three species, consistent with the center of accumulation hypothesis. While this study contributes toward understanding the biodiversity, ecology, and evolution of organisms in the Ryukyus and the Indo-West Pacific, it also has potential utility in establishing conservation strategies for anchialine fauna of the Pacific Basin in general.
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Affiliation(s)
- David A Weese
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, Alabama 36849
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15
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Bowen BW, Rocha LA, Toonen RJ, Karl SA. The origins of tropical marine biodiversity. Trends Ecol Evol 2013; 28:359-66. [DOI: 10.1016/j.tree.2013.01.018] [Citation(s) in RCA: 255] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 01/30/2013] [Accepted: 01/30/2013] [Indexed: 10/27/2022]
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16
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Horne JB, van Herwerden L. Long-term panmixia in a cosmopolitan Indo-Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species. J Evol Biol 2013; 26:783-99. [DOI: 10.1111/jeb.12092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 11/23/2012] [Indexed: 11/26/2022]
Affiliation(s)
- J. B. Horne
- Molecular Ecology and Evolution Laboratory; School of Tropical and Marine Biology; James Cook University; Townsville Qld Australia
- Centre of Marine Sciences; University of Algarve; Faro Portugal
| | - L. van Herwerden
- Molecular Ecology and Evolution Laboratory; School of Tropical and Marine Biology; James Cook University; Townsville Qld Australia
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Puckridge M, Last PR, White WT, Andreakis N. Phylogeography of the Indo-West Pacific maskrays (Dasyatidae, Neotrygon): a complex example of chondrichthyan radiation in the Cenozoic. Ecol Evol 2012; 3:217-32. [PMID: 23467194 PMCID: PMC3586632 DOI: 10.1002/ece3.448] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 11/14/2012] [Accepted: 11/15/2012] [Indexed: 12/03/2022] Open
Abstract
Maskrays of the genus Neotrygon (Dasyatidae) have dispersed widely in the Indo-West Pacific being represented largely by an assemblage of narrow-ranging coastal endemics. Phylogenetic reconstruction methods reproduced nearly identical and statistically robust topologies supporting the monophyly of the genus Neotrygon within the family Dasyatidae, the genus Taeniura being consistently basal to Neotrygon, and Dasyatis being polyphyletic to the genera Taeniurops and Pteroplatytrygon. The Neotrygon kuhlii complex, once considered to be an assemblage of color variants of the same biological species, is the most derived and widely dispersed subgroup of the genus. Mitochondrial (COI, 16S) and nuclear (RAG1) phylogenies used in synergy with molecular dating identified paleoclimatic fluctuations responsible for periods of vicariance and dispersal promoting population fragmentation and speciation in Neotrygon. Signatures of population differentiation exist in N. ningalooensis and N. annotata, yet a large-scale geological event, such as the collision between the Australian and Eurasian Plates, coupled with subsequent sea-level falls, appears to have separated a once homogeneous population of the ancestral form of N. kuhlii into southern Indian Ocean and northern Pacific taxa some 4–16 million years ago. Repeated climatic oscillations, and the subsequent establishment of land and shallow sea connections within and between Australia and parts of the Indo-Malay Archipelago, have both promoted speciation and established zones of secondary contact within the Indian and Pacific Ocean basins.
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Affiliation(s)
- Melody Puckridge
- Institute for Marine and Antarctic Studies, University of Tasmania Private Bag 129, Hobart, TAS, 7001, Australia ; Wealth from Oceans Flagship, CSIRO Marine and Atmospheric Research Castray Esplanade, Hobart, TAS, 7000, Australia
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Choat JH, klanten OS, Van Herwerden L, Robertson DR, Clements KD. Patterns and processes in the evolutionary history of parrotfishes (Family Labridae). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01959.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John. H. Choat
- School of Tropical and Marine Biology; James Cook University; Townsville QLD 4811 Australia
| | - Oya. S. klanten
- School of Tropical and Marine Biology; James Cook University; Townsville QLD 4811 Australia
- School of Medicine; The University of Sydney; Building F13 Sydney NSW 2006 Australia
| | - Lynne Van Herwerden
- School of Tropical and Marine Biology; James Cook University; Townsville QLD 4811 Australia
| | - D. Ross Robertson
- Smithsonian Tropical Research Institute; Ancon Balboa Republic of Panama
| | - Kendall D. Clements
- School of Biological Sciences; University of Auckland; Private Bag 92019 Auckland 1142 New Zealand
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Goetze E. Population differentiation in the open sea: insights from the pelagic copepod Pleuromamma xiphias. Integr Comp Biol 2012; 51:580-97. [PMID: 21940778 DOI: 10.1093/icb/icr104] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although a number of recent studies of marine holoplankton have reported significant genetic structure among populations, little is currently known about the biological and oceanographic processes that influence population connectivity in oceanic plankton. In order to examine how depth preferences influence dispersal in oceanic plankton, I characterized the genetic structure of a copepod with diel vertical migration (DVM) (Pleuromamma xiphias), throughout its global distribution, and compared these results to those expected given the interaction of this species' habitat depth with ocean circulation and bathymetry. Mitochondrial COI sequences from 651 individuals from 28 sites in the Indian, Pacific, and Atlantic Oceans revealed highly significant genetic differentiation both within and among ocean basins. Limited dispersal among distinct pelagic provinces seems to have played a major role in population differentiation in this species, with strong genetic breaks observed across known oceanographic fronts or current systems in all three ocean basins. The Indo-West Pacific (IWP) holds a highly distinct genetic population of this species that was sampled in both the western Pacific and eastern Indian Oceans. This suggests that the IWP does not act as a strong barrier to gene flow between basins, as expected, despite the relatively shallow water depth (<200 m) and vertically extensive (>400 m) diel migration of this species. A pattern of isolation by distance was observed in the Indian Ocean with genetic differentiation among samples down to spatial scales of ∼800 km, indicating that realized dispersal in P. xiphias occurs over much smaller spatial scales than in previously reported oceanic holoplankton. Given its highly regionalized population genetic structure, P. xiphias may have some capacity to adapt to local oceanographic conditions, and it should not be assumed that populations of this species in distinct pelagic biomes will respond in the same way to shared physical or climatic forcing.
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Affiliation(s)
- Erica Goetze
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
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Hodge JR, Read CI, van Herwerden L, Bellwood DR. The role of peripheral endemism in species diversification: Evidence from the coral reef fish genus Anampses (Family: Labridae). Mol Phylogenet Evol 2012; 62:653-63. [DOI: 10.1016/j.ympev.2011.11.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Revised: 11/09/2011] [Accepted: 11/09/2011] [Indexed: 10/15/2022]
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Gaither MR, Jones SA, Kelley C, Newman SJ, Sorenson L, Bowen BW. High connectivity in the deepwater snapper Pristipomoides filamentosus (Lutjanidae) across the Indo-Pacific with isolation of the Hawaiian archipelago. PLoS One 2011; 6:e28913. [PMID: 22216141 PMCID: PMC3245230 DOI: 10.1371/journal.pone.0028913] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/17/2011] [Indexed: 11/18/2022] Open
Abstract
In the tropical Indo-Pacific, most phylogeographic studies have focused on the shallow-water taxa that inhabit reefs to approximately 30 m depth. Little is known about the large predatory fishes, primarily snappers (subfamily Etelinae) and groupers (subfamily Epinephelinae) that occur at 100-400 m. These long-lived, slow-growing species support fisheries across the Indo-Pacific, yet no comprehensive genetic surveys within this group have been conducted. Here we contribute the first range-wide survey of a deepwater Indo-Pacific snapper, Pristipomoides filamentosus, with special focus on Hawai'i. We applied mtDNA cytochrome b and 11 microsatellite loci to 26 samples (N=1,222) collected across 17,000 km from Hawai'i to the western Indian Ocean. Results indicate that P. filamentosus is a highly dispersive species with low but significant population structure (mtDNA Φ(ST)=0.029, microsatellite F(ST)=0.029) due entirely to the isolation of Hawai'i. No population structure was detected across 14,000 km of the Indo-Pacific from Tonga in the Central Pacific to the Seychelles in the western Indian Ocean, a pattern rarely observed in reef species. Despite a long pelagic phase (60-180 days), interisland dispersal as adults, and extensive gene flow across the Indo-Pacific, P. filamentosus is unable to maintain population connectivity with Hawai'i. Coalescent analyses indicate that P. filamentosus may have colonized Hawai'i 26 K-52 K y ago against prevailing currents, with dispersal away from Hawai'i dominating migration estimates. P. filamentosus harbors low genetic diversity in Hawai'i, a common pattern in marine fishes, and our data indicate a single archipelago-wide stock. However, like the Hawaiian Grouper, Hyporthodus quernus, this snapper had several significant pairwise comparisons (F(ST)) clustered around the middle of the archipelago (St. Rogatien, Brooks Banks, Gardner) indicating that this region may be isolated or (more likely) receives input from Johnston Atoll to the south.
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Affiliation(s)
- Michelle R Gaither
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kane'ohe, Hawai'i, USA.
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Gaither MR, Bowen BW, Bordenave TR, Rocha LA, Newman SJ, Gomez JA, van Herwerden L, Craig MT. Phylogeography of the reef fish Cephalopholis argus (Epinephelidae) indicates Pleistocene isolation across the Indo-Pacific Barrier with contemporary overlap in The Coral Triangle. BMC Evol Biol 2011; 11:189. [PMID: 21722383 PMCID: PMC3145601 DOI: 10.1186/1471-2148-11-189] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 07/01/2011] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The Coral Triangle (CT), bounded by the Philippines, the Malay Peninsula, and New Guinea, is the epicenter of marine biodiversity. Hypotheses that explain the source of this rich biodiversity include 1) the center of origin, 2) the center of accumulation, and 3) the region of overlap. Here we contribute to the debate with a phylogeographic survey of a widely distributed reef fish, the Peacock Grouper (Cephalopholis argus; Epinephelidae) at 21 locations (N = 550) using DNA sequence data from mtDNA cytochrome b and two nuclear introns (gonadotropin-releasing hormone and S7 ribosomal protein). RESULTS Population structure was significant (ΦST = 0.297, P < 0.001; FST = 0.078, P < 0.001; FST = 0.099, P < 0.001 for the three loci, respectively) among five regions: French Polynesia, the central-west Pacific (Line Islands to northeastern Australia), Indo-Pacific boundary (Bali and Rowley Shoals), eastern Indian Ocean (Cocos/Keeling and Christmas Island), and western Indian Ocean (Diego Garcia, Oman, and Seychelles). A strong signal of isolation by distance was detected in both mtDNA (r = 0.749, P = 0.001) and the combined nuclear loci (r = 0.715, P < 0.001). We detected evidence of population expansion with migration toward the CT. Two clusters of haplotypes were detected in the mtDNA data (d = 0.008), corresponding to the Pacific and Indian Oceans, with a low level of introgression observed outside a mixing zone at the Pacific-Indian boundary. CONCLUSIONS We conclude that the Indo-Pacific Barrier, operating during low sea level associated with glaciation, defines the primary phylogeographic pattern in this species. These data support a scenario of isolation on the scale of 105 year glacial cycles, followed by population expansion toward the CT, and overlap of divergent lineages at the Pacific-Indian boundary. This pattern of isolation, divergence, and subsequent overlap likely contributes to species richness at the adjacent CT and is consistent with the region of overlap hypothesis.
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Affiliation(s)
- Michelle R Gaither
- Hawaii Institute of Marine Biology University of Hawaii PO Box 1346, Kaneohe, HI 96744, USA
| | - Brian W Bowen
- Hawaii Institute of Marine Biology University of Hawaii PO Box 1346, Kaneohe, HI 96744, USA
| | - Tiana-Rae Bordenave
- Hawaii Institute of Marine Biology University of Hawaii PO Box 1346, Kaneohe, HI 96744, USA
| | - Luiz A Rocha
- Department of Ichthyology California Academy of Sciences 55 Music Concourse Drive San Francisco, CA 94118, USA
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories Department of Fisheries Government of Western Australia P.O. Box 20, North Beach, WA 6920, Australia
| | - Juan A Gomez
- School of Marine & Tropical Biology James Cook University Townsville, QLD 4811, Australia
| | - Lynne van Herwerden
- School of Marine & Tropical Biology James Cook University Townsville, QLD 4811, Australia
| | - Matthew T Craig
- Department of Marine Sciences University of Puerto Rico Mayagüez P.O. Box 9000, Mayagüez PR 00681, USA
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Eble JA, Toonen RJ, Sorenson L, Basch LV, Papastamatiou YP, Bowen BW. Escaping paradise: Larval export from Hawaii in an Indo-Pacific reef fish, the Yellow Tang ( Zebrasoma flavescens). MARINE ECOLOGY PROGRESS SERIES 2011; 428:245-258. [PMID: 25505806 PMCID: PMC4260458 DOI: 10.3354/meps09083] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The depauperate marine ecosystems of the Hawaiian Archipelago share a high proportion of species with the southern and western Pacific, indicating historical and/or ongoing connections across the large oceanic expanse separating Hawaii from its nearest neighbors. The rate and direction of these interactions are, however, unknown. While previous biogeographic studies have consistently described Hawaii as a diversity sink, prevailing currents likely offer opportunities for larval export. To assess interactions between the remote reefs of the Hawaiian Archipelago and the species rich communities of the Central and West Pacific, we surveyed 14 nuclear microsatellite loci (nDNA; n = 857) and a 614 bp segment of mitochondrial cytochrome b (mtDNA; n = 654) in the Yellow Tang (Zebrasoma flavescens). Concordant frequency shifts in both nDNA and mtDNA reveal significant population differentiation among three West Pacific sites and Hawaii (nDNA F' CT = 0.116, mtDNA ϕ CT = 0.098, P < 0.001). SAMOVA analyses of microsatellite data additionally indicate fine scale differentiation within the 2600 km Hawaiian Archipelago (F' SC = 0.026; P < 0.001), with implications for management of this heavily-exploited aquarium fish. Mismatch analyses indicate the oldest contemporary populations are in the Hawaiian Archipelago (circa 318,000 y), with younger populations in the West Pacific (91,000 - 175,000 y). Estimates of Yellow Tang historical demography contradict expectations of Hawaii as a population sink, and instead indicate asymmetrical gene flow, with Hawaii exporting rather than importing Yellow Tang larvae.
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Affiliation(s)
- Jeff A. Eble
- Hawaii Institute of Marine Biology, School of Oceanography and Earth Science and Technology, University of Hawai’i, Kaneohe, HI 96744 USA
- Dept. of Zoology, University of Hawai’i, Honolulu, HI 96822 USA
- Corresponding author: , Forbes 410, 1140 E. South Campus Dr., Tucson AZ, 85721
| | - Robert J. Toonen
- Hawaii Institute of Marine Biology, School of Oceanography and Earth Science and Technology, University of Hawai’i, Kaneohe, HI 96744 USA
| | - Laurie Sorenson
- Virginia Institute of Marine Science, Gloucester Point, VA 23062 USA
| | - Larry V. Basch
- Ecology, Evolution, and Conservation Biology Program, University of Hawai’i, Honolulu, HI 96822 USA
| | - Yannis P. Papastamatiou
- Hawaii Institute of Marine Biology, School of Oceanography and Earth Science and Technology, University of Hawai’i, Kaneohe, HI 96744 USA
| | - Brian W. Bowen
- Hawaii Institute of Marine Biology, School of Oceanography and Earth Science and Technology, University of Hawai’i, Kaneohe, HI 96744 USA
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