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Panmictic stock structure of milkfish (Chanos chanos, Forsskål 1775) from Indian waters determined using mtDNA marker. J Genet 2022. [DOI: 10.1007/s12041-022-01395-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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2
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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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3
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Guo W, Banerjee AK, Wu H, Ng WL, Feng H, Qiao S, Liu Y, Huang Y. Contrasting Phylogeographic Patterns in Lumnitzera Mangroves Across the Indo-West Pacific. FRONTIERS IN PLANT SCIENCE 2021; 12:637009. [PMID: 34249031 PMCID: PMC8261646 DOI: 10.3389/fpls.2021.637009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/27/2021] [Indexed: 06/13/2023]
Abstract
Mangroves are ecologically important forest communities in tropical and subtropical coasts, the effective management of which requires understanding of their phylogeographic patterns. However, these patterns often vary among different species, even among ecologically similar taxa or congeneric species. Here, we investigated the levels and patterns of genetic variation within Lumnitzera consisting of two species (L. racemosa and L. littorea) with nearly sympatric ranges across the Indo-West Pacific (IWP) region by sequencing three chloroplast DNA regions (for both species) and genotyping 11 nuclear microsatellite loci (for L. littorea). Consistent with findings in studies on other mangrove species, we found that both L. racemosa and L. littorea showed relatively high genetic variation among populations but low genetic variation within populations. Haplotype network and genetic clustering analyses indicated two well-differentiated clades in both L. racemosa and L. littorea. The relationship between geographic and genetic distances and divergence time estimates of the haplotypes indicated that limited dispersal ability of the propagules, emergence of land barriers during ancient sea-level changes, and contemporary oceanic circulation pattern in the IWP influenced the current population structure of the two species. However, the position of genetic break was found to vary between the two species: in L. racemosa, strong divergence was observed between populations from the Indian Ocean and the Pacific Ocean possibly due to land barrier effect of the Malay Peninsula; in L. littorea, the phylogeographic pattern was created by a more eastward genetic break along the biogeographic barrier identified as the Huxley's line. Overall, our findings strongly supported previous hypothesis of mangrove species divergence and revealed that the two Lumnitzera species have different phylogeographic patterns despite their close genetic relationship and similar current geographic distribution. The findings also provided references for the management of Lumnitzera mangroves, especially for the threatened L. littorea.
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Affiliation(s)
- Wuxia Guo
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Achyut Kumar Banerjee
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Haidan Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Malaysia
| | - Hui Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sitan Qiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yelin Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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4
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Clark RD, Aardema ML, Andolfatto P, Barber PH, Hattori A, Hoey JA, Montes HR, Pinsky ML. Genomic signatures of spatially divergent selection at clownfish range margins. Proc Biol Sci 2021; 288:20210407. [PMID: 34102891 PMCID: PMC8187997 DOI: 10.1098/rspb.2021.0407] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/11/2021] [Indexed: 01/25/2023] Open
Abstract
Understanding how evolutionary forces interact to drive patterns of selection and distribute genetic variation across a species' range is of great interest in ecology and evolution, especially in an era of global change. While theory predicts how and when populations at range margins are likely to undergo local adaptation, empirical evidence testing these models remains sparse. Here, we address this knowledge gap by investigating the relationship between selection, gene flow and genetic drift in the yellowtail clownfish, Amphiprion clarkii, from the core to the northern periphery of the species range. Analyses reveal low genetic diversity at the range edge, gene flow from the core to the edge and genomic signatures of local adaptation at 56 single nucleotide polymorphisms in 25 candidate genes, most of which are significantly correlated with minimum annual sea surface temperature. Several of these candidate genes play a role in functions that are upregulated during cold stress, including protein turnover, metabolism and translation. Our results illustrate how spatially divergent selection spanning the range core to the periphery can occur despite the potential for strong genetic drift at the range edge and moderate gene flow from the core populations.
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Affiliation(s)
- René D. Clark
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
| | - Matthew L. Aardema
- Department of Biology, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5102, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY 10026, USA
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Akihisa Hattori
- Faculty of Liberal Arts and Education, Shiga University, 2-5-1 Hiratsu, Otsu, Shiga 520-0862, Japan
| | - Jennifer A. Hoey
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | | | - Malin L. Pinsky
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
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5
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Tang KL, Stiassny MLJ, Mayden RL, DeSalle R. Systematics of Damselfishes. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/i2020105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kevin L. Tang
- University of Michigan–Flint, Department of Biology, 303 East Kearsley St., Flint, Michigan 48502; . Send reprint requests to this address
| | - Melanie L. J. Stiassny
- American Museum of Natural History, Department of Ichthyology, Central Park West at 79th St., New York, New York 10024;
| | - Richard L. Mayden
- Saint Louis University, Department of Biology, 3507 Laclede Ave., St. Louis, Missouri 63103;
| | - Robert DeSalle
- American Museum of Natural History, Division of Invertebrate Zoology, Central Park West at 79th St., New York, New York 10024;
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6
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Gainsford A, Jones GP, Hobbs JA, Heindler FM, van Herwerden L. Species integrity, introgression, and genetic variation across a coral reef fish hybrid zone. Ecol Evol 2020; 10:11998-12014. [PMID: 33209265 PMCID: PMC7663085 DOI: 10.1002/ece3.6769] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 11/10/2022] Open
Abstract
Hybridization and introgression are evolutionarily significant phenomena breaking down species boundaries. "Hybrid zones" (regions of species overlap and hybridization) enable quantification of hybridization frequency and examination of mechanisms driving and maintaining gene flow. The hybrid anemonefish Amphiprion leucokranos is found where parent species (A. chrysopterus; A. sandaracinos) distributions overlap. Here, we examine geographic variation in hybridization and introgression, and potential impacts on parent species integrity through assessing relative abundance, social group composition, and genetic structure (mtDNA cytochrome b, 21 microsatellite loci) of taxa at three hybrid zone locations: Kimbe Bay (KB) and Kavieng (KA), Papua New Guinea; the Solomon Islands (SO). Relative abundances of and size disparities between parent species apparently drive hybridization frequency, introgression patterns, and genetic composition of taxa. Conspecific groups are most common in KB (65%) where parent species are similarly abundant. Conversely, mixed species groups dominate SO (82%), where A. chrysopterus is more abundant. Hybrids most commonly cohabit with A. sandaracinos in KB (17%), but with A. chrysopterus in KA (22%) and SO (50%). Genetic differentiation (nDNA) analyses indicate that parent species remain distinct, despite ongoing hybridization and hybrids are genetically similar to A. sandaracinos-resulting from persistent backcrossing with this smallest species. This study shows that hybridization outcomes may depend on the social and ecological context in which taxa hybridize, where relative abundance and disparate size of parent species explain the frequency and patterns of hybridization and introgression in the A. leucokranos hybrid zone, reflecting size-based dominance behaviors of anemonefish social groups.
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Affiliation(s)
- Ashton Gainsford
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQLDAustralia
- Faculty of Science and EngineeringJames Cook UniversityTownsvilleAustraliaAustralia
| | - Geoffrey P. Jones
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQLDAustralia
- Faculty of Science and EngineeringJames Cook UniversityTownsvilleAustraliaAustralia
| | - Jean‐Paul A. Hobbs
- School of Biological SciencesThe University of QueenslandBrisbaneQLDAustralia
| | | | - Lynne van Herwerden
- Faculty of Science and EngineeringJames Cook UniversityTownsvilleAustraliaAustralia
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7
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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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8
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Maas DL, Prost S, Bi K, Smith LL, Armstrong EE, Aji LP, Toha AHA, Gillespie RG, Becking LE. Rapid divergence of mussel populations despite incomplete barriers to dispersal. Mol Ecol 2018; 27:1556-1571. [DOI: 10.1111/mec.14556] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/25/2018] [Accepted: 02/26/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Diede L. Maas
- Department of Marine Animal Ecology; Wageningen University & Research; Wageningen The Netherlands
| | - Stefan Prost
- Department of Biology; Stanford University; Stanford CA USA
- Department of Integrative Biology; Center for Theoretical Evolutionary Genomics; University of California; Berkeley CA USA
| | - Ke Bi
- Museum of Vertebrate Zoology; University of California; Berkeley CA USA
- Computational Genomics Resource Laboratory; California Institute for Quantitative Biosciences; University of California; Berkley CA USA
| | - Lydia L. Smith
- Museum of Vertebrate Zoology; University of California; Berkeley CA USA
| | | | - Ludi P. Aji
- Research Centre for Oceanography; Indonesian Institute of Sciences; Jakarta Indonesia
| | | | - Rosemary G. Gillespie
- Department of Environmental Science, Policy, and Management; University of California; Berkeley CA USA
| | - Leontine E. Becking
- Department of Marine Animal Ecology; Wageningen University & Research; Wageningen The Netherlands
- Department of Environmental Science, Policy, and Management; University of California; Berkeley CA USA
- Wageningen Marine Research; Den Helder The Netherlands
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9
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Putra ING, Syamsuni YF, Subhan B, Pharmawati M, Madduppa H. Strong genetic differentiation in tropical seagrass Enhalus acoroides (Hydrocharitaceae) at the Indo-Malay Archipelago revealed by microsatellite DNA. PeerJ 2018; 6:e4315. [PMID: 29576933 PMCID: PMC5855881 DOI: 10.7717/peerj.4315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 01/11/2018] [Indexed: 11/20/2022] Open
Abstract
The Indo-Malay Archipelago is regarded as a barrier that separates organisms of the Indian and Pacific Oceans. Previous studies of marine biota from this region have found a variety of biogeographic barriers, seemingly dependent on taxon and methodology. Several hypotheses, such as emergence of the Sunda Shelf and recent physical oceanography, have been proposed to account for the genetic structuring of marine organisms in this region. Here, we used six microsatellite loci to infer genetic diversity, population differentiation and phylogeographic patterns of Enhalus acoroides across the Indo-Malay Archipelago. Heterozygosities were consistently high, and significant isolation-by-distance, consistent with restricted gene flow, was observed. Both a neighbour joining tree based on DA distance and Bayesian clustering revealed three major clusters of E. acoroides. Our results indicate that phylogeographic patterns of E. acoroides have possibly been influenced by glaciation and deglaciation during the Pleistocene. Recent physical oceanography such as the South Java Current and the Seasonally Reversing Current may also play a role in shaping the genetic patterns of E. acoroides.
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Affiliation(s)
- I Nyoman Giri Putra
- Department of Marine Science and Technology, Faculty Fisheries and Marine Sciences, Bogor Agricultural University (IPB), Bogor, Indonesia.,Department of Marine Science, Faculty of Marine Science and Fisheries, Udayana University, Bukit Jimbaran, Bali, Indonesia
| | | | - Beginer Subhan
- Department of Marine Science and Technology, Faculty Fisheries and Marine Sciences, Bogor Agricultural University (IPB), Bogor, Indonesia
| | - Made Pharmawati
- Biology Department, Faculty of Mathematics and Natural Sciences, Udayana University, Bukit Jimbaran, Bali, Indonesia
| | - Hawis Madduppa
- Department of Marine Science and Technology, Faculty Fisheries and Marine Sciences, Bogor Agricultural University (IPB), Bogor, Indonesia.,Center for Coastal and Marine Resources Studies, Bogor Agricultural University (IPB), Bogor, Indonesia
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10
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Cowman PF, Parravicini V, Kulbicki M, Floeter SR. The biogeography of tropical reef fishes: endemism and provinciality through time. Biol Rev Camb Philos Soc 2017; 92:2112-2130. [DOI: 10.1111/brv.12323] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/23/2017] [Accepted: 01/26/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Peter F. Cowman
- Department of Ecology and Evolutionary Biology; Yale University; New Haven CT 06511 U.S.A
- Centre of Excellence for Coral Reef Studies; James Cook University; Townsville 4811 Australia
| | - Valeriano Parravicini
- Ecole Pratique des Hautes Etudes, USR 3278 EPHE-CNRS-UPVD, Labex Corail, CRIOBE; 66860 Perpignan France
| | - Michel Kulbicki
- Institut de Recherche pour le développement (IRD), UMR Entropie-Labex CORAIL; Université de Perpignan; 66000 Perpignan France
| | - Sergio R. Floeter
- Depto. de Ecologia e Zoologia, Marine Macroecology and Biogeography Laboratory, CCB; Universidade Federal de Santa Catarina; Florianópolis 88040-900 Brazil
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11
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Hernawan UE, van Dijk KJ, Kendrick GA, Feng M, Biffin E, Lavery PS, McMahon K. Historical processes and contemporary ocean currents drive genetic structure in the seagrassThalassia hemprichiiin the Indo-Australian Archipelago. Mol Ecol 2017; 26:1008-1021. [DOI: 10.1111/mec.13966] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 11/22/2016] [Accepted: 12/08/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Udhi E. Hernawan
- School of Science and Centre for Marine Ecosystems Research; Edith Cowan University; Joondalup WA 6027 Australia
- UPT. LKBL-Tual; Research Centre for Oceanography (P2O); Indonesian Institute of Sciences (LIPI); Ancol Timur Jakarta 14430 Indonesia
| | - Kor-jent van Dijk
- School of Biological Sciences; The University of Adelaide; Adelaide SA 5005 Australia
| | - Gary A. Kendrick
- School of Plant Biology and The Ocean Institute; The University of Western Australia; Crawley WA 6009 Australia
| | - Ming Feng
- CSIRO Ocean and Atmosphere; Centre for Environment and Life Sciences; Floreat WA 6014 Australia
| | - Edward Biffin
- School of Biological Sciences; The University of Adelaide; Adelaide SA 5005 Australia
| | - Paul S. Lavery
- School of Science and Centre for Marine Ecosystems Research; Edith Cowan University; Joondalup WA 6027 Australia
| | - Kathryn McMahon
- School of Science and Centre for Marine Ecosystems Research; Edith Cowan University; Joondalup WA 6027 Australia
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Yang Y, Li J, Yang S, Li X, Fang L, Zhong C, Duke NC, Zhou R, Shi S. Effects of Pleistocene sea-level fluctuations on mangrove population dynamics: a lesson from Sonneratia alba. BMC Evol Biol 2017; 17:22. [PMID: 28100168 PMCID: PMC5241957 DOI: 10.1186/s12862-016-0849-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/08/2016] [Indexed: 11/21/2022] Open
Abstract
Background A large-scale systematical investigation of the influence of Pleistocene climate oscillation on mangrove population dynamics could enrich our knowledge about the evolutionary history during times of historical climate change, which in turn may provide important information for their conservation. Results In this study, phylogeography of a mangrove tree Sonneratia alba was studied by sequencing three chloroplast fragments and seven nuclear genes. A low level of genetic diversity at the population level was detected across its range, especially at the range margins, which was mainly attributed to the steep sea-level drop and associated climate fluctuations during the Pleistocene glacial periods. Extremely small effective population size (Ne) was inferred in populations from both eastern and western Malay Peninsula (44 and 396, respectively), mirroring the fragility of mangrove plants and their paucity of robustness against future climate perturbations and human activity. Two major genetic lineages of high divergence were identified in the two mangrove biodiversity centres: the Indo-Malesia and Australasia regions. The estimated splitting time between these two lineages was 3.153 million year ago (MYA), suggesting a role for pre-Pleistocene events in shaping the major diversity patterns of mangrove species. Within the Indo-Malesia region, a subdivision was implicated between the South China Sea (SCS) and the remaining area with a divergence time of 1.874 MYA, corresponding to glacial vicariance when the emerged Sunda Shelf halted genetic exchange between the western and eastern coasts of the Malay Peninsula during Pleistocene sea-level drops. Notably, genetic admixture was observed in populations at the boundary regions, especially in the two populations near the Malacca Strait, indicating secondary contact between divergent lineages during interglacial periods. These interregional genetic exchanges provided ample opportunity for the re-use of standing genetic variation, which could facilitate mangrove establishment and adaptation in new habitats, especially in the context of global climate changes. Conclusion Phylogeogrpahic analysis in this study reveal that Pleistocene sea-level fluctuations had profound influence on population differentiation of the mangrove tree S. alba. Our study highlights the fragility of mangrove plants and offers a guide for the conservation of coastal mangrove communities experiencing ongoing changes in sea-level. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0849-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuchen Yang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jianfang Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shuhuan Yang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xinnian Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Lu Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature Reserve, Haikou, 571129, China
| | - Norman C Duke
- Trop WATER, James Cook University, Townsville, Quennsland, Australia
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
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Becking LE, de Leeuw CA, Knegt B, Maas DL, de Voogd NJ, Abdunnur, Suyatna I, Peijnenburg KTCA. Highly divergent mussel lineages in isolated Indonesian marine lakes. PeerJ 2016; 4:e2496. [PMID: 27761314 PMCID: PMC5068364 DOI: 10.7717/peerj.2496] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 08/27/2016] [Indexed: 11/20/2022] Open
Abstract
Marine lakes, with populations in landlocked seawater and clearly delineated contours, have the potential to provide a unique model to study early stages of evolution in coastal marine taxa. Here we ask whether populations of the mussel Brachidontes from marine lakes in Berau, East Kalimantan (Indonesia) are isolated from each other and from the coastal mangrove systems. We analyzed sequence data of one mitochondrial marker (Cytochrome Oxidase I (COI)), and two nuclear markers (18S and 28S). In addition, we examined shell shape using a geometric morphometric approach. The Indonesian populations of Brachidontes spp. harbored four deeply diverged lineages (14–75% COI corrected net sequence divergence), two of which correspond to previously recorded lineages from marine lakes in Palau, 1,900 km away. These four lineages also showed significant differences in shell shape and constitute a species complex of at least four undescribed species. Each lake harbored a different lineage despite the fact that the lakes are separated from each other by only 2–6 km, while the two mangrove populations, at 20 km distance from each other, harbored the same lineage and shared haplotypes. Marine lakes thus represent isolated habitats. As each lake contained unique within lineage diversity (0.1–0.2%), we suggest that this may have resulted from in situdivergence due to isolation of founder populations after the formation of the lakes (6,000–12,000 years before present). Combined effects of stochastic processes, local adaptation and increased evolutionary rates could produce high levels of differentiation in small populations such as in marine lake environments. Such short-term isolation at small spatial scales may be an important contributing factor to the high marine biodiversity that is found in the Indo-Australian Archipelago.
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Affiliation(s)
- Leontine E Becking
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA; Department of Marine Animal Ecology, Wageningen University & Research, Wageningen, The Netherlands; Department of Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Christiaan A de Leeuw
- Department of Marine Animal Ecology, Wageningen University & Research, Wageningen, The Netherlands; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Bram Knegt
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam , Amsterdam , The Netherlands
| | - Diede L Maas
- Department of Marine Animal Ecology, Wageningen University & Research , Wageningen , The Netherlands
| | - Nicole J de Voogd
- Department of Marine Biodiversity, Naturalis Biodiversity Center , Leiden , The Netherlands
| | - Abdunnur
- Faculty of Fisheries and Marine Sciences, Mulawarman University , Samarinda , East Kalimantan , Indonesia
| | - Iwan Suyatna
- Faculty of Fisheries and Marine Sciences, Mulawarman University , Samarinda , East Kalimantan , Indonesia
| | - Katja T C A Peijnenburg
- Department of Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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Predator-prey interactions in the plankton: larval fish feeding on evasive copepods. Sci Rep 2016; 6:33585. [PMID: 27658849 PMCID: PMC5034258 DOI: 10.1038/srep33585] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/31/2016] [Indexed: 11/08/2022] Open
Abstract
Capture success and prey selectivity were investigated in clownfish Amphiprion ocellaris larvae using videography. Three prey types were tested using developmental stages (nauplii, copepodites and adults) of the copepod Parvocalanus crassirostris. Predatory abilities improved rapidly between days 1 and 14 post-hatch. Initially, capture success was limited to nauplii with few attacks on larger stages. Captures of copepodites were first observed at 3 dph, and of adults at 8 dph. Consistent strikes at the larger prey were observed on the day prior to successful captures (2 dph for copepodites, 7 dph for adults). Difference in capture success between nauplii and adults at 8 dph was an order of magnitude. Differences in capture success among prey types persisted but decreased to three-fold by 14 dph. Younger A. ocellaris attacked nauplii preferentially and avoided adult prey. Strike selectivity declined with age, and no selectivity was observed after 10 dph. However, numerically 50% of the ingested prey were still nauplii at 14 dph under the experimental conditions.
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15
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Li J, Yang Y, Chen Q, Fang L, He Z, Guo W, Qiao S, Wang Z, Guo M, Zhong C, Zhou R, Shi S. Pronounced genetic differentiation and recent secondary contact in the mangrove tree Lumnitzera racemosa revealed by population genomic analyses. Sci Rep 2016; 6:29486. [PMID: 27380895 PMCID: PMC4933931 DOI: 10.1038/srep29486] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 06/21/2016] [Indexed: 11/09/2022] Open
Abstract
Systematically investigating the impacts of Pleistocene sea-level fluctuations on mangrove plants may provide a better understanding of their demographic history and useful information for their conservation. Therefore, we conducted population genomic analyses of 88 nuclear genes to explore the population dynamics of a mangrove tree Lumnitzera racemosa across the Indo-West Pacific region. Our results revealed pronounced genetic differentiation in this species between the populations from the Indian Ocean and the Pacific Ocean, which may be attributable to the long-term isolation between the western and eastern coasts of the Malay Peninsula during sea-level drops in the Pleistocene glacial periods. The mixing of haplotypes from the two highly divergent groups was identified in a Cambodian population at almost all 88 nuclear genes, suggesting genetic admixture of the two lineages at the boundary region. Similar genetic admixture was also found in other populations from Southeast Asia based on the Bayesian clustering analysis of six nuclear genes, which suggests extensive and recent secondary contact of the two divergent lineages in Southeast Asia. Computer simulations indicated substantial migration from the Indian Ocean towards the South China Sea, which likely results in the genetic admixture in Southeast Asia.
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Affiliation(s)
- Jianfang Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Qipian Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Lu Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Wuxia Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Sitan Qiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhengzhen Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Miaomiao Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Cairong Zhong
- Hainan Dongzhai Harbour National Nature Reserve, Haikou 571129, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China
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16
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Cooke GM, Schlub TE, Sherwin WB, Ord TJ. Understanding the Spatial Scale of Genetic Connectivity at Sea: Unique Insights from a Land Fish and a Meta-Analysis. PLoS One 2016; 11:e0150991. [PMID: 27195493 PMCID: PMC4873183 DOI: 10.1371/journal.pone.0150991] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/21/2016] [Indexed: 11/19/2022] Open
Abstract
Quantifying the spatial scale of population connectivity is important for understanding the evolutionary potential of ecologically divergent populations and for designing conservation strategies to preserve those populations. For marine organisms like fish, the spatial scale of connectivity is generally set by a pelagic larval phase. This has complicated past estimates of connectivity because detailed information on larval movements are difficult to obtain. Genetic approaches provide a tractable alternative and have the added benefit of estimating directly the reproductive isolation of populations. In this study, we leveraged empirical estimates of genetic differentiation among populations with simulations and a meta-analysis to provide a general estimate of the spatial scale of genetic connectivity in marine environments. We used neutral genetic markers to first quantify the genetic differentiation of ecologically-isolated adult populations of a land dwelling fish, the Pacific leaping blenny (Alticus arnoldorum), where marine larval dispersal is the only probable means of connectivity among populations. We then compared these estimates to simulations of a range of marine dispersal scenarios and to collated FST and distance data from the literature for marine fish across diverse spatial scales. We found genetic connectivity at sea was extensive among marine populations and in the case of A. arnoldorum, apparently little affected by the presence of ecological barriers. We estimated that ~5000 km (with broad confidence intervals ranging from 810-11,692 km) was the spatial scale at which evolutionarily meaningful barriers to gene flow start to occur at sea, although substantially shorter distances are also possible for some taxa. In general, however, such a large estimate of connectivity has important implications for the evolutionary and conservation potential of many marine fish communities.
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Affiliation(s)
- Georgina M. Cooke
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052 NSW, Australia
- The Australian Museum, Australian Museum Research Institute, Ichthyology, 6 College Street, Sydney NSW 2010, Australia
| | - Timothy E. Schlub
- Sydney School of Public Health, Sydney Medical School, University of Sydney, 2006 NSW, Australia
| | - William B. Sherwin
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052 NSW, Australia
| | - Terry J. Ord
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052 NSW, Australia
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Yang Y, Duke NC, Peng F, Li J, Yang S, Zhong C, Zhou R, Shi S. Ancient Geographical Barriers Drive Differentiation among Sonneratia caseolaris Populations and Recent Divergence from S. lanceolata. FRONTIERS IN PLANT SCIENCE 2016; 7:1618. [PMID: 27833634 PMCID: PMC5080369 DOI: 10.3389/fpls.2016.01618] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 10/13/2016] [Indexed: 05/07/2023]
Abstract
Glacial vicariance is thought to influence population dynamics and speciation of many marine organisms. Mangroves, a plant group inhabiting intertidal zones, were also profoundly influenced by Pleistocene glaciations. In this study, we investigated phylogeographic patterns of a widespread mangrove species Sonneratia caseolaris and a narrowly distributed, closely related species S. lanceolata to infer their divergence histories and related it to historical geological events. We sequenced two chloroplast fragments and five nuclear genes for one population of S. lanceolata and 12 populations of S. caseolaris across the Indo-West Pacific (IWP) region to evaluate genetic differentiation and divergence time among them. Phylogenetic analysis based on sequences of nuclear ribosomal internal transcribed spacer and a nuclear gene rpl9 for all Sonneratia species indicate that S. lanceolata individuals are nested within S. caseolaris. We found strong genetic structure among geographic regions (South China Sea, the Indian Ocean, and eastern Australia) inhabited by S. caseolaris. We estimated that divergence between the Indo-Malesia and Australasia populations occurred 4.035 million years ago (MYA), prior to the onset of Pleistocene. BARRIERS analysis suggested that complex geographic features in the IWP region had largely shaped the phylogeographic patterns of S. caseolaris. Furthermore, haplotype analyses provided convincing evidence for secondary contact of the South China Sea and the Indian Ocean lineages at the Indo-Pacific boundary. Demographic history inference under isolation and migration (IM) model detected substantial gene flow from the Sri Lanka populations to the populations in the Java Island. Moreover, multi-locus sequence analysis indicated that S. lanceolata was most closely related to the Indian Ocean populations of S. caseolaris and the divergence time between them was 2.057 MYA, coinciding with the onset of the Pleistocene glaciation. Our results suggest that geographic isolation driven by the Pleistocene ice age resulted in the recent origin of S. lanceolata.
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Affiliation(s)
- Yuchen Yang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen UniversityGuangzhou, China
| | - Norman C. Duke
- Trop WATER, James Cook University, TownsvilleQLD, Australia
| | - Fangfang Peng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen UniversityGuangzhou, China
| | - Jianfang Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen UniversityGuangzhou, China
| | - Shuhuan Yang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen UniversityGuangzhou, China
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature ReserveHaikou, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen UniversityGuangzhou, China
- *Correspondence: Renchao Zhou, Suhua Shi,
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen UniversityGuangzhou, China
- *Correspondence: Renchao Zhou, Suhua Shi,
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18
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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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19
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Treml EA, Roberts J, Halpin PN, Possingham HP, Riginos C. The emergent geography of biophysical dispersal barriers across the Indo-West Pacific. DIVERS DISTRIB 2015. [DOI: 10.1111/ddi.12307] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Eric A. Treml
- School of BioSciences; University of Melbourne; Melbourne Vic. 3010 Australia
| | - Jason Roberts
- Marine Geospatial Ecology Laboratory; A324 LSRC Building; Nicholas School of the Environment; Duke University; Durham NC USA
| | - Patrick N. Halpin
- Marine Geospatial Ecology Laboratory; A324 LSRC Building; Nicholas School of the Environment; Duke University; Durham NC USA
| | - Hugh P. Possingham
- School of Biological Sciences; The University of Queensland; St. Lucia Qld 4072 Australia
| | - Cynthia Riginos
- School of Biological Sciences; The University of Queensland; St. Lucia Qld 4072 Australia
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20
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Stillman JH, Armstrong E. Genomics Are Transforming Our Understanding of Responses to Climate Change. Bioscience 2015. [DOI: 10.1093/biosci/biu219] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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21
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Gainsford A, van Herwerden L, Jones GP. Hierarchical behaviour, habitat use and species size differences shape evolutionary outcomes of hybridization in a coral reef fish. J Evol Biol 2015; 28:205-22. [DOI: 10.1111/jeb.12557] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 10/09/2014] [Accepted: 11/17/2014] [Indexed: 02/06/2023]
Affiliation(s)
- A. Gainsford
- College of Marine and Environmental Sciences; James Cook University; Townsville Qld Australia
- ARC Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld Australia
| | - L. van Herwerden
- College of Marine and Environmental Sciences; James Cook University; Townsville Qld Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture; James Cook University; Townsville Qld Australia
| | - G. P. Jones
- College of Marine and Environmental Sciences; James Cook University; Townsville Qld Australia
- ARC Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld Australia
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22
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Cowman PF. Historical factors that have shaped the evolution of tropical reef fishes: a review of phylogenies, biogeography, and remaining questions. Front Genet 2014; 5:394. [PMID: 25431581 PMCID: PMC4230204 DOI: 10.3389/fgene.2014.00394] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/27/2014] [Indexed: 12/21/2022] Open
Abstract
Biodiversity patterns across the marine tropics have intrigued evolutionary biologists and ecologists alike. Tropical coral reefs host 1/3 of all marine species of fish on 0.1% of the ocean's surface. Yet our understanding of how mechanistic processes have underpinned the generation of this diversity is limited. However, it has become clear that the biogeographic history of the marine tropics has played an important role in shaping the diversity of tropical reef fishes we see today. In the last decade, molecular phylogenies and age estimation techniques have provided a temporal framework in which the ancestral biogeographic origins of reef fish lineages have been inferred, but few have included fully sampled phylogenies or made inferences at a global scale. We are currently at a point where new sequencing technologies are accelerating the reconstruction and the resolution of the Fish Tree of Life. How will a complete phylogeny of fishes benefit the study of biodiversity in the tropics? Here, I review the literature concerning the evolutionary history of reef-associated fishes from a biogeographic perspective. I summarize the major biogeographic and climatic events over the last 65 million years that have regionalized the tropical marine belt and what effect they have had on the molecular record of fishes and global biodiversity patterns. By examining recent phylogenetic trees of major reef associated groups, I identify gaps to be filled in order to obtain a clearer picture of the origins of coral reef fish assemblages. Finally, I discuss questions that remain to be answered and new approaches to uncover the mechanistic processes that underpin the evolution of biodiversity on coral reefs.
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Affiliation(s)
- Peter F Cowman
- Department of Ecology and Evolutionary Biology, Yale University New Haven, CT, USA
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23
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Van Der Meij SE, Reijnen BT. The curious case ofNeotroglocarcinus dawydoffi(Decapoda, Cryptochiridae): unforeseen biogeographic patterns resulting from isolation. SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.946979] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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24
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Bogorodsky SV, Last PR, Alpermann TJ, Mal AO. Records of Himantura granulata(Dasyatidae) and Rhinoptera jayakari(Rhinopteridae) from the Red Sea. ZOOLOGY IN THE MIDDLE EAST 2014. [DOI: 10.1080/09397140.2014.914719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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Interspecific, spatial and temporal variability of self-recruitment in anemonefishes. PLoS One 2014; 9:e90648. [PMID: 24587406 PMCID: PMC3938785 DOI: 10.1371/journal.pone.0090648] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 02/03/2014] [Indexed: 11/24/2022] Open
Abstract
Polymorphic microsatellite DNA parentage analysis was used to investigate the spatio-temporal variability of self-recruitment in populations of two anemonefishes: Amphiprion ocellaris and A. perideraion. Tissue samples of A. ocellaris (n = 364) and A. perideraion (n = 105) were collected from fringing reefs around two small islands (Barrang Lompo and Samalona) in Spermonde Archipelago, Indonesia. Specimens were genotyped based on seven microsatellite loci for A. ocellaris and five microsatellite loci for A. perideraion, and parentage assignment as well as site fidelity were calculated. Both species showed high levels of self-recruitment: 65.2% of juvenile A. ocellaris in Samalona were the progeny of parents from the same island, while on Barrang Lompo 47.4% of A. ocellaris and 46.9% of A. perideraion juveniles had parents from that island. Self-recruitment of A. ocellaris in Barrang Lompo varied from 44% to 52% between the two sampling periods. The site fidelity of A. ocellaris juveniles that returned to their reef site in Barang Lompo was up to 44%, while for A. perideraion up to 19%. In Samalona, the percentage of juveniles that returned to their natal reef site ranged from 8% to 11%. Exchange of progeny between the two study islands, located 7.5 km apart, was also detected via parentage assignments. The larger Samalona adult population of A. ocellaris was identified as the parents of 21% of Barrang Lompo juveniles, while the smaller adult population on Barrang Lompo were the parents of only 4% of Samalona juveniles. High self-recruitment and recruitment to nearby island reefs have important implications for management and conservation of anemonefishes. Small MPAs, preferably on every island/reef, should ensure that a part of the population is protected to enable replenishment by the highly localised recruitment behaviour observed in these species.
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Chan SW, Cheang CC, Chirapart A, Gerung G, Tharith C, Ang P. Homogeneous population of the brown alga Sargassum polycystum in Southeast Asia: possible role of recent expansion and asexual propagation. PLoS One 2013; 8:e77662. [PMID: 24147050 PMCID: PMC3798308 DOI: 10.1371/journal.pone.0077662] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/12/2013] [Indexed: 11/18/2022] Open
Abstract
Southeast Asia has been known as one of the biodiversity hotspots in the world. Repeated glacial cycles during Pleistocene were believed to cause isolation of marine taxa in refugia, resulting in diversification among lineages. Recently, ocean current was also found to be another factor affecting gene flow by restricting larval dispersal in animals. Macroalgae are unique in having mode of reproduction that differs from that of animals. Our study on the phylogeographical pattern of the brown macroalga Sargassum polycystum using nuclear Internal Transcribed Spacer 2 (ITS2), plastidal RuBisCO spacer (Rub spacer) and mitochondrial cytochrome oxidase subunit-III (Cox3) as molecular markers revealed genetic homogeneity across 27 sites in Southeast Asia and western Pacific, in sharp contrast to that revealed from most animal studies. Our data suggested that S. polycystum persisted in single refugium during Pleistocene in a panmixia pattern. Expansion occurred more recently after the Last Glacial Maximum and recolonization of the newly flooded Sunda Shelf could have involved asexual propagation of the species. High dispersal ability through floating fronds carrying developing germlings may also contribute to the low genetic diversity of the species.
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Affiliation(s)
- Sze Wai Chan
- Marine Science Laboratory, Chinese University of Hong Kong, N.T., Hong Kong SAR, China
| | - Chi Chiu Cheang
- Marine Science Laboratory, Chinese University of Hong Kong, N.T., Hong Kong SAR, China
| | - Anong Chirapart
- Algal Bioresources Research Center, Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Grevo Gerung
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado, Indonesia
| | - Chea Tharith
- Research and Development Institute (MFReDI), Fisheries Administration, Phnom Penh, Cambodia
| | - Put Ang
- Marine Science Laboratory, Chinese University of Hong Kong, N.T., Hong Kong SAR, China
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27
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Taillebois L, Castelin M, Ovenden JR, Bonillo C, Keith P. Contrasting genetic structure among populations of two amphidromous fish species (Sicydiinae) in the Central West Pacific. PLoS One 2013; 8:e75465. [PMID: 24130714 PMCID: PMC3794023 DOI: 10.1371/journal.pone.0075465] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 08/15/2013] [Indexed: 11/18/2022] Open
Abstract
Both present-day and past processes can shape connectivity of populations. Pleistocene vicariant events and dispersal have shaped the present distribution and connectivity patterns of aquatic species in the Indo-Pacific region. In particular, the processes that have shaped distribution of amphidromous goby species still remain unknown. Previous studies show that phylogeographic breaks are observed between populations in the Indian and Pacific Oceans where the shallow Sunda shelf constituted a geographical barrier to dispersal, or that the large spans of open ocean that isolate the Hawaiian or Polynesian Islands are also barriers for amphidromous species even though they have great dispersal capacity. Here we assess past and present genetic structure of populations of two amphidromous fish (gobies of the Sicydiinae) that are widely distributed in the Central West Pacific and which have similar pelagic larval durations. We analysed sections of mitochondrial COI, Cytb and nuclear Rhodospine genes in individuals sampled from different locations across their entire known range. Similar to other Sicydiinae fish, intraspecific mtDNA genetic diversity was high for all species (haplotype diversity between 0.9–0.96). Spatial analyses of genetic variation in Sicyopus zosterophorum demonstrated strong isolation across the Torres Strait, which was a geologically intermittent land barrier linking Australia to Papua New Guinea. There was a clear genetic break between the northwestern and the southwestern clusters in Si. zosterophorum (φST = 0.67502 for COI) and coalescent analyses revealed that the two populations split at 306 Kyr BP (95% HPD 79–625 Kyr BP), which is consistent with a Pleistocene separation caused by the Torres Strait barrier. However, this geographical barrier did not seem to affect Sm. fehlmanni. Historical and demographic hypotheses are raised to explain the different patterns of population structure and distribution between these species. Strategies aiming to conserve amphidromous fish should consider the presence of cryptic evolutionary lineages to prevent stock depletion.
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Affiliation(s)
- Laura Taillebois
- Milieux et Peuplements Aquatiques - UMR 7208 (MNHN, CNRS, IRD, UPMC), Muséum national d'Histoire naturelle, Paris, France ; Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
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28
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Becking LE, Erpenbeck D, Peijnenburg KTCA, de Voogd NJ. Phylogeography of the sponge Suberites diversicolor in Indonesia: insights into the evolution of marine lake populations. PLoS One 2013; 8:e75996. [PMID: 24098416 PMCID: PMC3788070 DOI: 10.1371/journal.pone.0075996] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 08/09/2013] [Indexed: 11/19/2022] Open
Abstract
The existence of multiple independently derived populations in landlocked marine lakes provides an opportunity for fundamental research into the role of isolation in population divergence and speciation in marine taxa. Marine lakes are landlocked water bodies that maintain a marine character through narrow submarine connections to the sea and could be regarded as the marine equivalents of terrestrial islands. The sponge Suberites diversicolor (Porifera: Demospongiae: Suberitidae) is typical of marine lake habitats in the Indo-Australian Archipelago. Four molecular markers (two mitochondrial and two nuclear) were employed to study genetic structure of populations within and between marine lakes in Indonesia and three coastal locations in Indonesia, Singapore and Australia. Within populations of S. diversicolor two strongly divergent lineages (A & B) (COI: p = 0.4% and ITS: p = 7.3%) were found, that may constitute cryptic species. Lineage A only occurred in Kakaban lake (East Kalimantan), while lineage B was present in all sampled populations. Within lineage B, we found low levels of genetic diversity in lakes, though there was spatial genetic population structuring. The Australian population is genetically differentiated from the Indonesian populations. Within Indonesia we did not record an East-West barrier, which has frequently been reported for other marine invertebrates. Kakaban lake is the largest and most isolated marine lake in Indonesia and contains the highest genetic diversity with genetic variants not observed elsewhere. Kakaban lake may be an area where multiple putative refugia populations have come into secondary contact, resulting in high levels of genetic diversity and a high number of endemic species.
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Affiliation(s)
- Leontine E. Becking
- Naturalis Biodiversity Center, Department Marine Zoology, Leiden, The Netherlands
- Institute for Marine Resources and Ecosystem Studies (IMARES), Maritime Department, Den Helder, The Netherlands
- * E-mail:
| | - Dirk Erpenbeck
- Department of Earth- and Environmental Sciences, Palaeontology & Geobiology & GeoBio-Center, Ludwig-Maximilians-University, Munich, Germany
| | - Katja T. C. A. Peijnenburg
- Naturalis Biodiversity Center, Department Marine Zoology, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Nicole J. de Voogd
- Naturalis Biodiversity Center, Department Marine Zoology, Leiden, The Netherlands
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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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Tian C, Yang M, Liang XF, Cao L, Zheng H, Zhao C, Zhu K, Yuan Y. Population genetic structure of Siniperca chuatsi in the middle reach of the Yangtze River inferred from mitochondrial DNA and microsatellite loci. ACTA ACUST UNITED AC 2013; 26:61-7. [PMID: 23919325 DOI: 10.3109/19401736.2013.823169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Chinese mandarin fish (Siniperca chuatsi) is currently one of the most important economic freshwater fish in China, whereas the wild resource has declined dramatically in recent years. In this study, we examined the genetic structure and diversity of five populations from the middle reach of the Yangtze River using mitochondrial cytochrome b sequences and microsatellite markers. This research revealed high genetic diversity and low genetic differentiation of S. chuatsi from these regions. The pairwise Fst values of the two markers showed low and no-significant differentiation among populations. AMOVA analysis of two markers and the haplotype genealogy of the Cytb gene confirmed these results. The STRUCTURE analysis of the microsatellite marker implied that the dam upon the tributary of the Yangtze River blocked the gene flow among those regions. This research will be useful in breeding programs and conservation management of this species.
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Affiliation(s)
- Changxu Tian
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan , Hubei , China and
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Lind CE, Evans BS, Elphinstone MS, Taylor JJU, Jerry DR. Phylogeography of a pearl oyster (Pinctada maxima) across the Indo-Australian Archipelago: evidence of strong regional structure and population expansions but no phylogenetic breaks. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01960.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Curtis E. Lind
- Aquaculture Genetics Research Group; School of Marine & Tropical Biology; James Cook University; Townsville Qld 4811 Australia
- Fish Breeding and Genetics Group; The WorldFish Center; PO Box 500 GPO 10670 Penang Malaysia
| | - Brad S. Evans
- Aquaculture Genetics Research Group; School of Marine & Tropical Biology; James Cook University; Townsville Qld 4811 Australia
| | - Martin S. Elphinstone
- Centre for Plant Conservation Genetics; Southern Cross University; Lismore NSW 2480 Australia
| | | | - Dean R. Jerry
- Aquaculture Genetics Research Group; School of Marine & Tropical Biology; James Cook University; Townsville Qld 4811 Australia
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High similarity of genetic population structure in the false clown anemonefish (Amphiprion ocellaris) found in microsatellite and mitochondrial control region analysis. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0318-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Barber P, Cheng S, Erdmann M, Tenggardjaja K. Evolution and conservation of marine biodiversity in the Coral Triangle. CRUSTACEAN ISSUES 2011. [DOI: 10.1201/b11113-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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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, Rocha LA, Craig MT, Bowen BW. Not All Larvae Stay Close to Home: Insights into Marine Population Connectivity with a Focus on the Brown Surgeonfish ( Acanthurus nigrofuscus). JOURNAL OF MARINE BIOLOGY 2011; 2011:518516. [PMID: 25505914 PMCID: PMC4260469 DOI: 10.1155/2011/518516] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Recent reports of localized larval recruitment in predominately small-range fishes are countered by studies that show high genetic connectivity across large oceanic distances. This discrepancy may result from the different timescales over which genetic and demographic processes operate or rather may indicate regular long-distance dispersal in some species. Here, we contribute an analysis of mtDNA cytochrome b diversity in the widely distributed Brown Surgeonfish (Acanthurus nigrofuscus; N = 560), which revealed significant genetic structure only at the extremes of the range (ΦCT = 0.452; P < .001). Collections from Hawaii to the Eastern Indian Ocean comprise one large, undifferentiated population. This pattern of limited genetic subdivision across reefs of the central Indo-Pacific has been observed in a number of large-range reef fishes. Conversely, small-range fishes are often deeply structured over the same area. These findings demonstrate population connectivity differences among species at biogeographic and evolutionary timescales, which likely translates into differences in dispersal ability at ecological and demographic timescales. While interspecific differences in population connectivity complicate the design of management strategies, the integration of multiscale connectivity patterns into marine resource planning will help ensure long-term ecosystem stability by preserving functionally diverse communities.
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Affiliation(s)
- Jeff A. Eble
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, P.O. Box 1346, Kaneohe, HI 96744, USA
| | - Luiz A. Rocha
- Marine Science Institute, University of Texas at Austin, Port Aransas, TX 78373, USA
| | - Matthew T. Craig
- Department of Marine Sciences, University of Puerto Rico Mayagüez, P.O. Box 9000, Mayagüez, PR 00681, USA
| | - Brian W. Bowen
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, P.O. Box 1346, Kaneohe, HI 96744, USA
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