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Liu J, Lindstrom AJ, Chen YS, Nathan R, Gong X. Congruence between ocean-dispersal modelling and phylogeography explains recent evolutionary history of Cycas species with buoyant seeds. THE NEW PHYTOLOGIST 2021; 232:1863-1875. [PMID: 34342898 DOI: 10.1111/nph.17663] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/29/2021] [Indexed: 05/25/2023]
Abstract
Ocean currents play a significant role in driving the long-distance dispersal (LDD), spatial distribution and phylogeographic patterns of many organisms. Integrating phylogeographic analyses and mechanistic ocean current modelling can provide novel insights into the evolutionary history of terrestrial littoral species but has been rarely applied in this context. We focused on a group of Cycas that have buoyant seeds and occupy coastal habitats. By integrating evidence from mechanistic simulations and whole plastomic data, we examined the role of ocean circulation in shaping the phylogeography of these Cycas species. Plastomes of the studied Cycas species showed extreme conservatism, following a post-Pleistocene divergence. Phylogenies revealed three subclades, corresponding to the Pacific Ocean, Sunda Shelf and Indian Ocean. The ocean modelling results indicate that hotspots of seed stranding coincide well with the contemporary distribution of the Cycas species and that drifting trajectories from the three subclades are largely confined to separate regions. These findings suggest that ocean current systems, by driving long-distance dispersal, have shaped the distribution and phylogeography for Cycas with buoyant seeds. This study highlights how the combination of genomic data and ocean drift modelling can help explain phylogeographic patterns and diversity in terrestrial littoral ecosystems.
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Affiliation(s)
- Jian Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Anders J Lindstrom
- Global Biodiversity Conservancy, 144/124 Moo3, Soi Bua Thong, Bangsalae, Sattahip, Chonburi, 20250, Thailand
| | - Yong-Sheng Chen
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Ran Nathan
- Movement Ecology Laboratory, Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Xun Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Takeuchi T, Masaoka T, Aoki H, Koyanagi R, Fujie M, Satoh N. Divergent northern and southern populations and demographic history of the pearl oyster in the western Pacific revealed with genomic SNPs. Evol Appl 2020; 13:837-853. [PMID: 32211071 PMCID: PMC7086055 DOI: 10.1111/eva.12905] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 12/26/2022] Open
Abstract
In the open ocean without terrain boundaries, marine invertebrates with pelagic larvae can migrate long distances using ocean currents, suggesting reduced genetic diversification. Contrary to this assumption, however, genetic differentiation is often observed in marine invertebrates. In the present study, we sought to explain how population structure is established in the western Pacific Ocean, where the strong Kuroshio Current maintains high levels of gene flow from south to north, presumably promoting genetic homogeneity. We determined the population structure of the pearl oyster, Pinctada fucata, in the Indo-Pacific Ocean using genome-wide genotyping data from multiple sampling localities. Cluster analysis showed that the western Pacific population is distinct from that of the Indian Ocean, and that it is divided into northern (Japanese mainland) and southern (Nansei Islands, China, and Cambodia) populations. Genetic differentiation of P. fucata can be explained by geographic barriers in the Indian Ocean and a local lagoon, and by environmental gradients of sea surface temperature (SST) and oxygen concentration in the western Pacific. A genome scan showed evidence of adaptive evolution in genomic loci, possibly associated with changes in environmental factors, including SST and oxygen concentration. Furthermore, Bayesian simulation demonstrated that the past population expansion and division are congruent with ocean warming after the last glacial period. It is highly likely that the environmental gradient forms a genetic barrier that diversifies P. fucata populations in the western Pacific. This hypothesis helps to explain genetic differentiation and possible speciation of marine invertebrates.
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Affiliation(s)
- Takeshi Takeuchi
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Tetsuji Masaoka
- Aquaculture Technology DivisionNational Research Institute of Aquaculture, Fisheries Research and Education AgencyTamaki‐choJapan
| | - Hideo Aoki
- Mie Prefecture Fisheries Research InstituteShimaJapan
| | - Ryo Koyanagi
- DNA Sequencing SectionOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Manabu Fujie
- DNA Sequencing SectionOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Noriyuki Satoh
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
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Burn D, Matthews S, Caballes CF, Chandler JF, Pratchett MS. Biogeographical variation in diurnal behaviour of Acanthaster planci versus Acanthaster cf. solaris. PLoS One 2020; 15:e0228796. [PMID: 32078663 PMCID: PMC7032693 DOI: 10.1371/journal.pone.0228796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/22/2020] [Indexed: 11/24/2022] Open
Abstract
Crown-of-thorns starfish (CoTS; Acanthaster spp.) are among the most extensively studied coral reef taxa, largely owing to their devastating impacts on live coral cover during population outbreaks. Much of this research has however, been conducted in the western Pacific, although it is now apparent that there are several distinct species of Acanthaster spp. across the Indo-Pacific. The purpose of this study was to test for biogeographical variation in behaviour, comparing between Acanthaster planci at Lankanfushi Island in the Maldives and Acanthaster cf. solaris at Rib Reef on Australia's Great Barrier Reef. The extent to which CoTS were exposed (cf. concealed within or beneath coral substrates) was substantially higher (63.14%) for A. planci at Lankanfushi Island, compared to 28.55% for A. cf. solaris at Rib Reef, regardless of time of day. More importantly, only 52% of individuals were exposed at night at Rib Reef compared to >97% at reefs around Lankanfushi Island. Biogeographic variation in the behaviour of Acanthaster spp. was independent of differences in the size structure of starfish and coral cover at specific study sites, but may be attributable to other environmental factors such as habitat complexity or prey availability. This is the first study to explicitly test for biogeographical differences in the biology and behaviour of Acanthaster spp., potentially linked to species-specific differences in the causes and explanations of population outbreaks. However, we did not find evidence at this stage of differences in behavior among regions, rather behavioural differences observed were most likely products of different environments.
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Affiliation(s)
- Deborah Burn
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Samuel Matthews
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Ciemon F. Caballes
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Ultra Coral Australia, Paget, Queensland, Australia
| | - Josie F. Chandler
- Gili Lankanfushi Resort, Lankanfushi Island, North Male Atoll, Maldives
| | - Morgan S. Pratchett
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
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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: 1.6] [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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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: 20] [Impact Index Per Article: 2.5] [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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Otwoma LM, Kochzius M. Genetic Population Structure of the Coral Reef Sea Star Linckia laevigata in the Western Indian Ocean and Indo-West Pacific. PLoS One 2016; 11:e0165552. [PMID: 27798700 PMCID: PMC5087890 DOI: 10.1371/journal.pone.0165552] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/13/2016] [Indexed: 11/18/2022] Open
Abstract
The coral reef sea star Linckia laevigata is common on shallow water coral reefs of the Indo-West Pacific. Its large geographic distribution and comprehensive data from previous studies makes it suitable to examine genetic differentiation and connectivity over large geographical scales. Based on partial sequences of the mitochondrial cytochrome oxidase I (COI) gene this study investigates the genetic population structure and connectivity of L. laevigata in the Western Indian Ocean (WIO) and compares it to previous studies in the Indo-Malay-Philippines Archipelago (IMPA). A total of 138 samples were collected from nine locations in the WIO. AMOVA revealed a low but significant ΦST-value of 0.024 for the WIO populations. In the hierarchical AMOVA, the following grouping rejected the hypothesis of panmixia: (1) Kenya (Watamu, Mombasa, Diani) and Tanzanian Island populations (Misali and Jambiani) and (2) the rest of the WIO sites (mainland Tanzania and Madagascar; ΦCT = 0.03). The genetic population structure was stronger and more significant (ΦST = 0.13) in the comparative analysis of WIO and IMPA populations. Three clades were identified in the haplotype network. The strong genetic differentiation (ΦCT = 0.199, P < 0.001) suggests that Indo-West Pacific populations of L. laevigata can be grouped into four biogeographic regions: (1) WIO (2) Eastern Indian Ocean (3) IMPA and (4) Western Pacific. The findings of this study support the existence of a genetic break in the Indo-West Pacific consistent with the effect of lowered sea level during the Pleistocene, which limited gene flow between the Pacific and Indian Ocean.
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Affiliation(s)
- Levy Michael Otwoma
- Kenya Marine and Fisheries Research Institute, P.O. BOX 81651, Mombasa, Kenya
- Marine Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Marc Kochzius
- Marine Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
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Li X, Duke NC, Yang Y, Huang L, Zhu Y, Zhang Z, Zhou R, Zhong C, Huang Y, Shi S. Re-Evaluation of Phylogenetic Relationships among Species of the Mangrove Genus Avicennia from Indo-West Pacific Based on Multilocus Analyses. PLoS One 2016; 11:e0164453. [PMID: 27716800 PMCID: PMC5055292 DOI: 10.1371/journal.pone.0164453] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/26/2016] [Indexed: 01/31/2023] Open
Abstract
Avicennia L. (Avicenniaceae), one of the most diverse mangrove genera, is distributed widely in tropical and subtropical intertidal zones worldwide. Five species of Avicennia in the Indo-West Pacific region have been previously described. However, their phylogenetic relationships were determined based on morphological and allozyme data. To enhance our understanding of evolutionary patterns in the clade, we carried out a molecular phylogenetic study using wide sampling and multiple loci. Our results support two monophyletic clades across all species worldwide in Avicennia: an Atlantic-East Pacific (AEP) lineage and an Indo-West Pacific (IWP) lineage. This split is in line with biogeographic distribution of the clade. Focusing on the IWP branch, we reconstructed a detailed phylogenetic tree based on sequences from 25 nuclear genes. The results identified three distinct subclades, (1) A. rumphiana and A. alba, (2) A. officinalis and A. integra, and (3) the A. marina complex, with high bootstrap support. The results strongly corresponded to two morphological traits in floral structure: stigma position in relation to the anthers and style length. Using Bayesian dating methods we estimated diversification of the IWP lineage was dated to late Miocene (c. 6.0 million years ago) and may have been driven largely by the fluctuating sea levels since that time.
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Affiliation(s)
- Xinnian Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Norman C. Duke
- Trop WATER, James Cook University, Townsville, Queensland, Australia
| | - Yuchen Yang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lishi Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuxiang Zhu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhang Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature Reserve, Haikou, Hainan, China
| | - Yelin Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (YH); (SS)
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (YH); (SS)
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Tusso S, Morcinek K, Vogler C, Schupp PJ, Caballes CF, Vargas S, Wörheide G. Genetic structure of the crown-of-thorns seastar in the Pacific Ocean, with focus on Guam. PeerJ 2016; 4:e1970. [PMID: 27168979 PMCID: PMC4860296 DOI: 10.7717/peerj.1970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 04/04/2016] [Indexed: 11/20/2022] Open
Abstract
Population outbreaks of the corallivorous crown-of-thorns seastar (COTS), Acanthaster 'planci' L., are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared samples from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations sampled were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island; (2) Japan, Philippines, GBR and Vanuatu; and (3) Johnston Atoll, which was significantly different from all other localities. The lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island suggests potential long-distance dispersal of COTS in the Pacific.
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Affiliation(s)
- Sergio Tusso
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München , München , Germany
| | - Kerstin Morcinek
- Department of Anatomy (Neuroanatomy), University of Cologne , Köln , Germany
| | - Catherine Vogler
- Environment Department, Pöyry Switzerland Ltd. , Zurich , Switzerland
| | - Peter J Schupp
- Environmental Biochemistry, Carl-von-Ossietzky University Oldenburg, ICBM-Terramare , Wilhelmshaven , Germany
| | - Ciemon F Caballes
- ARC Centre of Excellence for Coral Reef Studies, James Cook University , Townsville, Queensland , Australia
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München , München , Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany; SNSB-Bavarian State Collections of Palaeontology and Geology, München, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
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Wee AKS, Takayama K, Chua JL, Asakawa T, Meenakshisundaram SH, Onrizal, Adjie B, Ardli ER, Sungkaew S, Malekal NB, Tung NX, Salmo SG, Yllano OB, Saleh MN, Soe KK, Tateishi Y, Watano Y, Baba S, Webb EL, Kajita T. Genetic differentiation and phylogeography of partially sympatric species complex Rhizophora mucronata Lam. and R. stylosa Griff. using SSR markers. BMC Evol Biol 2015; 15:57. [PMID: 25888261 PMCID: PMC4389924 DOI: 10.1186/s12862-015-0331-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 03/04/2015] [Indexed: 11/10/2022] Open
Abstract
Background Mangrove forests are ecologically important but globally threatened intertidal plant communities. Effective mangrove conservation requires the determination of species identity, management units, and genetic structure. Here, we investigate the genetic distinctiveness and genetic structure of an iconic but yet taxonomically confusing species complex Rhizophora mucronata and R. stylosa across their distributional range, by employing a suite of 20 informative nuclear SSR markers. Results Our results demonstrated the general genetic distinctiveness of R. mucronata and R. stylosa, and potential hybridization or introgression between them. We investigated the population genetics of each species without the putative hybrids, and found strong genetic structure between oceanic regions in both R. mucronata and R. stylosa. In R. mucronata, a strong divergence was detected between populations from the Indian Ocean region (Indian Ocean and Andaman Sea) and the Pacific Ocean region (Malacca Strait, South China Sea and Northwest Pacific Ocean). In R. stylosa, the genetic break was located more eastward, between populations from South and East China Sea and populations from the Southwest Pacific Ocean. The location of these genetic breaks coincided with the boundaries of oceanic currents, thus suggesting that oceanic circulation patterns might have acted as a cryptic barrier to gene flow. Conclusions Our findings have important implications on the conservation of mangroves, especially relating to replanting efforts and the definition of evolutionary significant units in Rhizophora species. We outlined the genetic structure and identified geographical areas that require further investigations for both R. mucronata and R. stylosa. These results serve as the foundation for the conservation genetics of R. mucronata and R. stylosa and highlighted the need to recognize the genetic distinctiveness of closely-related species, determine their respective genetic structure, and avoid artificially promoting hybridization in mangrove restoration programmes. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0331-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alison K S Wee
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan. .,Present Address: Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China.
| | - Koji Takayama
- The University Museum, The University of Tokyo, Hongo 7-3-1, Tokyo, 113-0033, Japan.
| | - Jasher L Chua
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
| | - Takeshi Asakawa
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
| | | | - Onrizal
- Forestry Sciences Department, Universitas Sumatera Utara, Medan, Indonesia.
| | - Bayu Adjie
- Bali Botanical Garden, Indonesian Institute of Sciences, Bali, Indonesia.
| | | | - Sarawood Sungkaew
- Forest Biology Department, Faculty of Forestry, Kasetsart University, Bangkok, Thailand.
| | - Norhaslinda Binti Malekal
- Institute for Tropical Biology and Conservation, Universiti Malaysia Kota Kinabalu, Kota Kinabalu, Malaysia.
| | - Nguyen Xuan Tung
- Mangrove Ecosystem Research Centre, Hanoi National University of Education, Hanoi, Vietnam.
| | - Severino G Salmo
- Department of Environmental Science, School of Science and Engineering, Ateneo de Manila University, Quezon City, Philippines.
| | - Orlex Baylen Yllano
- Biology Department, College of Science and Technology, Adventist University of the Philippines, Silang, 4118, Cavite, Philippines.
| | - M Nazre Saleh
- Department of Forest Production, Faculty of Forestry, Universiti Putra Malaysia, Serdang, Malaysia.
| | - Khin Khin Soe
- Department of Botany, University of Yangon, Yangon, Myanmar.
| | - Yoichi Tateishi
- Faculty of Education, University of the Ryukyus, Senbaru, Okinawa, Japan.
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
| | - Shigeyuki Baba
- Tropical Biosphere Research Center, University of the Ryukyus, Iriomote, Okinawa, Japan. .,International Society for Mangrove Ecosystems (ISME), c/o Faculty of Agriculture, University of the Ryukyus, Senbaru, Okinawa, 903-0129, Japan.
| | - Edward L Webb
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
| | - Tadashi Kajita
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
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Jackson AM, Semmens BX, Sadovy de Mitcheson Y, Nemeth RS, Heppell SA, Bush PG, Aguilar-Perera A, Claydon JAB, Calosso MC, Sealey KS, Schärer MT, Bernardi G. Population structure and phylogeography in Nassau grouper (Epinephelus striatus), a mass-aggregating marine fish. PLoS One 2014; 9:e97508. [PMID: 24830641 PMCID: PMC4022523 DOI: 10.1371/journal.pone.0097508] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 04/18/2014] [Indexed: 11/19/2022] Open
Abstract
To address patterns of genetic connectivity in a mass-aggregating marine fish, we analyzed genetic variation in mitochondrial DNA (mtDNA), microsatellites, and single nucleotide polymorphisms (SNPs) for Nassau grouper (Epinephelus striatus). We expected Nassau grouper to exhibit genetic differentiation among its subpopulations due to its reproductive behavior and retentive oceanographic conditions experienced across the Caribbean basin. All samples were genotyped for two mitochondrial markers and 9 microsatellite loci, and a subset of samples were genotyped for 4,234 SNPs. We found evidence of genetic differentiation in a Caribbean-wide study of this mass-aggregating marine fish using mtDNA (FST = 0.206, p<0.001), microsatellites (FST = 0.002, p = 0.004) and SNPs (FST = 0.002, p = 0.014), and identified three potential barriers to larval dispersal. Genetically isolated regions identified in our work mirror those seen for other invertebrate and fish species in the Caribbean basin. Oceanographic regimes in the Caribbean may largely explain patterns of genetic differentiation among Nassau grouper subpopulations. Regional patterns observed warrant standardization of fisheries management and conservation initiatives among countries within genetically isolated regions.
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Affiliation(s)
- Alexis M. Jackson
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
| | - Brice X. Semmens
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | | | - Richard S. Nemeth
- Department of Zoology/Marine Biology, University of the Virgin Islands, St. Thomas, Virgin Islands, United States of America
| | - Scott A. Heppell
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
| | - Phillippe G. Bush
- Protection and Conservation Unit, Cayman Islands Department of the Environment, Grand Cayman, British West Indies
| | - Alfonso Aguilar-Perera
- Departmento de Biología Marina, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - John A. B. Claydon
- The School for Field Studies, Center for Marine Resource Studies, South Caicos, Turks and Caicos Islands
| | - Marta C. Calosso
- The School for Field Studies, Center for Marine Resource Studies, South Caicos, Turks and Caicos Islands
| | - Kathleen S. Sealey
- Department of Biology, University of Miami, Coral Gables, Florida, United States of America
| | | | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
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11
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Phylogeography of the crown-of-thorns starfish in the Indian Ocean. PLoS One 2012; 7:e43499. [PMID: 22927975 PMCID: PMC3424128 DOI: 10.1371/journal.pone.0043499] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 07/24/2012] [Indexed: 01/01/2023] Open
Abstract
Background Understanding the limits and population dynamics of closely related sibling species in the marine realm is particularly relevant in organisms that require management. The crown-of-thorns starfish Acanthaster planci, recently shown to be a species complex of at least four closely related species, is a coral predator infamous for its outbreaks that have devastated reefs throughout much of its Indo-Pacific distribution. Methodology/Principal Findings In this first Indian Ocean-wide genetic study of a marine organism we investigated the genetic structure and inferred the paleohistory of the two Indian Ocean sister-species of Acanthaster planci using mitochondrial DNA sequence analyses. We suggest that the first of two main diversification events led to the formation of a Southern and Northern Indian Ocean sister-species in the late Pliocene-early Pleistocene. The second led to the formation of two internal clades within each species around the onset of the last interglacial. The subsequent demographic history of the two lineages strongly differed, the Southern Indian Ocean sister-species showing a signature of recent population expansion and hardly any regional structure, whereas the Northern Indian Ocean sister-species apparently maintained a constant size with highly differentiated regional groupings that were asymmetrically connected by gene flow. Conclusions/Significance Past and present surface circulation patterns in conjunction with ocean primary productivity were identified as the processes most likely to have shaped the genetic structure between and within the two Indian Ocean lineages. This knowledge will help to understand the biological or ecological differences of the two sibling species and therefore aid in developing strategies to manage population outbreaks of this coral predator in the Indian Ocean.
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12
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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: 4.9] [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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Vogler C, Benzie J, Lessios H, Barber P, Wörheide G. A threat to coral reefs multiplied? Four species of crown-of-thorns starfish. Biol Lett 2009; 4:696-9. [PMID: 18832058 DOI: 10.1098/rsbl.2008.0454] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In the face of ever-increasing threats to coral reef ecosystems, it is essential to understand the impact of natural predators in order to devise appropriate management strategies. Destructive population explosions of the crown-of-thorns starfish Acanthaster planci have devastated coral reefs throughout the Indo-Pacific for decades. But despite extensive research, the causes of outbreaks are still unclear. An important consideration in this research is that A. planci has been regarded as a single taxonomic entity. Using molecular data from its entire distribution, we find that A. planci is in fact a species complex. This discovery has important consequences for future coral reef research, and might prove critical for successful reef conservation management.
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Affiliation(s)
- Catherine Vogler
- Courant Research Center Geobiology, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
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Wörheide G, Epp LS, Macis L. Deep genetic divergences among Indo-Pacific populations of the coral reef sponge Leucetta chagosensis (Leucettidae): founder effects, vicariance, or both? BMC Evol Biol 2008; 8:24. [PMID: 18221552 PMCID: PMC2267160 DOI: 10.1186/1471-2148-8-24] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 01/26/2008] [Indexed: 11/26/2022] Open
Abstract
Background An increasing number of studies demonstrate that genetic differentiation and speciation in the sea occur over much smaller spatial scales than previously appreciated given the wide distribution range of many morphologically defined coral reef invertebrate species and the presumed dispersal-enhancing qualities of ocean currents. However, knowledge about the processes that lead to population divergence and speciation is often lacking despite being essential for the understanding, conservation, and management of marine biodiversity. Sponges, a highly diverse, ecologically and economically important reef-invertebrate taxon, exhibit spatial trends in the Indo-West Pacific that are not universally reflected in other marine phyla. So far, however, processes generating those unexpected patterns are not understood. Results We unraveled the phylogeographic structure of the widespread Indo-Pacific coral reef sponge Leucetta chagosensis across its known geographic range using two nuclear markers: the rDNA internal transcribed spacers (ITS 1&2) and a fragment of the 28S gene, as well as the second intron of the ATP synthetase beta subunit-gene (ATPSb-iII). This enabled the detection of several deeply divergent clades congruent over both loci, one containing specimens from the Indian Ocean (Red Sea and Maldives), another one from the Philippines, and two other large and substructured NW Pacific and SW Pacific clades with an area of overlap in the Great Barrier Reef/Coral Sea. Reciprocally monophyletic populations were observed from the Philippines, Red Sea, Maldives, Japan, Samoa, and Polynesia, demonstrating long-standing isolation. Populations along the South Equatorial Current in the south-western Pacific showed isolation-by-distance effects. Overall, the results pointed towards stepping-stone dispersal with some putative long-distance exchange, consistent with expectations from low dispersal capabilities. Conclusion We argue that both founder and vicariance events during the late Pliocene and Pleistocene were responsible to varying degrees for generating the deep phylogeographic structure. This structure was perpetuated largely as a result of the life history of L. chagosensis, resulting in high levels of regional isolation. Reciprocally monophyletic populations constitute putative sibling (cryptic) species, while population para- and polyphyly may indicate incipient speciation processes. The genetic diversity and biodiversity of tropical Indo-Pacific sponges appears to be substantially underestimated since the high level of genetic divergence is not necessarily manifested at the morphological level.
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Affiliation(s)
- Gert Wörheide
- Courant Research Center Geobiology, Georg-August-Universität Göttingen, Goldschmidtstr. 3, D-37077 Göttingen, Germany.
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Lessios HA, Kane J, Robertson DR. Phylogeography of the pantropical sea urchin Tripneustes: contrasting patterns of population structure between oceans. Evolution 2004; 57:2026-36. [PMID: 14575324 DOI: 10.1111/j.0014-3820.2003.tb00382.x] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To understand how allopatric speciation proceeds, we need information on barriers to gene flow, their antiquity, and their efficacy. For marine organisms with planktonic larvae, much of this information can only be obtained through the determination of divergence between populations. We evaluated the importance of ocean barriers by studying the mitochondrial DNA phylogeography of Tripneustes, a pantropical genus of shallow water sea urchin. A region of cytochrome oxidase I (COI) was sequenced in 187 individuals from locations around the globe. The COI phylogeny agreed with a previously published phylogeny of bindin that barriers important to the evolution of Tripneustes are: (1) the cold water upwelling close to the tip of South Africa, (2) the Isthmus of Panama, (3) the long stretch of deep water separating the eastern from the western Atlantic, and (4) the freshwater plume of the Orinoco and the Amazon rivers between the Caribbean and the coast of Brazil. These barriers have previously been shown to be important in at least a subset of the shallow water marine organisms in which phylogeography has been studied. In contrast, the Eastern Pacific Barrier, 5000 km of deep water between the central and the eastern Pacific that has caused the deepest splits in other genera of sea urchins, is remarkably unimportant as a cause of genetic subdivision in Tripneustes. There is also no discernible subdivision between the Pacific and Indian Ocean populations of this genus. The most common COI haplotype is found in the eastern, central, and western Pacific as well as the Indian Ocean. Morphology, COI, and bindin data agree that T. depressus from the eastern Pacific and T. gratilla from the western Pacific are, in fact, the same species. The distribution of haplotype differences in the Indo-Pacific exhibits characteristics expected from a sea urchin genus with ephemeral local populations, but with high fecundity, dispersal, and growth: there is little phylogenetic structure, and mismatch distributions conform to models of recent population expansion on a nearly global scale. Yet, comparisons between local populations produce large and significant F(ST) values, indicating nonrandom haplotype distribution. This apparent local differentiation is only weakly reflected in regional divergence, and there is no evidence of isolation by distance in correlations between F(ST) values and either geographical or current distance. Thus, Tripneustes in the Indo-Pacific (but not in the Atlantic) seems to be one large metapopulation spanning two oceans and containing chaotic, nonequilibrium local variation, produced by the haphazard arrival of larvae or by unpredictable local extinction.
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Affiliation(s)
- H A Lessios
- Smithsonian Tropical Research Institute, Box 2072, Balboa, Panama.
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Uthicke S, Benzie JAH. Gene flow and population history in high dispersal marine invertebrates: mitochondrial DNA analysis of Holothuria nobilis (Echinodermata: Holothuroidea) populations from the Indo-Pacific. Mol Ecol 2003; 12:2635-48. [PMID: 12969467 DOI: 10.1046/j.1365-294x.2003.01954.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The sea cucumber, Holothuria nobilis, has a long-lived planktotrophic larvae, and previous allozyme surveys have suggested that high dispersal is realized. In contrast, recent ecological studies indicate that dispersal is low. To reconcile these data, and to investigate the evolution of this Indo-Pacific species, we screened geographical variation in 559 bp of a mitochondrial gene (COI) in 360 samples from the Australasian region and La Réunion. Sequences from La Réunion differed by > 7% from others and may constitute another species. Haplotype diversity in other samples was high (0.942, SD = 0.007), but haplotypes were closely related (mean nucleotide diversity: 0.0075, SD = 0.0041). AMOVA, pairwise FST values and exact tests did not detect significant population structure. Nested clade analysis showed that one of two main clades was over-represented in west Australia, whereas the other was more common in the northern Great Barrier Reef. Isolation-by-distance was identified as the main determinant of population structure at several clade levels. Contiguous range expansion was inferred for evolutionary older clade levels and this may correspond to a late Pleistocene (88 000-193 000 years ago) population expansion inferred from haplotype mismatch distributions. Thus, the population genetic structures detected are likely to be formed prior to the last ice age, with some indications for high dispersal on shorter time scales.
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Affiliation(s)
- S Uthicke
- Australian Institute of Marine Science, PMB no. 3, Townsville, Queensland 4810, Australia.
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