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Jeena NS, Rahuman S, Sebastian W, Kumar R, Sajeela KA, Kizhakudan JK, Menon KK, Roul SK, Gopalakrishnan A, Radhakrishnan EV. Mitogenomic recognition of incognito lineages in the mud spiny lobster Panulirus polyphagus (Herbst, 1793): A tale of unique genetic structuring and diversification. Int J Biol Macromol 2024:134327. [PMID: 39098694 DOI: 10.1016/j.ijbiomac.2024.134327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
This study provides the first documentation of three deep conspecific lineages within Panulirus polyphagus in the Indian Ocean, bridging the gap in genetic research. Comparative mitogenomics between lineages (L) at both species and family levels, evolutionary relationships and heterogeneity of sequence divergence within Decapoda, and divergence time estimation were performed. The characterized mitogenomes ranged from 15,685-15,705 bp in size and exhibited a typical pancrustacean pattern. Among the three lineages, L1 predominated the Bay of Bengal, L2 the Arabian Sea, and L2.a, a less common lineage genetically closer to L2, was restricted to the latter region. A minor lineage L1.a, was observed in the Coral Triangle area. All PCGs displayed evidence of purifying selection across species and family levels. The largest genetic distance (K2P) between lineages was 9 %, notably between L1.a and L2.a. The phylogenetic tree subdivided the Achelates into Palinuridae and Scyllaridae, and the topology demonstrated a distinct pattern of lineage diversification within P. polyphagus. AliGROOVE analyzes revealed no discernible divergence in Decapoda. The diversification of P. polyphagus appears to have occurred during Miocene, with further diversification in Pliocene. Furthermore, genetic stocks and population connectivity recognized here will provide valuable insight for spatial management planning of this dwindling resource.
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Affiliation(s)
- N S Jeena
- Marine Biotechnology, Fish Nutrition and Health Division, CMFRI, Kochi, Kerala, India.
| | - Summaya Rahuman
- Marine Biotechnology, Fish Nutrition and Health Division, CMFRI, Kochi, Kerala, India
| | - Wilson Sebastian
- Centre for Marine Living Resources and Ecology (CMLRE), Kochi, Kerala, India
| | - Rajan Kumar
- Shellfish Fisheries Division, Regional Centre of CMFRI, Veraval, Gujarat, India
| | - K A Sajeela
- Marine Biotechnology, Fish Nutrition and Health Division, CMFRI, Kochi, Kerala, India
| | - Joe K Kizhakudan
- Mariculture Division, Regional Centre of CMFRI, Visakhapatnam, Andhra Pradesh, India
| | | | - Subal Kumar Roul
- Finfish Fisheries Division, Regional Centre of CMFRI, Digha, West Bengal, India
| | - A Gopalakrishnan
- Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India
| | - E V Radhakrishnan
- Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India
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2
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Briones C, Nuñez JJ, Pérez M, Garrido O, Campos B, Godoy K, Hartley R, Oyarzún PA, Guiñez R. Linking Acrosome Size and Genetic Divergence in an Inter-Oceanic Mussel from the Pacific and Atlantic Coasts: A Case of Incipient Speciation? Animals (Basel) 2024; 14:674. [PMID: 38473058 DOI: 10.3390/ani14050674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
In recent years, advances in analyses of the sperm morphology and genetics of Perumytilus purpuratus have allowed to two evolutionary scenarios for this mussel to be suggested: (1) the scenario of cryptic species and (2) the scenario of incipient or in progress speciation. For a better understanding of the evolutionary history of P. purpuratus, we performed extensive sampling along a latitudinal gradient of ca. 7180 km of coastline-from the Southern Pacific Ocean to the Atlantic Ocean-and we delved deeper into the sperm morphology of P. purpuratus, exploring its association with the phylogeny and population genetics to determine whether the variability in sperm traits between the northern and southern regions was a signal of cryptic or incipient species. Overall, our results showed that sperm sizes were strongly correlated with the genetic structure in males of P. purpuratus. We identified at 37° S on the Pacific coast a coincident break of both sperm size and genetic disruption that can be explained by historical events and postglacial recolonization as causal phenomena for the observed divergences. Furthermore, evidence of genetic admixture between lineages was found at 38° S, suggesting the presence of an introgressive hybridization zone and incomplete reproductive isolation in an in fraganti or incipient speciation process.
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Affiliation(s)
- Carolina Briones
- Instituto de Ciencias Naturales Alexander von Humbodt, Facultad de Ciencias del Mar y de Recursos Biológicos, Universidad de Antofagasta, Angamos 601, Antofagasta 1270300, Chile
| | - José J Nuñez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia 5090000, Chile
| | - Montse Pérez
- AquaCOV, Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas (IEO, CSIC), 36390 Vigo, Spain
| | - Orlando Garrido
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia 5090000, Chile
| | | | - Karina Godoy
- Núcleo Científico y Tecnológico de Biorecursos (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
| | - Ricardo Hartley
- Instituto de Investigación y Postgrado, Facultad de Medicina y Ciencias de la Salud, Universidad Central de Chile, Santiago 8330507, Chile
| | - Pablo A Oyarzún
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay 2340000, Chile
| | - Ricardo Guiñez
- Instituto de Ciencias Naturales Alexander von Humbodt, Facultad de Ciencias del Mar y de Recursos Biológicos, Universidad de Antofagasta, Angamos 601, Antofagasta 1270300, Chile
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3
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Kagawa O, Hirota SK, Saito T, Uchida S, Watanabe H, Miyazoe R, Yamaguchi T, Matsuno T, Araki K, Wakasugi H, Suzuki S, Kobayashi G, Miyazaki H, Suyama Y, Hanyuda T, Chiba S. Host-Shift Speciation Proceeded with Gene Flow in Algae Covering Shells. Am Nat 2023; 202:721-732. [PMID: 37963116 DOI: 10.1086/726221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
AbstractHost shifts represent the advancement of a novel niche and often lead to speciation in symbionts. However, its mechanisms are not well understood. Here, we focused on the alga Pseudocladophora conchopheria growing on the shells of intertidal snails. Previous surveys have shown that the alga has host specificity-only attaching to the shell of Lunella correensis-but we discovered that the alga attaches to the shells of multiple sympatric snails. A genome-wide single-nucleotide polymorphism analysis (MIG-seq) was performed to determine whether host-associated speciation occurred in the algae. As a result, there was no gene flow or limited gene flow among the algae from different hosts, and some algae were genetically differentiated among hosts. In addition, the demographic estimate revealed that speciation with gene flow occurred between the algae from different hosts. Therefore, these results support the idea that host-shift speciation gradually proceeded with gene flow in the algae, providing insight into the early evolution of host shifts.
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4
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Petak C, Frati L, Brennan RS, Pespeni MH. Whole-Genome Sequencing Reveals That Regulatory and Low Pleiotropy Variants Underlie Local Adaptation to Environmental Variability in Purple Sea Urchins. Am Nat 2023; 202:571-586. [PMID: 37792925 DOI: 10.1086/726013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
AbstractOrganisms experience environments that vary across both space and time. Such environmental heterogeneity shapes standing genetic variation and may influence species' capacity to adapt to rapid environmental change. However, we know little about the kind of genetic variation that is involved in local adaptation to environmental variability. To address this gap, we sequenced the whole genomes of 140 purple sea urchins (Strongylocentrotus purpuratus) from seven populations that vary in their degree of pH variability. Despite no evidence of global population structure, we found a suite of single-nucleotide polymorphisms (SNPs) tightly correlated with local pH variability (outlier SNPs), which were overrepresented in regions putatively involved in gene regulation (long noncoding RNA and enhancers), supporting the idea that variation in regulatory regions is important for local adaptation to variability. In addition, outliers in genes were found to be (i) enriched for biomineralization and ion homeostasis functions related to low pH response, (ii) less central to the protein-protein interaction network, and (iii) underrepresented among genes highly expressed during early development. Taken together, these results suggest that loci that underlie local adaptation to pH variability in purple sea urchins fall in regions with potentially low pleiotropic effects (based on analyses involving regulatory regions, network centrality, and expression time) involved in low pH response (based on functional enrichment).
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Lasley RM, Evans N, Paulay G, Michonneau F, Windsor A, Irwansyah, Ng PKL. Allopatric mosaics in the Indo-West Pacific crab subfamily Chlorodiellinae reveal correlated patterns of sympatry, genetic divergence, and genitalic disparity. Mol Phylogenet Evol 2023; 181:107710. [PMID: 36707010 DOI: 10.1016/j.ympev.2023.107710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/31/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023]
Abstract
Molecular studies have revealed that many species once thought to be wide-ranging in the Indo-West Pacific contain allopatric mosaics of endemic lineages. These lineages provide compelling evidence that substantial time is needed to evolve isolating mechanisms sufficient to permit successful secondary sympatry, and that divergence is initiated in allopatry. In this context, questions arise regarding the nature, timing, and origin of isolating mechanisms that permit secondary sympatry. We present a phylogeny of the crab subfamily Chlorodiellinae which displays allopatric mosaics within species. These allopatric lineages typically do not have divergent male genitalia, while older sympatric lineages do. We tested the relationship between genetic distance (proxy for time), sympatry, and the divergence of male genitalic morphology. Our results suggest that male genitalic divergence is not involved in the initiation of speciation in chlorodielline crabs, having likely occurred only after isolation began in allopatry. However, morphological evolution of genitalia seemingly does play an important role in completing the process of speciation in these crabs.
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Affiliation(s)
- Robert M Lasley
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA; University of Guam, EPSCoR, Mangilao 96926, Guam; National Museum of Natural History, Smithsonian Institution, Suitland, MD 20746, USA.
| | - Nathaniel Evans
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA; National Museum of Natural History, Smithsonian Institution, Suitland, MD 20746, USA; Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Gustav Paulay
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
| | - Francois Michonneau
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
| | - Amanda Windsor
- National Museum of Natural History, Smithsonian Institution, Suitland, MD 20746, USA
| | - Irwansyah
- Syiah Kuala University, Aceh 23111, Indonesia
| | - Peter K L Ng
- Lee Kong Chian Natural History Museum, National University of Singapore, 117377, Singapore
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6
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Peres PA, Bracken-Grissom H, Timm LE, Mantelatto FL. Genomic Analyses Implicate the Amazon-Orinoco Plume as the Driver of Cryptic Speciation in a Swimming Crab. Genes (Basel) 2022; 13:genes13122263. [PMID: 36553531 PMCID: PMC9777557 DOI: 10.3390/genes13122263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/04/2022] Open
Abstract
The Amazon-Orinoco plume (AOP) is the world's largest freshwater and sediment discharge into the ocean. Previous studies limited to mtDNA suggest that the swimming crab Callinectes ornatus Ordway, 1863 exists as two distinct genetic clusters separated by the AOP. However, questions concerning migration, diversification time, and species delimitation are unresolved. Densely sampling markers across the genome (SNPs) could elucidate the evolutionary processes within this species. Here, we combined mtDNA data and ddRAD-seq to explore the diversification patterns and processes within the swimming crab C. ornatus. We show great genetic differentiation between groups on the north and south sides of the plume but also signs of hybridization. Demographic modeling indicates the divergence between groups starting around 8 Mya following the AOP's formation. After a period of isolation, we detect two incidences of secondary contact with stronger migration in concordance with the North Brazil Current flow. Our results suggest speciation with gene flow explained by the interplay among the AOP, oceanographic currents, and long larval dispersal. This work represents the first investigation employing ddRAD-seq in a marine invertebrate species with distribution encompassing the north and south Atlantic and sheds light on the role of the AOP in the diversification of a marine species.
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Affiliation(s)
- Pedro A. Peres
- Department of Biology, Institute of Environment, Florida International University (FIU), Miami, FL 33199, USA
- Laboratory of Bioecology and Systematics of Crustaceans (LBSC), Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto 14040-901, Brazil
- Correspondence:
| | - Heather Bracken-Grissom
- Department of Biology, Institute of Environment, Florida International University (FIU), Miami, FL 33199, USA
- Department of Invertebrate Zoology, National Museum of Natural History-Smithsonian, Washington, WA 20013-7012, USA
| | - Laura E. Timm
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
- Auke Bay Laboratories, Alaska Fisheries Science Center, NOAA National Marine Fisheries Service, Juneau, AK 99801, USA
| | - Fernando L. Mantelatto
- Laboratory of Bioecology and Systematics of Crustaceans (LBSC), Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto 14040-901, Brazil
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7
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Zhang J, Richards ZT, Adam AAS, Chan CX, Shinzato C, Gilmour J, Thomas L, Strugnell JM, Miller DJ, Cooke I. Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum. Mol Biol Evol 2022; 39:msac201. [PMID: 36219871 PMCID: PMC9578555 DOI: 10.1093/molbev/msac201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Climate change threatens the survival of coral reefs on a global scale, primarily through mass bleaching and mortality as a result of marine heatwaves. While these short-term effects are clear, predicting the fate of coral reefs over the coming century is a major challenge. One way to understand the longer-term effects of rapid climate change is to examine the response of coral populations to past climate shifts. Coastal and shallow-water marine ecosystems such as coral reefs have been reshaped many times by sea-level changes during the Pleistocene, yet, few studies have directly linked this with its consequences on population demographics, dispersal, and adaptation. Here we use powerful analytical techniques, afforded by haplotype phased whole-genomes, to establish such links for the reef-building coral, Acropora digitifera. We show that three genetically distinct populations are present in northwestern Australia, and that their rapid divergence since the last glacial maximum (LGM) can be explained by a combination of founder-effects and restricted gene flow. Signatures of selective sweeps, too strong to be explained by demographic history, are present in all three populations and overlap with genes that show different patterns of functional enrichment between inshore and offshore habitats. In contrast to rapid divergence in the host, we find that photosymbiont communities are largely undifferentiated between corals from all three locations, spanning almost 1000 km, indicating that selection on host genes and not acquisition of novel symbionts, has been the primary driver of adaptation for this species in northwestern Australia.
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Affiliation(s)
- Jia Zhang
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
- Collections and Research, Western Australian Museum, 49 Kew Street Welshpool, WA 6106, Australia
| | - Arne A S Adam
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Cheong Xin Chan
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, QLD 4072, Australia
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo277-8564, Chiba, Japan
| | - James Gilmour
- Australia Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA, 6009, Australia
| | - Luke Thomas
- Australia Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA, 6009, Australia
- Oceans Graduate School, The UWA Oceans Institute, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jan M Strugnell
- Department of Marine Biology and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
| | - David J Miller
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
- Marine Climate Change Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan 904-0495
| | - Ira Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
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8
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Davis KE, De Grave S, Delmer C, Payne ARD, Mitchell S, Wills MA. Ecological Transitions and the Shape of the Decapod Tree of Life. Integr Comp Biol 2022; 62:332-344. [PMID: 35612997 DOI: 10.1093/icb/icac052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 11/14/2022] Open
Abstract
Understanding the processes that shaped the distribution of species richness across the Tree of Life is a central macroevolutionary research agenda. Major ecological innovations, including transitions between habitats, may help to explain the striking asymmetries of diversity that are often observed between sister clades. Here, we test the impact of such transitions on speciation rates across decapod crustaceans, modelling diversification dynamics within a phylogenetic framework. Our results show that, while terrestrial lineages have higher speciation rates than either marine or freshwater lineages, there is no difference between mean speciation rates in marine and freshwater lineages across Decapoda. Partitioning our data by infraorder reveals that those clades with habitat heterogeneity have higher speciation rates in freshwater and terrestrial lineages, with freshwater rates up to 1.5 times faster than marine rates, and terrestrial rates approximately four times faster. This averaging out of marine and freshwater speciation rates results from the varying contributions of different clades to average speciation rates. However, with the exception of Caridea, we find no evidence for any causal relationship between habitat and speciation rate. Our results demonstrate that while statistical generalisations about ecological traits and evolutionary rates are valuable, there are many exceptions. Hence, while freshwater and terrestrial lineages typically speciate faster than their marine relatives, there are many atypically slow freshwater lineages and fast marine lineages across Decapoda. Future work on diversification patterns will benefit from the inclusion of fossil data, as well as additional ecological factors.
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Affiliation(s)
- Katie E Davis
- University of York, Department of Biology York, North Yorkshire, UK
| | - Sammy De Grave
- Oxford University Museum of Natural History, Oxford, Oxfordshire, UK
| | - Cyrille Delmer
- University of Bath, Department of Biology & Biochemistry, Bath, Bath and North East Somerset, UK
| | - Alexander R D Payne
- University of York, Leverhulme Centre for Anthropocene Biodiversity, York, North Yorkshire, UK
| | - Steve Mitchell
- University of Bath, Department of Biology & Biochemistry, Bath, Bath and North East Somerset, UK
| | - Matthew A Wills
- University of Bath, Department of Biology & Biochemistry, Bath, Bath and North East Somerset, UK
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9
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Yamaguchi R. Intermediate dispersal hypothesis of species diversity: New insights. Ecol Res 2022. [DOI: 10.1111/1440-1703.12313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryo Yamaguchi
- Department of Advanced Transdisciplinary Science Hokkaido University Sapporo Japan
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10
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Liu X, Schjøtt SR, Granquist SM, Rosing-Asvid A, Dietz R, Teilmann J, Galatius A, Cammen K, O Corry-Crowe G, Harding K, Härkönen T, Hall A, Carroll EL, Kobayashi Y, Hammill M, Stenson G, Frie AK, Lydersen C, Kovacs KM, Andersen LW, Hoffman JI, Goodman SJ, Vieira FG, Heller R, Moltke I, Tange Olsen M. Origin and expansion of the world's most widespread pinniped: range-wide population genomics of the harbour seal (Phoca vitulina). Mol Ecol 2022; 31:1682-1699. [PMID: 35068013 PMCID: PMC9306526 DOI: 10.1111/mec.16365] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
The harbour seal (Phoca vitulina) is the most widely distributed pinniped, occupying a wide variety of habitats and climatic zones across the Northern Hemisphere. Intriguingly, the harbour seal is also one of the most philopatric seals, raising questions as to how it colonised virtually the whole of the Northern Hemisphere. To shed light on the origin, remarkable range expansion, population structure and genetic diversity of this species, we used genotyping-by-sequencing to analyse ~13,500 biallelic SNPs from 286 individuals sampled from 22 localities across the species' range. Our results point to a Northeast Pacific origin, colonisation of the North Atlantic via the Canadian Arctic, and subsequent stepping-stone range expansions across the North Atlantic from North America to Europe, accompanied by a successive loss of genetic diversity. Our analyses further revealed a deep divergence between modern North Pacific and North Atlantic harbour seals, with finer-scale genetic structure at regional and local scales consistent with strong philopatry. The study provides new insights into the harbour seal's remarkable ability to colonise and adapt to a wide range of habitats. Furthermore, it has implications for current harbour seal subspecies delineations and highlights the need for international and national red lists and management plans to ensure the protection of genetically and demographically isolated populations.
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Affiliation(s)
- Xiaodong Liu
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | | | - Sandra M Granquist
- Icelandic Seal Centre, Höfðabraut 6, 530, Hvammstangi, Iceland.,Marine and Freshwater Research Institute, Institute of Freshwater Fisheries Fornubúðir 5, 220, Hafnarfjörður, Iceland
| | | | - Rune Dietz
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Jonas Teilmann
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Anders Galatius
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | | | - Greg O Corry-Crowe
- Wildlife Evolution and Behavior Program, Florida Atlantic University, USA
| | - Karin Harding
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
| | | | - Ailsa Hall
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St. Andrews, UK, KY16 8LB
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Yumi Kobayashi
- Laboratory of Animal Ecology, Research Faculty of Agriculture, Hokkaido University, Japan
| | - Mike Hammill
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, P.O. Box 1000, Mont-Joli, QC, Canada
| | - Garry Stenson
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, P.O. Box 5667, St. John's NL, Canada
| | | | | | - Kit M Kovacs
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
| | | | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, 33501, Bielefeld, Germany.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Simon J Goodman
- School of Biology, Faculty of Biological Sciences, University of Leeds, UK
| | - Filipe G Vieira
- Center for Genomic Medicine, Copenhagen University Hospitalet, Denmark
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | - Ida Moltke
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | - Morten Tange Olsen
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Denmark
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11
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Disentangling the Taxonomic Status of Caprella penantis sensu stricto (Amphipoda: Caprellidae) Using an Integrative Approach. Life (Basel) 2022; 12:life12020155. [PMID: 35207443 PMCID: PMC8878143 DOI: 10.3390/life12020155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 11/21/2022] Open
Abstract
Despite its importance in intertidal and shallow-water marine ecosystems, Caprella penantis continues to be one of the most taxonomically challenging amphipods in the world. A recent molecular study focusing on C. penantis sensu stricto pointed out the existence of three highly divergent lineages, indicating the possible existence of a process of ongoing speciation and, thus, casting doubt on the taxonomic status of this species. In the present study, we used an integrative approach to continue to shed light on the taxonomy and distribution of this caprellid. To this end, we combined morphological and genetic data (COI and 18S) and included, for the first time, populations from its type locality. Our analyses provide strong evidence of the existence of potentially three distinct species, genetically and geographically restricted, within C. penantis sensu stricto, with the distribution of the true C. penantis sensu stricto restricted to the UK (type locality), the northern coast of the Iberian Peninsula, and the Azores. Results show the co-occurrence of two of these species in a locality of northern Portugal and indicate the existence of distinct evolutionary and diversification patterns along the eastern Atlantic region. Overall, our study highlights the use of an integrative approach to properly assess species boundaries and unravel hidden biodiversity in amphipods.
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12
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Hirase S, Yamasaki YY, Sekino M, Nishisako M, Ikeda M, Hara M, Merilä J, Kikuchi K. Genomic Evidence for Speciation with Gene Flow in Broadcast Spawning Marine Invertebrates. Mol Biol Evol 2021; 38:4683-4699. [PMID: 34311468 PMCID: PMC8557453 DOI: 10.1093/molbev/msab194] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
How early stages of speciation in free-spawning marine invertebrates proceed is poorly understood. The Western Pacific abalones, Haliotis discus, H. madaka, and H. gigantea, occur in sympatry with shared breeding season and are capable of producing viable F1 hybrids in spite of being ecologically differentiated. Population genomic analyses revealed that although the three species are genetically distinct, there is evidence for historical and ongoing gene flow among these species. Evidence from demographic modeling suggests that reproductive isolation among the three species started to build in allopatry and has proceeded with gene flow, possibly driven by ecological selection. We identified 27 differentiation islands between the closely related H. discus and H. madaka characterized by high FST and dA, but not high dXY values, as well as high genetic diversity in one H. madaka population. These genomic signatures suggest differentiation driven by recent ecological divergent selection in presence of gene flow outside of the genomic islands of differentiation. The differentiation islands showed low polymorphism in H. gigantea, and both high FST, dXY, and dA values between H. discus and H. gigantea, as well as between H. madaka and H. gigantea. Collectively, the Western Pacific abalones appear to occupy the early stages speciation continuum, and the differentiation islands associated with ecological divergence among the abalones do not appear to have acted as barrier loci to gene flow in the younger divergences but appear to do so in older divergences.
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Affiliation(s)
- Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Maisaka, Hamamatsu, Shizuoka, Japan
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masashi Sekino
- Bioinformatics and Biosciences Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Masato Nishisako
- Laboratory of Integrative Aquatic Biology, Graduate School of Agricultural Sciences, Tohoku University, Onagawa, Miyagi, Japan
| | - Minoru Ikeda
- Laboratory of Integrative Aquatic Biology, Graduate School of Agricultural Sciences, Tohoku University, Onagawa, Miyagi, Japan
| | - Motoyuki Hara
- Tohoku Ecosystem-Associated Marine Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Research Division of Ecology and Biodiversity, Faculty of Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Maisaka, Hamamatsu, Shizuoka, Japan
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13
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Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving under the surface. J Evol Biol 2021; 34:4-15. [PMID: 33460491 DOI: 10.1111/jeb.13756] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 12/28/2022]
Abstract
Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model-based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.
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Affiliation(s)
- Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Kerstin Johannesson
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Sean Stankowski
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.,IST Austria, Klosterneuburg, Austria
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14
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Warren DL, Eytan RI, Dornburg A, Iglesias TL, Brandley MC, Wainwright PC. Reevaluating claims of ecological speciation in Halichoeres bivittatus. Ecol Evol 2021; 11:11449-11456. [PMID: 34429932 PMCID: PMC8366890 DOI: 10.1002/ece3.7936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/17/2021] [Accepted: 07/07/2021] [Indexed: 11/11/2022] Open
Abstract
Allopatry has traditionally been viewed as the primary driver of speciation in marine taxa, but the geography of the marine environment and the larval dispersal capabilities of many marine organisms render this view somewhat questionable. In marine fishes, one of the earliest and most highly cited empirical examples of ecological speciation with gene flow is the slippery dick wrasse, Halichoeres bivittatus. Evidence for this cryptic or incipient speciation event was primarily in the form of a deep divergence in a single mitochondrial locus between the northern and southern Gulf of Mexico, combined with a finding that these two haplotypes were associated with different habitat types ("tropical" vs. "subtropical") in the Florida Keys and Bermuda, where they overlap. Here, we examine habitat assortment in the Florida Keys using a broader sampling of populations and habitat types than were available for the original study. We find no evidence to support the claim that haplotype frequencies differ between habitat types, and little evidence to support any differences between populations in the Keys. These results undermine claims of ecological speciation with gene flow in Halichoeres bivittatus. Future claims of this type should be supported by multiple lines of evidence that illuminate potential mechanisms and allow researchers to rule out alternative explanations for spatial patterns of genetic differences.
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Affiliation(s)
- Dan L. Warren
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Ron I. Eytan
- Department of Marine BiologyTexas A&M University at GalvestonGalvestonTexasUSA
| | - Alex Dornburg
- Department of Bioinformatics and GenomicsUniversity of North Carolina CharlotteCharlotteNorth CarolinaUSA
| | - Teresa L. Iglesias
- Animal Resources SectionOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Matthew C. Brandley
- Section of Amphibians and ReptilesCarnegie Museum of Natural HistoryPittsburghPAUSA
- Powdermill Nature ReserveCarnegie Museum of Natural HistoryRectorPennsylvaniaUSA
| | - Peter C. Wainwright
- Department of Evolution and EcologyUniversity of CaliforniaDavisCaliforniaUSA
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15
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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: 2] [Impact Index Per Article: 0.7] [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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16
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Geography is more important than life history in the recent diversification of the tiger salamander complex. Proc Natl Acad Sci U S A 2021; 118:2014719118. [PMID: 33888580 DOI: 10.1073/pnas.2014719118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by model-based population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and the Mexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research.
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17
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Nam BH, Kim H, Seol D, Kim H, Noh ES, Kim EM, Noh JK, Kim YO, Park JY, Kwak W. Genotyping-by-Sequencing of the regional Pacific abalone (Haliotis discus) genomes reveals population structures and patterns of gene flow. PLoS One 2021; 16:e0247815. [PMID: 33826655 PMCID: PMC8026068 DOI: 10.1371/journal.pone.0247815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 02/12/2021] [Indexed: 01/05/2023] Open
Abstract
Continuous monitoring of the present genetic status is essential to preserve the genetic resource of wild populations. In this study, we sequenced regional Pacific abalone Haliotis discus samples from three different locations around the Korean peninsula to assess population structure, utilizing Genotyping-by-Sequencing (GBS) method. Using PstI enzyme for genome reduction, we demonstrated the resultant library represented the whole genome region with even spacing, and as a result 16,603 single nucleotide variants (SNVs) were produced. Genetic diversity and population structure were investigated using several methods, and a strong genetic heterogeneity was observed in the Korean abalone populations. Additionally, by comparison of the variant sets among population groups, we were able to discover 26 Korean abalone population-specific SNVs, potentially associated with phenotype differences. This is the first study demonstrating the feasibility of GBS for population genetic study on H. discus. Our results will provide valuable data for the genetic conservation and management of wild abalone populations in Korea and help future GBS studies on the marine mollusks.
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Affiliation(s)
- Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Hyaekang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Genome, Inc, Seoul, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Genome, Inc, Seoul, Republic of Korea
| | - Eun Soo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Eun Mi Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jae Koo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Woori Kwak
- Genome, Inc, Seoul, Republic of Korea
- * E-mail:
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18
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Li C, Olave M, Hou Y, Qin G, Schneider RF, Gao Z, Tu X, Wang X, Qi F, Nater A, Kautt AF, Wan S, Zhang Y, Liu Y, Zhang H, Zhang B, Zhang H, Qu M, Liu S, Chen Z, Zhong J, Zhang H, Meng L, Wang K, Yin J, Huang L, Venkatesh B, Meyer A, Lu X, Lin Q. Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution. Nat Commun 2021; 12:1094. [PMID: 33597547 PMCID: PMC7889852 DOI: 10.1038/s41467-021-21379-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/25/2021] [Indexed: 01/31/2023] Open
Abstract
Seahorses have a circum-global distribution in tropical to temperate coastal waters. Yet, seahorses show many adaptations for a sedentary, cryptic lifestyle: they require specific habitats, such as seagrass, kelp or coral reefs, lack pelvic and caudal fins, and give birth to directly developed offspring without pronounced pelagic larval stage, rendering long-range dispersal by conventional means inefficient. Here we investigate seahorses' worldwide dispersal and biogeographic patterns based on a de novo genome assembly of Hippocampus erectus as well as 358 re-sequenced genomes from 21 species. Seahorses evolved in the late Oligocene and subsequent circum-global colonization routes are identified and linked to changing dynamics in ocean currents and paleo-temporal seaway openings. Furthermore, the genetic basis of the recurring "bony spines" adaptive phenotype is linked to independent substitutions in a key developmental gene. Analyses thus suggest that rafting via ocean currents compensates for poor dispersal and rapid adaptation facilitates colonizing new habitats.
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Affiliation(s)
- Chunyan Li
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China ,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China ,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Melisa Olave
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany ,grid.423606.50000 0001 1945 2152Present Address: Argentine Dryland Research Institute, National Council for Scientific and Technical Research (IADIZA-CONICET), Mendoza, Argentina
| | - Yali Hou
- grid.464209.d0000 0004 0644 6935Beijing Institute of Genomics, Chinese Academy of Sciences; China National Center for Bioinformation, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Geng Qin
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China ,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Ralf F. Schneider
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany ,Marine Ecology, Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Zexia Gao
- grid.35155.370000 0004 1790 4137College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | | | - Xin Wang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Furong Qi
- grid.464209.d0000 0004 0644 6935Beijing Institute of Genomics, Chinese Academy of Sciences; China National Center for Bioinformation, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Alexander Nater
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas F. Kautt
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany ,grid.38142.3c000000041936754XPresent Address: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Shiming Wan
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Yanhong Zhang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Yali Liu
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Huixian Zhang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Bo Zhang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Hao Zhang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Meng Qu
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Shuaishuai Liu
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Zeyu Chen
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.419010.d0000 0004 1792 7072State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Jia Zhong
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | | | - Kai Wang
- grid.443651.1School of Agriculture, Ludong University, Yantai, China
| | - Jianping Yin
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Liangmin Huang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Byrappa Venkatesh
- grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Axel Meyer
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany
| | - Xuemei Lu
- grid.419010.d0000 0004 1792 7072State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Qiang Lin
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China ,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China ,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
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19
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Amaral AR, Chanfana C, Smith BD, Mansur R, Collins T, Baldwin R, Minton G, Parra GJ, Krützen M, Jefferson TA, Karczmarski L, Guissamulo A, Brownell RL, Rosenbaum HC. Genomics of Population Differentiation in Humpback Dolphins, Sousa spp. in the Indo-Pacific Ocean. J Hered 2020; 111:652-660. [PMID: 33475708 DOI: 10.1093/jhered/esaa055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Speciation is a fundamental process in evolution and crucial to the formation of biodiversity. It is a continuous and complex process, which can involve multiple interacting barriers leading to heterogeneous genomic landscapes with various peaks of divergence among populations. In this study, we used a population genomics approach to gain insights on the speciation process and to understand the population structure within the genus Sousa across its distribution in the Indo-Pacific region. We found 5 distinct clusters, corresponding to S. plumbea along the eastern African coast and the Arabian Sea, the Bangladesh population, S. chinensis off Thailand and S. sahulensis off Australian waters. We suggest that the high level of differentiation found, even across geographically close areas, is likely determined by different oceanographic features such as sea surface temperature and primary productivity.
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Affiliation(s)
- Ana R Amaral
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY.,Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Cátia Chanfana
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Brian D Smith
- Wildlife Conservation Society, Ocean Giants Program, Bronx, NY
| | - Rubaiyat Mansur
- Wildlife Conservation Society, Ocean Giants Program, Bronx, NY
| | - Tim Collins
- Wildlife Conservation Society, Ocean Giants Program, Bronx, NY
| | | | - Gianna Minton
- Megaptera Marine Conservation, The Hague, The Netherlands
| | - Guido J Parra
- Cetacean Ecology, Behaviour and Evolution Lab, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, CH Zurich, Switzerland
| | | | - Leszek Karczmarski
- Division of Cetacean Ecology and Division of Comparative Behavioural Ecology, Cetacea Research Institute, Lantau, Hong Kong.,Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, Pretoria, South Africa
| | - Almeida Guissamulo
- Universidade Eduardo Mondlane, Museu de Historia Natural, Praca Travessia do Zambeze, Maputo, Mozambique
| | - Robert L Brownell
- NOAA Fisheries, Southwest Fisheries Science Center, La Jolla Shores Drive, La Jolla, CA
| | - Howard C Rosenbaum
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY.,Wildlife Conservation Society, Ocean Giants Program, Bronx, NY
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20
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Population history and genomic admixture of sea snakes of the genus Laticauda in the West Pacific. Mol Phylogenet Evol 2020; 155:107005. [PMID: 33160037 DOI: 10.1016/j.ympev.2020.107005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 11/23/2022]
Abstract
Speciation in the open ocean has long been studied, but it remains largely elusive what factors promote or inhibit speciation in such an open environment. Marine amniotes, which evolved from terrestrial ancestors, provide valuable opportunities for studying speciation in the ocean because of their evident aquatic origins. Sea snakes are phylogenetically related to terrestrial elapid snakes and consist of two monophyletic groups (Hydrophiini and Laticaudini). These two groups migrated from land to water almost at the same time, but species diversities are remarkably different: there are approx. 60 species in 16 genera described for hydrophiins, whereas only eight species in the genus Laticauda are described for laticaudins. Here, we provide a high-quality reference genome assembly of a laticaudin L. colubrina with a scaffold N50 value of 40 Mbp, and focused on laticaudins to consider why they have seldom speciated. We performed whole-genome shotgun sequencing of several species of laticaudins sampled in their southmost (Vanuatu) and northmost (Ryukyu) habitats. Demographic histories of Vanuatu and Ryukyu populations suggest that populations of broadly distributed major species are geographically structured. Each species is genetically clearly distinguished, but there is a considerable amount of gene flow between two sibling species distributed sympatrically in Vanuatu. In addition, inter-species genomic admixture is ubiquitously observed among laticaudins even between phylogenetically distant species. Broad distribution of major species combined with such genetic mixability might have prevented laticaudins from genetic isolation and speciation.
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21
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Dorant Y, Cayuela H, Wellband K, Laporte M, Rougemont Q, Mérot C, Normandeau E, Rochette R, Bernatchez L. Copy number variants outperform SNPs to reveal genotype–temperature association in a marine species. Mol Ecol 2020; 29:4765-4782. [DOI: 10.1111/mec.15565] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Yann Dorant
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Hugo Cayuela
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Kyle Wellband
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Claire Mérot
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Rémy Rochette
- Department of Biology University of New Brunswick Saint John NB Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
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22
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Cayuela H, Rougemont Q, Laporte M, Mérot C, Normandeau E, Dorant Y, Tørresen OK, Hoff SNK, Jentoft S, Sirois P, Castonguay M, Jansen T, Praebel K, Clément M, Bernatchez L. Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish. Mol Ecol 2020; 29:2379-2398. [DOI: 10.1111/mec.15499] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Siv Nam Khang Hoff
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Pascal Sirois
- Département des sciences fondamentales Université du Québec à Chicoutimi Chicoutimi QC Canada
| | - Martin Castonguay
- Fisheries and Oceans Canada Institut Maurice‐Lamontagne Mont‐Joli QC Canada
| | - Teunis Jansen
- GINR‐Greenland Institute of Natural Resources Nuuk Greenland
- DTU Aqua‐National Institute of Aquatic Resources Technical University of Denmark Charlottenlund Castle, Charlottenlund Denmark
| | - Kim Praebel
- Norwegian College of Fishery Science Faculty of Biosciences, Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
| | - Marie Clément
- Center for Fisheries Ecosystems Research Fisheries and Marine Institute of Memorial University of Newfoundland St. John's NL Canada
- Labrador Institute of Memorial University of Newfoundland Happy Valley‐Goose Bay NL Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
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23
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Beaugrand G, Kirby R, Goberville E. The mathematical influence on global patterns of biodiversity. Ecol Evol 2020; 10:6494-6511. [PMID: 32724528 PMCID: PMC7381758 DOI: 10.1002/ece3.6385] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 02/19/2020] [Accepted: 03/19/2020] [Indexed: 01/25/2023] Open
Abstract
Although we understand how species evolve, we do not appreciate how this process has filled an empty world to create current patterns of biodiversity. Here, we conduct a numerical experiment to determine why biodiversity varies spatially on our planet. We show that spatial patterns of biodiversity are mathematically constrained and arise from the interaction between the species' ecological niches and environmental variability that propagates to the community level. Our results allow us to explain key biological observations such as (a) latitudinal biodiversity gradients (LBGs) and especially why oceanic LBGs primarily peak at midlatitudes while terrestrial LBGs generally exhibit a maximum at the equator, (b) the greater biodiversity on land even though life first evolved in the sea, (c) the greater species richness at the seabed than at the sea surface, and (d) the higher neritic (i.e., species occurring in areas with a bathymetry lower than 200 m) than oceanic (i.e., species occurring in areas with a bathymetry higher than 200 m) biodiversity. Our results suggest that a mathematical constraint originating from a fundamental ecological interaction, that is, the niche-environment interaction, fixes the number of species that can establish regionally by speciation or migration.
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Affiliation(s)
- Gregory Beaugrand
- LOGLaboratoire d'Océanologie et de GéosciencesCNRSUMR 8187WimereuxFrance
| | | | - Eric Goberville
- Unité Biologie des Organismes et Ecosystèmes Aquatiques (BOREA)Muséum National d’Histoire NaturelleSorbonne UniversitéUniversité de Caen NormandieUniversité des AntillesCNRSIRDParisFrance
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24
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Peres PA, Mantelatto FL. Salinity tolerance explains the contrasting phylogeographic patterns of two swimming crabs species along the tropical western Atlantic. Evol Ecol 2020. [DOI: 10.1007/s10682-020-10057-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Melo DCM, Lira SMA, Moreira APB, Freitas L, Lima CAD, Thompson F, Bertrand A, Silva AC, Neumann-Leitão S. Genetic diversity and connectivity of Flaccisagitta enflata (Chaetognatha: Sagittidae) in the tropical Atlantic ocean (northeastern Brazil). PLoS One 2020; 15:e0231574. [PMID: 32374742 PMCID: PMC7202658 DOI: 10.1371/journal.pone.0231574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 03/26/2020] [Indexed: 11/18/2022] Open
Abstract
The phylogeography of the holoplanktonic chaetognath Flaccisagitta enflata was investigated in the Tropical Western Atlantic (TWA). Considering the cosmopolitan range of this species and the fact that its entire life cycle is planktonic, the central hypothesis of this study is that F. enflata exhibits connectivity due to its high dispersal capacity, forming a panmictic population among the study sites. The evaluated areas included neritic (Port of Recife–PR, and Tamandaré - TA) and oceanic (Fernando de Noronha Archipelago—FN, Rocas Atoll—RA, Guará seamount—GS and Saint Peter and Saint Paul’s Archipelago—SPSPA) locations of the Brazilian Blue Amazon. We used COI gene sequences as molecular marker. Partial sequences (425 bp) were obtained for 116 specimens and employed to reconstruct the phylogeny, build an haplotype network, evaluate gene flow through a migration model, and estimate diversity indices, population structuring and demographic history. High levels of haplotype diversity (mean: 0.98) and moderate to high levels of nucleotide diversity (mean: 0.023) were observed. The phylogeny and the haplotype network topologies showed some geographic clustering, indicating local structuring in GS and PR. This finding was supported by the AMOVA high global Φst (0.033, significant) and some pairwise Φst comparisons (7 out of 15 were significantly >0). Significant differences suggested lower levels of connectivity when GS population was compared to those of FN and SPSPA; as well as when TA was compared to FN. These results might be related to particularities of the oceanic dynamics which rules the TWA, sustaining such dissimilarities. Structuring was also observed between PR and all oceanic locations. We hypothesize that the topography of the port inlet, enclosured by a reef barrier, may constrain the water turnover ratio and thus migration rates of F. enflata in the TWA. Accordingly, Migrate-N yielded a four metapopulations model (PR ⇌ TA ⇌ SPSPA+FN ⇌ GS+RA) as the best (highest probability; ~0.90) to represent the structuring of F. enflata in the TWA. Therefore, the null hypothesis of one randomly mating population cannot be accepted. The demographic evaluation demonstrated that the neutral hypothesis of stable populations may not be rejected for most of the locations. This work is the start point to broaden the knowledge on the phylogeography and population genetic structure of a numerically dominant species in the Western Atlantic, with key role in the marine trophic web.
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Affiliation(s)
- Danielle C. M. Melo
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife, Brazil
- * E-mail:
| | - Simone M. A. Lira
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife, Brazil
- Programa de pós-graduação em Ecologia, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | - Ana Paula B. Moreira
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucas Freitas
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, São Paulo, Brazil
| | - Camilla A. D. Lima
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife, Brazil
| | - Fabiano Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- SAGE—COPPE, Centro de Gestão Tecnológica—CT2, Rio de Janeiro, Brazil
| | - Arnaud Bertrand
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife, Brazil
- Departamento de Pesca e Aquicultura, Universidade Federal Rural de Pernambuco, Recife, Brazil
- MARBEC, CNRS, Ifremer, IRD, Institut de Recherche pour le Développement (IRD), Université Montpellier, Sète, France
| | - Alex C. Silva
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife, Brazil
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Lombal AJ, O'dwyer JE, Friesen V, Woehler EJ, Burridge CP. Identifying mechanisms of genetic differentiation among populations in vagile species: historical factors dominate genetic differentiation in seabirds. Biol Rev Camb Philos Soc 2020; 95:625-651. [PMID: 32022401 DOI: 10.1111/brv.12580] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 12/23/2019] [Accepted: 01/08/2020] [Indexed: 01/01/2023]
Abstract
Elucidating the factors underlying the origin and maintenance of genetic variation among populations is crucial for our understanding of their ecology and evolution, and also to help identify conservation priorities. While intrinsic movement has been hypothesized as the major determinant of population genetic structuring in abundant vagile species, growing evidence indicates that vagility does not always predict genetic differentiation. However, identifying the determinants of genetic structuring can be challenging, and these are largely unknown for most vagile species. Although, in principle, levels of gene flow can be inferred from neutral allele frequency divergence among populations, underlying assumptions may be unrealistic. Moreover, molecular studies have suggested that contemporary gene flow has often not overridden historical influences on population genetic structure, which indicates potential inadequacies of any interpretations that fail to consider the influence of history in shaping that structure. This exhaustive review of the theoretical and empirical literature investigates the determinants of population genetic differentiation using seabirds as a model system for vagile taxa. Seabirds provide a tractable group within which to identify the determinants of genetic differentiation, given their widespread distribution in marine habitats and an abundance of ecological and genetic studies conducted on this group. Herein we evaluate mitochondrial DNA (mtDNA) variation in 73 seabird species. Lack of mutation-drift equilibrium observed in 19% of species coincided with lower estimates of genetic differentiation, suggesting that dynamic demographic histories can often lead to erroneous interpretations of contemporary gene flow, even in vagile species. Presence of land across the species sampling range, or sampling of breeding colonies representing ice-free Pleistocene refuge zones, appear to be associated with genetic differentiation in Tropical and Southern Temperate species, respectively, indicating that long-term barriers and persistence of populations are important for their genetic structuring. Conversely, biotic factors commonly considered to influence population genetic structure, such as spatial segregation during foraging, were inconsistently associated with population genetic differentiation. In light of these results, we recommend that genetic studies should consider potential historical events when identifying determinants of genetic differentiation among populations to avoid overestimating the role of contemporary factors, even for highly vagile taxa.
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Affiliation(s)
- Anicee J Lombal
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - James E O'dwyer
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Vicki Friesen
- Department of Biology, Queen's University, 99 University Avenue, Kingston, OL, K7L 3N6, Canada
| | - Eric J Woehler
- Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Hobart, TAS, 7004, Australia
| | - Christopher P Burridge
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
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27
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Ashby B, Shaw AK, Kokko H. An inordinate fondness for species with intermediate dispersal abilities. OIKOS 2019. [DOI: 10.1111/oik.06704] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ben Ashby
- Dept of Mathematical Sciences, Univ. of Bath Bath BA2 7AY UK
| | - Allison K. Shaw
- Dept of Ecology, Evolution and Behavior, Univ. of Minnesota St. Paul MN USA
| | - Hanna Kokko
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Zurich Switzerland
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Abstract
Speciation-the origin of new species-has been one of the most active areas of research in evolutionary biology, both during, and since the Modern Synthesis. While the Modern Synthesis certainly shaped research on speciation in significant ways, providing a core framework, and set of categories and methods to work with, the history of work on speciation since the mid-twentieth century is a history of divergence and diversification. This piece traces this divergence, through both theoretical advances, and empirical insights into how different lineages, with different genetics and ecological conditions, are shaped by very different modes of diversification.
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Pirog A, Ravigné V, Fontaine MC, Rieux A, Gilabert A, Cliff G, Clua E, Daly R, Heithaus MR, Kiszka JJ, Matich P, Nevill JEG, Smoothey AF, Temple AJ, Berggren P, Jaquemet S, Magalon H. Population structure, connectivity, and demographic history of an apex marine predator, the bull shark Carcharhinus leucas. Ecol Evol 2019; 9:12980-13000. [PMID: 31871624 PMCID: PMC6912899 DOI: 10.1002/ece3.5597] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 07/23/2019] [Accepted: 07/28/2019] [Indexed: 01/16/2023] Open
Abstract
Knowledge of population structure, connectivity, and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas. This large-bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures. We investigated the bull shark's global population structure and demographic history by analyzing the genetic diversity of 370 individuals from 11 different locations using 25 microsatellite loci and three mitochondrial genes (CR, nd4, and cytb). Both types of markers revealed clustering between sharks from the Western Atlantic and those from the Western Pacific and the Western Indian Ocean, with no contemporary gene flow. Microsatellite data suggested low differentiation between the Western Indian Ocean and the Western Pacific, but substantial differentiation was found using mitochondrial DNA. Integrating information from both types of markers and using Bayesian computation with a random forest procedure (ABC-RF), this discordance was found to be due to a complete lack of contemporary gene flow. High genetic connectivity was found both within the Western Indian Ocean and within the Western Pacific. In conclusion, these results suggest important structuring of bull shark populations globally with important gene flow occurring along coastlines, highlighting the need for management and conservation plans on regional scales rather than oceanic basin scale.
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Affiliation(s)
- Agathe Pirog
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint DenisFrance
| | | | - Michaël C. Fontaine
- Laboratoire MIVEGEC (Université de Montpellier UMR CNRS 5290, IRD 229)Centre IRD de MontpellierMontpellierFrance
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | | | | | - Geremy Cliff
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Eric Clua
- EPHECNRS UPVDUSR 3278 CRIOBEPSL Research UniversityPerpignanFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
| | - Ryan Daly
- Oceanographic Research InstituteDurbanSouth Africa
- South African Institute for Aquatic BiodiversityGrahamstownSouth Africa
| | - Michael R. Heithaus
- Department of Biological SciencesFlorida International UniversityNorth MiamiFLUSA
| | - Jeremy J. Kiszka
- Department of Biological SciencesFlorida International UniversityNorth MiamiFLUSA
| | - Philip Matich
- Department of Biological SciencesFlorida International UniversityNorth MiamiFLUSA
| | | | - Amy F. Smoothey
- NSW Department of Primary IndustriesSydney Institute of Marine ScienceMosmanNSWAustralia
| | - Andrew J. Temple
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Per Berggren
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Sébastien Jaquemet
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint DenisFrance
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint DenisFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
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Pepato AR, Vidigal THDA, Klimov PB. Evaluating the boundaries of marine biogeographic regions of the Southwestern Atlantic using halacarid mites (Halacaridae), meiobenthic organisms with a low dispersal potential. Ecol Evol 2019; 9:13359-13374. [PMID: 31871650 PMCID: PMC6912894 DOI: 10.1002/ece3.5791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/05/2019] [Indexed: 11/07/2022] Open
Abstract
AIM We evaluated traditional biogeographic boundaries of coastal marine regions in Southwestern Atlantic using DNA sequence data from common, rocky-shore inhabiting, marine mites of the genera Agauopsis and Rhombognathus, family Halacaridae. METHODS We investigated geographic population genetic structure using CO1 gene sequences, estimated divergence times using a multigene dataset and absolute time-calibrated molecular clock analyses, and performed environmental niche modeling (ENM) of common marine mite species. RESULTS Agauopsis legionium has a shallow history (2.01 Ma) with four geographically differentiated groups. Two of them corresponded to the traditional Amazonian and Northeastern ecoregions, but the boundary between the two other groups was inferred at the Abrolhos Plateau, not Cabo Frio. Rhombognathus levigatoides s. lat. was represented by two cryptic species that diverged 7.22 (multilocus data) or 10.01 Ma (CO1-only analyses), with their boundary, again at the Abrolhos Plateau. ENM showed that A. legionium has suitable habitats scattered along the coast, while the two R. levigatoides cryptic species differ considerably in their niches, especially in parameters related to upwelling. This indicates that genetic isolation associated with the Abrolhos Plateau occurred in both lineages, but for the R. levigatoides species complex, ecological niche specialization was also an important factor. MAIN CONCLUSIONS Our study suggests that the major biogeographic boundary in the Southwestern Atlantic lies not at Cabo Frio but at the Abrolhos Plateau. There two biogeographically relevant factors meet (a) changes in current directions (which limit dispersal) and (b) abrupt changes in environmental parameters associated with the South Atlantic Central Waters (SACW) upwelling (offering distinct ecological niches). We suggest that our result represents a general biogeographic pattern because a barrier at the Abrolhos Plateau was found previously for the fish genus Macrodon (phylogeographic data), prosobranch mollusks, ascidians, and reef fishes (community-level data).
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Affiliation(s)
- Almir R. Pepato
- Departamento de ZoologiaInstituto de Ciências BiológicasUFMGBelo HorizonteBrazil
- Tyumen State UniversityTyumenRussia
| | | | - Pavel B. Klimov
- Tyumen State UniversityTyumenRussia
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
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Population co-divergence in common cuttlefish (Sepia officinalis) and its dicyemid parasite in the Mediterranean Sea. Sci Rep 2019; 9:14300. [PMID: 31586090 PMCID: PMC6778094 DOI: 10.1038/s41598-019-50555-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/12/2019] [Indexed: 12/22/2022] Open
Abstract
Population structure and biogeography of marine organisms are formed by different drivers than in terrestrial organisms. Yet, very little information is available even for common marine organisms and even less for their associated parasites. Here we report the first analysis of population structure of both a cephalopod host (Sepia officinalis) and its dicyemid parasite, based on a homologous molecular marker (cytochrome oxidase I). We show that the population of common cuttlefish in the Mediterranean area is fragmented into subpopulations, with some areas featuring restricted level of gene flow. Amongst the studied areas, Sardinia was genetically the most diverse and Cyprus the most isolated. At a larger scale, across the Mediterranean, the population structure of the parasite shows co-diversification pattern with its host, but a slower rate of diversification. Differences between the two counterparts are more obvious at a finer scale, where parasite populations show increased level of fragmentation and lower local diversities. This discrepancy can be caused by local extinctions and replacements taking place more frequently in the dicyemid populations, due to their parasitic lifestyle.
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Nakov T, Beaulieu JM, Alverson AJ. Diatoms diversify and turn over faster in freshwater than marine environments*. Evolution 2019; 73:2497-2511. [DOI: 10.1111/evo.13832] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/05/2019] [Accepted: 07/18/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Teofil Nakov
- Department of Biological Sciences University of Arkansas Fayetteville 1 University of Arkansas, SCEN 601 Fayetteville AR 72701
| | - Jeremy M. Beaulieu
- Department of Biological Sciences University of Arkansas Fayetteville 1 University of Arkansas, SCEN 601 Fayetteville AR 72701
| | - Andrew J. Alverson
- Department of Biological Sciences University of Arkansas Fayetteville 1 University of Arkansas, SCEN 601 Fayetteville AR 72701
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Population genetic structure of Etroplus suratensis Bloch, 1790 in South India: preliminary evidence of founder haplotypes shared among populations. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2019. [DOI: 10.1016/j.japb.2019.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Moreira C, Correia AT, Vaz-Pires P, Froufe E. Genetic diversity and population structure of the blue jack mackerel Trachurus picturatus across its western distribution. JOURNAL OF FISH BIOLOGY 2019; 94:725-731. [PMID: 30895622 DOI: 10.1111/jfb.13944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/01/2019] [Indexed: 06/09/2023]
Abstract
Blue jack mackerel Trachurus picturatus collected at six sampling locations of the north-east Atlantic Ocean (Azores, Madeira, Canaries, and Matosinhos, Peniche and Portimão, mainland Portugal) and one location in the Mediterranean (Sicily), were used to examine the genetic structure of this species. Three mitochondrial gene regions (cytochrome c oxidase subunit I, cytochrome b and control region) were used to study the genetic structure of the species in Macaronesia, as well as to compare the genetic diversity of this region with published results from its eastern distribution. All markers indicated the absence of genetic structure among populations, with high indices of genetic diversity. These results suggest that the species went through a bottleneck event, followed by a recent population expansion. Moreover, the comparison with previously published results from the T. picturatus Mediterranean distribution suggests the existence of a single panmictic population throughout the species' full range. This was, however, an unexpected result since other methodologies have shown the presence of, at least, three different population-units in the NE Atlantic Ocean.
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Affiliation(s)
- Cláudia Moreira
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Alberto T Correia
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos, Portugal
- Faculdade de Ciências da Saúde, Universidade Fernando Pessoa (FCS/UFP), Porto, Portugal
| | - Paulo Vaz-Pires
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Elsa Froufe
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos, Portugal
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35
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Peres PA, Azevedo-Silva M, Andrade SCS, Leite FPP. Is there host-associated differentiation in marine herbivorous amphipods? Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Pedro A Peres
- Department of Animal Biology, Institute of Biology, University of Campinas (UNICAMP), Brazil
| | - Marianne Azevedo-Silva
- Department of Animal Biology, Institute of Biology, University of Campinas (UNICAMP), Brazil
| | - Sónia C S Andrade
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), Brazil
| | - Fosca P P Leite
- Department of Animal Biology, Institute of Biology, University of Campinas (UNICAMP), Brazil
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36
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Flaviani F, Schroeder DC, Lebret K, Balestreri C, Highfield AC, Schroeder JL, Thorpe SE, Moore K, Pasckiewicz K, Pfaff MC, Rybicki EP. Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current. Front Microbiol 2018; 9:1474. [PMID: 30065704 PMCID: PMC6056678 DOI: 10.3389/fmicb.2018.01474] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/13/2018] [Indexed: 12/13/2022] Open
Abstract
Microbes occupy diverse ecological niches and only through recent advances in next generation sequencing technologies have the true microbial diversity been revealed. Furthermore, lack of perceivable marine barriers to genetic dispersal (i.e., mountains or islands) has allowed the speculation that organisms that can be easily transported by currents and therefore proliferate everywhere. That said, ocean currents are now commonly being recognized as barriers for microbial dispersal. Here we analyzed samples collected from a total of six stations, four located in the Indian Ocean, and two in the Southern Ocean. Amplicon sequencing was used to characterize both prokaryotic and eukaryotic plankton communities, while shotgun sequencing was used for the combined environmental DNA (eDNA), microbial eDNA (meDNA), and viral fractions. We found that Cyanobacteria dominated the prokaryotic component in the South-West Indian Ocean, while γ-Proteobacteria dominated the South-East Indian Ocean. A combination of γ- and α-Proteobacteria dominated the Southern Ocean. Alveolates dominated almost exclusively the eukaryotic component, with variation in the ratio of Protoalveolata and Dinoflagellata depending on station. However, an increase in haptophyte relative abundance was observed in the Southern Ocean. Similarly, the viral fraction was dominated by members of the order Caudovirales across all stations; however, a higher presence of nucleocytoplasmic large DNA viruses (mainly chloroviruses and mimiviruses) was observed in the Southern Ocean. To our knowledge, this is the first that a statistical difference in the microbiome (from viruses to protists) between the subtropical Indian and Southern Oceans. We also show that not all phylotypes can be found everywhere, and that meDNA is not a suitable resource for monitoring aquatic microbial diversity.
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Affiliation(s)
- Flavia Flaviani
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa.,Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom
| | - Declan C Schroeder
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom.,School of Biological Sciences, University of Reading, Reading, United Kingdom.,College of Veterinary Medicine, University of Minnesota Twin Cities, Minneapolis, MN, United States
| | - Karen Lebret
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom.,Limnology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Cecilia Balestreri
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom
| | - Andrea C Highfield
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom
| | - Joanna L Schroeder
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom
| | - Sally E Thorpe
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Karen Moore
- Exeter Sequencing Service, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Konrad Pasckiewicz
- Exeter Sequencing Service, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Maya C Pfaff
- Department of Environmental Affairs, Oceans and Coasts, Cape Town, South Africa
| | - Edward P Rybicki
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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37
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Lait LA, Carr SM. Intraspecific mitogenomics of three marine species-at-risk: Atlantic, spotted, and northern wolffish (Anarhichas spp.). Genome 2018; 61:625-634. [PMID: 30001499 DOI: 10.1139/gen-2018-0043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
High-resolution mitogenomics of within-species relationships can answer such phylogeographic questions as how species survived the most recent glaciation, as well as identify contemporary factors such as physical barriers, isolation, and gene flow. We examined the mitogenomic population structure of three at-risk species of wolffish: Atlantic (Anarhichas lupus), spotted (A. minor), and northern (A. denticulatus). These species are extensively sympatric across the North Atlantic but exhibit very different life history strategies, a combination that results in concordant and discordant patterns of genetic variation and structure. Wolffish haplogroups were not structured geographically: Atlantic and spotted wolffish each comprised three shallow clades, whereas northern wolffish comprised two deeper but unstructured lineages. We suggest that wolffish species survived in isolation in multiple glacial refugia, either refugia within refugia (Atlantic and spotted wolffish) or more distant refugia (northern wolffish), followed by secondary admixture upon post-glacial recolonisation of the North Atlantic.
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Affiliation(s)
- Linda A Lait
- a Genetics, Evolution, and Molecular Systematics Laboratory, Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.,b Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Steven M Carr
- a Genetics, Evolution, and Molecular Systematics Laboratory, Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada
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38
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Nakov T, Beaulieu JM, Alverson AJ. Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta). THE NEW PHYTOLOGIST 2018; 219:462-473. [PMID: 29624698 PMCID: PMC6099383 DOI: 10.1111/nph.15137] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/02/2018] [Indexed: 05/08/2023]
Abstract
Patterns of species richness are commonly linked to life history strategies. In diatoms, an exceptionally diverse lineage of photosynthetic heterokonts important for global photosynthesis and burial of atmospheric carbon, lineages with different locomotory and reproductive traits differ dramatically in species richness, but any potential association between life history strategy and diversification has not been tested in a phylogenetic framework. We constructed a time-calibrated, 11-gene, 1151-taxon phylogeny of diatoms - the most inclusive diatom species tree to date. We used this phylogeny, together with a comprehensive inventory of first-last occurrences of Cenozoic fossil diatoms, to estimate ranges of expected species richness, diversification and its variation through time and across lineages. Diversification rates varied with life history traits. Although anisogamous lineages diversified faster than oogamous ones, this increase was restricted to a nested clade with active motility in the vegetative cells. We propose that the evolution of motility in vegetative cells, following an earlier transition from oogamy to anisogamy, facilitated outcrossing and improved utilization of habitat complexity, ultimately leading to enhanced opportunity for adaptive divergence across a variety of novel habitats. Together, these contributed to a species radiation that gave rise to the majority of present-day diatom diversity.
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Affiliation(s)
- Teofil Nakov
- University of Arkansas1 University of Arkansas, SCEN 601FayettevilleAR72701‐1201USA
| | - Jeremy M. Beaulieu
- University of Arkansas1 University of Arkansas, SCEN 601FayettevilleAR72701‐1201USA
| | - Andrew J. Alverson
- University of Arkansas1 University of Arkansas, SCEN 601FayettevilleAR72701‐1201USA
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39
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Lait LA, Marshall HD, Carr SM. Phylogeographic mitogenomics of Atlantic cod Gadus morhua: Variation in and among trans-Atlantic, trans-Laurentian, Northern cod, and landlocked fjord populations. Ecol Evol 2018; 8:6420-6437. [PMID: 30038745 PMCID: PMC6053584 DOI: 10.1002/ece3.3873] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 12/21/2017] [Accepted: 01/01/2018] [Indexed: 01/16/2023] Open
Abstract
The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High-resolution, whole-genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans-Atlantic comparisons (ΦST = .029-.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000-.060) or defined management stocks (ΦST = .000-.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans-Atlantic phylogeography versus absence of such structure within various partitions of trans-Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near-identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153-.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200-250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations.
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Affiliation(s)
- Linda A. Lait
- Genetics, Evolution, and Molecular Systematics LaboratoryDepartment of BiologyMemorial University of NewfoundlandSt. John'sNLCanada
- Centre for Biodiversity Genomics, Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - H. Dawn Marshall
- Genetics, Evolution, and Molecular Systematics LaboratoryDepartment of BiologyMemorial University of NewfoundlandSt. John'sNLCanada
| | - Steven M. Carr
- Genetics, Evolution, and Molecular Systematics LaboratoryDepartment of BiologyMemorial University of NewfoundlandSt. John'sNLCanada
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40
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López-Márquez V, Acevedo I, Manjón-Cabeza ME, García-Jiménez R, Templado J, Machordom A. Looking for morphological evidence of cryptic species in Asterina Nardo, 1834 (Echinodermata: Asteroidea). The redescription of Asterina pancerii (Gasco, 1870) and the description of two new species. INVERTEBR SYST 2018. [DOI: 10.1071/is17024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Three species of the genus Asterina are known to inhabit the Mediterranean Sea and the north-eastern Atlantic Ocean: Asterina gibbosa (Pennant, 1777), A. pancerii (Gasco, 1870) and A. phylactica Emson & Crump, 1979. Differentiation of these species has primarily been based only on subtle characters (some highly debatable), such as colour or size. Therefore, this study aimed to review the morphological data characterising members of the genus, to incorporate new characters that may clarify morphological analyses and to couple morphological data with molecular evidence of differentiation based on the analysis of partial sequences of the cytochromec oxidase subunitI (COI) and 18S rDNA (18S) genes and two anonymous nuclear loci (AgX2 and AgX5). The different lineages and cryptic species identified from the molecular analysis were then morphologically characterised, which was challenging given the limited number of diagnostic characters. Two of the five monophyletic lineages obtained molecularly (COI divergence >4%), further supported by differences in morphological characters and reproductive behaviour, are proposed as new species: Asterina martinbarriosi, sp. nov. from the Canary Islands, Spain (eastern central Atlantic Ocean) and Asterina vicentae, sp. nov. from Tarragona, north-eastern Spain (western Mediterranean Sea).
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41
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Pu C, Li H, Zhu A, Chen Y, Zhao Y, Zhan A. Phylogeography in Nassarius mud snails: Complex patterns in congeneric species. PLoS One 2017; 12:e0180728. [PMID: 28704536 PMCID: PMC5507531 DOI: 10.1371/journal.pone.0180728] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 06/20/2017] [Indexed: 11/19/2022] Open
Abstract
One major goal for phylogeographical studies is to elucidate respective roles of multiple evolutionary and ecological forces that shape the current distribution patterns. In marine and coastal ecosystems, it has been generated a common realization that species with enormous population size and pelagic larval stages can disperse across broad geographical scales, leading to weak or even no phylogeographical structure across large geographical scales. However, the violation of such realization has been frequently reported, and it remains largely unexplored on mechanisms responsible for various phylogeographical patterns observed in different species at varied geographical scales. Here, we used a species-rich genus Nassarius to assess and compare phylogeographical patterns in congeneric species, and discuss causes and consequences underlying varied phylogeographical patterns. Interestingly, we observed complex phylogeographical patterns both within single species and across multiple species, and multiple analyses showed varied levels of genetic heterogeneity among sites within and across species. Available evidence suggests that related species with similar biological characteristics may not be necessary to result in consistent phylogeographical patterns. Multiple factors, including larval ecology, interactions between dispersal and natural selection, and human activity-mediated dispersal, can partially explain the complex patterns observed in this study. Deep investigations should be performed on these factors, particularly their respective roles in determining evolutionary/ecological processes to form phylogeographical patterns in species with high dispersal capacities in marine and coastal ecosystems.
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Affiliation(s)
- Chuanliang Pu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Haitao Li
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, Guangdong, China
| | - Aijia Zhu
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, Guangdong, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Yan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
- * E-mail:
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42
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Silva G, Cunha RL, Ramos A, Castilho R. Wandering behaviour prevents inter and intra oceanic speciation in a coastal pelagic fish. Sci Rep 2017; 7:2893. [PMID: 28588244 PMCID: PMC5460251 DOI: 10.1038/s41598-017-02945-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/26/2017] [Indexed: 11/25/2022] Open
Abstract
Small pelagic fishes have the ability to disperse over long distances and may present complex evolutionary histories. Here, Old World Anchovies (OWA) were used as a model system to understand genetic patterns and connectivity of fish between the Atlantic and Pacific basins. We surveyed 16 locations worldwide using mtDNA and 8 microsatellite loci for genetic parameters, and mtDNA (cyt b; 16S) and nuclear (RAG1; RAG2) regions for dating major lineage-splitting events within Engraulidae family. The OWA genetic divergences (0-0.4%) are compatible with intra-specific divergence, showing evidence of both ancient and contemporary admixture between the Pacific and Atlantic populations, enhanced by high asymmetrical migration from the Pacific to the Atlantic. The estimated divergence between Atlantic and Pacific anchovies (0.67 [0.53-0.80] Ma) matches a severe drop of sea temperature during the Günz glacial stage of the Pleistocene. Our results support an alternative evolutionary scenario for the OWA, suggesting a coastal migration along south Asia, Middle East and eastern Africa continental platforms, followed by the colonization of the Atlantic via the Cape of the Good Hope.
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Affiliation(s)
- Gonçalo Silva
- Centre of Marine Sciences, CCMAR, University of Algarve, Gambelas, 8005-139, Faro, Portugal.
- MARE - Marine and Environmental Sciences Centre; ISPA - Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041, Lisboa, Portugal.
| | - Regina L Cunha
- Centre of Marine Sciences, CCMAR, University of Algarve, Gambelas, 8005-139, Faro, Portugal
| | - Ana Ramos
- Centre of Marine Sciences, CCMAR, University of Algarve, Gambelas, 8005-139, Faro, Portugal
| | - Rita Castilho
- Centre of Marine Sciences, CCMAR, University of Algarve, Gambelas, 8005-139, Faro, Portugal
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43
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Costello MJ, Chaudhary C. Marine Biodiversity, Biogeography, Deep-Sea Gradients, and Conservation. Curr Biol 2017; 27:R511-R527. [DOI: 10.1016/j.cub.2017.04.060] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Shulman MJ, Bermingham E. EARLY LIFE HISTORIES, OCEAN CURRENTS, AND THE POPULATION GENETICS OF CARIBBEAN REEF FISHES. Evolution 2017; 49:897-910. [DOI: 10.1111/j.1558-5646.1995.tb02325.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/1993] [Accepted: 07/06/1994] [Indexed: 12/01/2022]
Affiliation(s)
- Myra J. Shulman
- Department of Biology University of California Los Angeles California 90024‐1606
| | - Eldredge Bermingham
- Smithsonian Tropical Research Institute Apartado 2072 Balboa Republic of Panama
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45
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Howard DJ, Gregory PG, Chu J, Cain ML. CONSPECIFIC SPERM PRECEDENCE IS AN EFFECTIVE BARRIER TO HYBRIDIZATION BETWEEN CLOSELY RELATED SPECIES. Evolution 2017; 52:511-516. [PMID: 28568320 DOI: 10.1111/j.1558-5646.1998.tb01650.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/1997] [Accepted: 01/28/1998] [Indexed: 11/28/2022]
Abstract
Conspecific sperm precedence is widespread in animals, appears to evolve rapidly, and is thought to have the potential to prevent hybridization between closely related species. However, to date no study has tested the isolating potential of such a barrier in mixed populations of two taxa under conditions in which other potential barriers to gene flow are controlled for or are prevented from operating. We tested the isolating potential of conspecific sperm precedence in the ground crickets Allonemobius fasciatus and A. socius in population cage experiments in which the frequency of the two species was varied. Despite the observation of abundant interspecific matings, the proportions of hybrid progeny were low and differed statistically from the proportions expected in the absence of conspecific sperm precedence. The results demonstrate that conspecific sperm precedence can severely limit gene flow between closely related species, even when one species is less abundant than the other.
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Affiliation(s)
- Daniel J Howard
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, 88003-8001
| | - Pamela G Gregory
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, 88003-8001.,Department of Biology, Mahasarakham University, 269/2 Mating District, Maha Sarakham, 44000, Thailand
| | - Jiming Chu
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, 88003-8001
| | - Michael L Cain
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, 88003-8001
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46
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Peterson MA, Denno RF. THE INFLUENCE OF INTRASPECIFIC VARIATION IN DISPERSAL STRATEGIES ON THE GENETIC STRUCTURE OF PLANTHOPPER POPULATIONS. Evolution 2017; 51:1189-1206. [PMID: 28565487 DOI: 10.1111/j.1558-5646.1997.tb03967.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/1996] [Accepted: 03/06/1997] [Indexed: 11/30/2022]
Abstract
The hypothesis that levels of gene flow among populations are correlated with dispersal ability has typically been tested by comparing gene flow among species that differ in dispersal abilities, an approach that potentially confounds dispersal ability with other species-specific differences. In this study, we take advantage of geographic variation in the dispersal strategies of two wing-dimorphic planthopper species, Prokelisia marginata and P. dolus, to examine for the first time whether levels of gene flow among populations are correlated with intraspecific variation in dispersal ability. We found that in both of these coastal salt marsh-inhabiting species, population-genetic subdivision, as assessed using allozyme electrophoresis, parallels geographic variation in the proportion of flight-capable adults (macropters) in a population; in regions where levels of macroptery are high, population genetic subdivision is less than in regions where levels of macroptery are low. We found no evidence that geographic variation in dispersal capability influences the degree to which gene flow declines with distance in either species. Thus, both species provided evidence that intraspecific variation in dispersal strategies influences the genetic structure of populations, and that this effect is manifested in population-genetic structure at the scale of large, coastal regions, rather than in genetic isolation by distance within a region. This conclusion was supported by interspecific comparisons revealing that: (1) population-genetic structure (GST ) of the two Prokelisia species correlated negatively with the mean proportion of flight-capable adults within a region; and (2) there was no evidence that the degree of isolation by distance increased with decreasing dispersal capability. Populations of the relatively sedentary P. dolus clustered by geographic region (using Nei's distances), but this was not the case for the more mobile P. marginata. Furthermore, gene flow among the two major regions we surveyed (Atlantic and Gulf Coasts) has been substantial in P. marginata, but relatively less in P. dolus. The results for P. marginata suggest that differences in the dispersal strategies of Atlantic and Gulf Coast populations occur despite extensive gene flow. We argue that gene flow is biased from Atlantic to Gulf Coast populations, indicating that selection favoring a reduction in flight capability must be intense along the Gulf. Together, the results of this study provide the first rigorous evidence of a negative relationship within a species between dispersal ability and the genetic structure of populations. Furthermore, regional variation in dispersal ability is apparently maintained by selective differences that outweigh high levels of gene flow among regions.
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Affiliation(s)
- Merrill A Peterson
- Department of Entomology, University of Maryland, College Park, Maryland, 20742
| | - Robert F Denno
- Department of Entomology, University of Maryland, College Park, Maryland, 20742
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47
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Palumbi SR, Grabowsky G, Duda T, Geyer L, Tachino N. SPECIATION AND POPULATION GENETIC STRUCTURE IN TROPICAL PACIFIC SEA URCHINS. Evolution 2017; 51:1506-1517. [DOI: 10.1111/j.1558-5646.1997.tb01474.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/1996] [Accepted: 06/11/1997] [Indexed: 11/27/2022]
Affiliation(s)
- Stephen R. Palumbi
- Department of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts 02138
| | - Gail Grabowsky
- Department of Biology Chaminade University Honolulu Hawaii 96822
| | - Thomas Duda
- Department of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts 02138
| | - Laura Geyer
- Department of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts 02138
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48
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Hellberg ME. RELATIONSHIPS BETWEEN INFERRED LEVELS OF GENE FLOW AND GEOGRAPHIC DISTANCE IN A PHILOPATRIC CORAL, BALANOPHYLLIA ELEGANS. Evolution 2017; 48:1829-1854. [DOI: 10.1111/j.1558-5646.1994.tb02218.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/1992] [Accepted: 08/17/1993] [Indexed: 12/01/2022]
Affiliation(s)
- Michael E. Hellberg
- Department of Zoology and Center for Population Biology; University of California; Davis California 95616
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49
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Hellberg ME. SYMPATRIC SEA SHELLS ALONG THE SEA'S SHORE: THE GEOGRAPHY OF SPECIATION IN THE MARINE GASTROPOD TEGULA. Evolution 2017; 52:1311-1324. [PMID: 28565375 DOI: 10.1111/j.1558-5646.1998.tb02013.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/1997] [Accepted: 06/02/1998] [Indexed: 11/29/2022]
Abstract
Uncertainty and controversy surround the geographical and ecological circumstances that create genetic differences between populations that eventually lead to reproductive isolation. Two aspects of marine organisms further complicate this situation: (1) many species possess planktonic larvae capable of great dispersal; and (2) obvious barriers to movement between populations are rare. Past studies of speciation in the sea have focussed on identifying the effects of past land barriers and on biogeographical breakpoints. However, assessing the role such undeniable barriers actually play in the initial divergence leading to reproductive isolation requires phylogenetic studies of recent radiations living in varying degrees of sympatry and allopatry to see which barriers (if any) tend to separate sister species. Here I infer phylogenetic relationship between 23 species of the marine snail Tegula using DNA sequences from two regions of the mitochondrial genome: cytochrome c oxidase I (COI) and the small ribosomal subunit (12S) These snails possess planktonic larvae with moderate dispersal capabilities and have speciated rapidly with over 40 extant species arising since the genus first appeared in the mid-Miocene (about 15 M.Y.B.P.). Trees constructed from the COI and 12S regions (which yielded 205 and 137 phylogenetically informative sites, respectively) were robust with respect to tree-building method, bootstrapping, and the relative weightings of transitions, transversions, and gaps Within clades where all extant species have been sampled, five of six identified sister species pairs broadly coexist on the same side of biogeographical boundaries. These data suggest strong geographical barriers to gene flow may not always be required for speciation in the sea; transient allopatry or even ecological barriers may suffice. A survey of the geographic distributions of marine radiations suggests that coastal distributions may favor the sympatry of sister taxa more than island distributions do.
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Affiliation(s)
- Michael E Hellberg
- Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California, 92093-0202
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50
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Marko PB. HISTORICAL ALLOPATRY AND THE BIOGEOGRAPHY OF SPECIATION IN THE PROSOBRANCH SNAIL GENUS NUCELLA. Evolution 2017; 52:757-774. [PMID: 28565241 DOI: 10.1111/j.1558-5646.1998.tb03700.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/1997] [Accepted: 03/06/1998] [Indexed: 12/01/2022]
Affiliation(s)
- Peter B. Marko
- Section of Evolution and Ecology and Center for Population Biology; University of California; Davis California 95616
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