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Peluso L, Faúndez J, Navarrete SA, Broitman BR, Aiken CM, Saenz-Agudelo P. Oceanographical-driven dispersal and environmental variation explain genetic structure in an upwelling coastal ecosystem. Sci Rep 2024; 14:21942. [PMID: 39304706 DOI: 10.1038/s41598-024-72841-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 09/11/2024] [Indexed: 09/22/2024] Open
Abstract
The seascape comprises multiple environmental variables that interact with species biology to determine patterns of spatial genetic variation. The environment imposes spatially variable selective forces together with homogenizing and diverging drivers that facilitate or restrict dispersal, which is a complex, time-dependent process. Understanding how the seascape influences spatial patterns of genetic variation remains elusive, particularly in coastal upwelling systems. Here, we combine genome-wide SNP data, Lagrangian larval dispersal simulated over a hydrodynamic model, and ocean environmental information to quantify the relative contribution of ocean circulation and environmental heterogeneity as drivers of the spatial genetic structure of two congeneric intertidal limpets, Scurria scurra and S. araucana, along the central coast of Chile. We find that a genetic break observed in both limpet species coincides with a break in connectivity shown by the Lagrangian dispersal, suggesting that mean ocean circulation is an important seascape feature, in particular for S. scurra. For S. araucana, environmental variation appears as a better predictor of genetic structure than ocean circulation. Overall, our study shows broad patterns of seascape forcing on genetic diversity and contributes to our understanding of the complex ecological and evolutionary interactions along coastal upwelling systems.
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Affiliation(s)
- Lívia Peluso
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Escuela de Graduados, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Juan Faúndez
- Departamento de Oceanografía y Medio Ambiente, Instituto de Fomento Pesquero, Valparaíso, Chile
- Facultad de Ciencias Biológicas, Estación Costera de Investigaciones Marinas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sergio A Navarrete
- Coastal Socio-Ecological Millennium Institute, SECOS, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millenium Nucleus for Ecology and Conservation of Temperate Mesophotic Reef Ecosystems (NUTME), Valparaíso, Chile
- Facultad de Ciencias Biológicas, Estación Costera de Investigaciones Marinas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Oceanographic Research, COPAS-COASTAL, Universidad de Concepción, Concepción, Chile
- Marine Energy Research and Innovation Energy, MERIC, Estación Costera de Investigaciones Marinas, P. Universidad Católica de Chile, Santiago, Chile
| | - Bernardo R Broitman
- Departamento de Ciencias, Facultad de Artes Liberales, Universidad Adolfo Ibáñez, Viña del Mar, Santiago, Chile
- Coastal Socio-Ecological Millennium Institute, SECOS, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Nucleus UPWELL, Santiago, Chile
| | - Christopher M Aiken
- Coastal Marine Ecosystems Research Centre, CQUniversity, Gladstone, Australia
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.
- Millenium Nucleus for Ecology and Conservation of Temperate Mesophotic Reef Ecosystems (NUTME), Valparaíso, Chile.
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2
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Nandanpawar P, Sahoo B, Sahoo L, Murmu K, Reang D, Kumar AP, Chaudhari A, Das P. Unveiling population structure and selection signatures of riverine and genetically improved rohu, Labeo rohita using genome wide SNPs. Mol Biol Rep 2024; 51:926. [PMID: 39167228 DOI: 10.1007/s11033-024-09866-y] [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] [Received: 07/01/2024] [Accepted: 08/14/2024] [Indexed: 08/23/2024]
Abstract
BACKGROUND Captive breeding, along with artificial selection can significantly impact population structure by influencing allele frequencies and driving populations towards specific adaptation. Selective sweeps are powerful forces in shaping genetic variation within populations and can drive rapid spread of beneficial alleles while simultaneously reducing genetic diversity in localized regions of the genome. The present work was undertaken to assess the genetic structure and consequences of artificial selection in 10th generation of genetically improved rohu by comparing with wild populations. METHODS AND RESULTS The present study used 11,022 high-quality genome wide SNPs to compare the population genetic structure and signatures of selection between Jayanti rohu population and its wild counterpart. Outlier analysis revealed presence of 14 adaptive SNPs, out of which 5 were classified to be under decisive selection pressure. Notably, Jayanti rohu (JR) displayed 297 private alleles exclusive to its population. Chromosomes 7 and 16 emerged as potential hotspots containing a majority of the identified SNPs. Structure and principal component analysis revealed two distinct clusters, effectively distinguishing the JR and wild rohu populations. Phylogenetic analysis indicated a separate cluster of JR population distant from wild groups. CONCLUSION The results of present study shall help in elucidating patterns of genetic variation and characterizing selection signatures associated with captive bred and natural populations of rohu. The genomic resources generated through this work shall be helpful in improving the traceability of selectively bred germplasm for developing future strategies of genetic management.
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Affiliation(s)
- Priyanka Nandanpawar
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India.
| | - Bismay Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Lakshman Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Khuntia Murmu
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Dhalongsaih Reang
- ICAR-Central Institute of Fisheries Education, Panch Marg, Versova, Mumbai, Maharashtra, 400 061, India
| | - Annam Pavan Kumar
- ICAR-Central Institute of Fisheries Education, Panch Marg, Versova, Mumbai, Maharashtra, 400 061, India
| | - Aparna Chaudhari
- ICAR-Central Institute of Fisheries Education, Panch Marg, Versova, Mumbai, Maharashtra, 400 061, India
| | - Paramananda Das
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
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3
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Montalvo LD, Kimball RT, Austin JD, Robinson SK. Unraveling the genomic landscape of Campylorhynchus wrens along western Ecuador's precipitation gradient: Insights into hybridization, isolation by distance, and isolation by the environment. Ecol Evol 2024; 14:e11661. [PMID: 38994212 PMCID: PMC11237350 DOI: 10.1002/ece3.11661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 05/31/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024] Open
Abstract
Environmental gradients have the potential to influence genetic differentiation among populations ultimately leading to allopatric speciation. However, environmental gradients can also facilitate hybridization between closely related taxa. We investigated a putative hybrid zone in western Ecuador, involving two polytypic wren species (Aves: Troglodytidae), Campylorhynchus zonatus and C. fasciatus. Our study addressed two primary questions: (1) Is there evidence of population structure and genetic admixture between these taxa in western Ecuador? and (2) What are the relative contributions of isolation by distance and isolation by the environment to the observed genetic differentiation along the environmental gradient in this region? We analyzed 4409 single-nucleotide polymorphisms (SNPs) from 112 blood samples sequenced using ddRadSeq and a de novo assembly. The optimum number of genetic clusters ranged from 2 to 4, aligning with geographic origins, known phylogenetics, and physical or ecological constraints. We observed notable transitions in admixture proportions along the environmental gradient in western Ecuador between C. z. brevirostris and the northern and southern genetic clusters of C. f. pallescens. Genetic differentiation between the two C. f. pallescens populations could be attributed to an unreported potential physical barrier in central western Ecuador, where the proximity of the Andes to the coastline restricts lowland habitats, limiting dispersal and gene flow, especially among dry-habitat specialists. The observed admixture in C. f. pallescens suggests that this subspecies may be a hybrid between C. z. brevirostris and C. fasciatus, with varying degrees of admixture in western Ecuador and northwestern Peru. We found evidence of isolation by distance, while isolation by the environment was less pronounced but still significant for annual mean precipitation and precipitation seasonality. This study enhances our understanding of avian population genomics in tropical regions.
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Affiliation(s)
- Luis Daniel Montalvo
- Florida Museum of Natural History University of Florida Gainesville Florida USA
- Department of Biology University of Florida Gainesville Florida USA
| | | | - James D Austin
- Department of Wildlife Ecology and Conservation University of Florida Gainesville Florida USA
| | - Scott K Robinson
- Florida Museum of Natural History University of Florida Gainesville Florida USA
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Villalobos R, Aylagas E, Pearman JK, Curdia J, Coker D, Bell AC, Brown SD, Rowe K, Lozano-Cortés D, Rabaoui LJ, Marshell A, Qurban M, Jones B, Berumen ML, Carvalho S. Biodiversity patterns of the coral reef cryptobiota around the Arabian Peninsula. Sci Rep 2024; 14:9532. [PMID: 38664507 PMCID: PMC11045746 DOI: 10.1038/s41598-024-60336-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024] Open
Abstract
The Arabian Peninsula accounts for approximately 6% of the world's coral reefs. Some thrive in extreme environments of temperature and salinity. Using 51 Autonomous Reef Monitoring Structure (ARMS), a standardized non-destructive monitoring device, we investigated the spatial patterns of coral reef cryptobenthic diversity in four ecoregions around the Arabian Peninsula and analyzed how geographical and/or environmental drivers shape those patterns. The mitochondrial cytochrome c oxidase subunit I (COI) gene was used to identify Amplicon Sequence Variants and assign taxonomy of the cryptobenthic organisms collected from the sessile and mobile fractions of each ARMS. Cryptobenthic communities sampled from the two ecoregions in the Red Sea showed to be more diverse than those inhabiting the Arabian (Persian) Gulf and the Gulf of Oman. Geographic distance revealed a stronger relationship with beta diversity in the Mantel partial correlation than environmental distance. However, the two mobile fractions (106-500 µm and 500-2000 µm) also had a significant correlation between environmental distance and beta diversity. In our study, dispersal limitations explained the beta diversity patterns in the selected reefs, supporting the neutral theory of ecology. Still, increasing differences in environmental variables (environmental filtering) also had an effect on the distribution patterns of assemblages inhabiting reefs within short geographic distances. The influence of geographical distance in the cryptofauna assemblages makes these relevant, yet usually ignored, communities in reef functioning vulnerable to large scale coastal development and should be considered in ecosystem management of such projects.
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Affiliation(s)
- Rodrigo Villalobos
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Eva Aylagas
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - John K Pearman
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Joao Curdia
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Darren Coker
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Alyssa Clothilde Bell
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Shannon D Brown
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington, Seattle, WA, USA
| | - Katherine Rowe
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- School of Science, The University of Waikato, Hamilton, New Zealand
| | | | - Lotfi J Rabaoui
- Center for Environment & Marine Studies, Research Institute, King Fahd University of Petroleum and Minerals, 31261, Dhahran, Eastern Province, Kingdom of Saudi Arabia
- National Center for Wildlife, Riyadh, Saudi Arabia
| | - Alyssa Marshell
- Sultan Qaboos University, Al Seeb Al Khoudh SQU SEPS, 123, Muscat, Oman
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7053, Australia
| | - Mohammad Qurban
- Center for Environment & Marine Studies, Research Institute, King Fahd University of Petroleum and Minerals, 31261, Dhahran, Eastern Province, Kingdom of Saudi Arabia
- Ministry of Environment, Water and Agriculture, Riyadh, Saudi Arabia
| | - Burton Jones
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Michael Lee Berumen
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Susana Carvalho
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia.
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Friis G, Smith EG, Lovelock CE, Ortega A, Marshell A, Duarte CM, Burt JA. Rapid diversification of grey mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula. Mol Ecol 2024; 33:e17260. [PMID: 38197286 DOI: 10.1111/mec.17260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 11/13/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024]
Abstract
Biological systems occurring in ecologically heterogeneous and spatially discontinuous habitats provide an ideal opportunity to investigate the relative roles of neutral and selective factors in driving lineage diversification. The grey mangroves (Avicennia marina) of Arabia occur at the northern edge of the species' range and are subject to variable, often extreme, environmental conditions, as well as historic large fluctuations in habitat availability and connectivity resulting from Quaternary glacial cycles. Here, we analyse fully sequenced genomes sampled from 19 locations across the Red Sea, the Arabian Sea and the Persian/Arabian Gulf (PAG) to reconstruct the evolutionary history of the species in the region and to identify adaptive mechanisms of lineage diversification. Population structure and phylogenetic analyses revealed marked genetic structure correlating with geographic distance and highly supported clades among and within the seas surrounding the Arabian Peninsula. Demographic modelling showed times of divergence consistent with recent periods of geographic isolation and low marine connectivity during glaciations, suggesting the presence of (cryptic) glacial refugia in the Red Sea and the PAG. Significant migration was detected within the Red Sea and the PAG, and across the Strait of Hormuz to the Arabian Sea, suggesting gene flow upon secondary contact among populations. Genetic-environment association analyses revealed high levels of adaptive divergence and detected signs of multi-loci local adaptation driven by temperature extremes and hypersalinity. These results support a process of rapid diversification resulting from the combined effects of historical factors and ecological selection and reveal mangrove peripheral environments as relevant drivers of lineage diversity.
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Affiliation(s)
- Guillermo Friis
- Center for Genomics and Systems Biology (CGSB) and Mubadala ACCESS Center, New York University - Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Edward G Smith
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Catherine E Lovelock
- School of Environment, The University of Queensland, St Lucia, Queensland, Australia
| | - Alejandra Ortega
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Alyssa Marshell
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - John A Burt
- Center for Genomics and Systems Biology (CGSB) and Mubadala ACCESS Center, New York University - Abu Dhabi, Abu Dhabi, United Arab Emirates
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Li J, Zhang C, Mipam TD, Zhou Q, Chen S. Effects of Climatic Change on Phylogeography and Ecological Niche of the Endemic Herb Elymus breviaristatus on the Qinghai-Tibet Plateau. PLANTS (BASEL, SWITZERLAND) 2023; 12:3326. [PMID: 37765492 PMCID: PMC10535585 DOI: 10.3390/plants12183326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
Past climatic and topographic variations have created strong biogeographic barriers for alpine species and are key drivers of the distribution of genetic variation and population dynamics of species on the Qinghai-Tibet Plateau (QTP). Therefore, to better conserve and use germplasm resources, it is crucial to understand the distribution and differentiation of genetic variation within species. Elymus breviaristatus, an ecologically important rare grass species with strong resistance, is restricted to a limited area of the QTP. In this study, we investigated the phylogeography of E. breviaristatus using five chloroplast genes and spacer regions in natural populations distributed along the eastern QTP. We identified a total of 25 haplotypes among 216 individuals from 18 E. breviaristatus populations, which were further classified into four haplogroups based on geographical distribution and haplotype network analysis. Notably, we did not observe any signs of population expansion. High genetic diversity was exhibited at both species and population levels, with precipitation being the main limiting factor for population genetic diversity levels. Higher genetic diversity was exhibited by populations located near the Mekong-Salween Divide genetic barrier, suggesting that they may have served as a glacial refuge. The significant pattern of genetic differentiation by environmental isolation highlights the influence of heterogeneous environments on the genetic structure of E. breviaristatus populations. Additionally, the results of ecological niche models indicated that the geographic distribution of E. breviaristatus populations has decreased rapidly since the Last Glacial Maximum but is not threatened by future global warming.
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Affiliation(s)
- Jin Li
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu 610041, China
| | | | - Tserang Donko Mipam
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu 610041, China
| | - Qingping Zhou
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu 610041, China
| | - Shiyong Chen
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu 610041, China
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
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Hancock ZB, Toczydlowski RH, Bradburd GS. A spatial approach to jointly estimate Wright's neighborhood size and long-term effective population size. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.10.532094. [PMID: 36945591 PMCID: PMC10029013 DOI: 10.1101/2023.03.10.532094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Spatially continuous patterns of genetic differentiation, which are common in nature, are often poorly described by existing population genetic theory or methods that assume panmixia or discrete, clearly definable populations. There is therefore a need for statistical approaches in population genetics that can accommodate continuous geographic structure, and that ideally use georeferenced individuals as the unit of analysis, rather than populations or subpopulations. In addition, researchers are often interested describing the diversity of a population distributed continuously in space, and this diversity is intimately linked to the dispersal potential of the organism. A statistical model that leverages information from patterns of isolation-by-distance to jointly infer parameters that control local demography (such as Wright's neighborhood size), and the long-term effective size (Ne) of a population would be useful. Here, we introduce such a model that uses individual-level pairwise genetic and geographic distances to infer Wright's neighborhood size and long-term Ne. We demonstrate the utility of our model by applying it to complex, forward-time demographic simulations as well as an empirical dataset of the Red Sea clownfish (Amphiprion bicinctus). The model performed well on simulated data relative to alternative approaches and produced reasonable empirical results given the natural history of clownfish. The resulting inferences provide important insights into the population genetic dynamics of spatially structure populations.
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Affiliation(s)
- Zachary B. Hancock
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 481103, USA
| | | | - Gideon S. Bradburd
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 481103, USA
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8
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Fitz KS, Montes HR, Thompson DM, Pinsky ML. Isolation-by-distance and isolation-by-oceanography in Maroon Anemonefish ( Amphiprion biaculeatus). Evol Appl 2023; 16:379-392. [PMID: 36793687 PMCID: PMC9923474 DOI: 10.1111/eva.13448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/27/2022] [Accepted: 07/07/2022] [Indexed: 11/29/2022] Open
Abstract
Obtaining dispersal estimates for a species is key to understanding local adaptation and population dynamics and to implementing conservation actions. Genetic isolation-by-distance (IBD) patterns can be used for estimating dispersal, and these patterns are especially useful for marine species in which few other methods are available. In this study, we genotyped coral reef fish (Amphiprion biaculeatus) at 16 microsatellite loci across eight sites across 210 km in the central Philippines to generate fine-scale estimates of dispersal. All sites except for one followed IBD patterns. Using IBD theory, we estimated a larval dispersal kernel spread of 8.9 km (95% confidence interval of 2.3-18.4 km). Genetic distance to the remaining site correlated strongly with the inverse probability of larval dispersal from an oceanographic model. Ocean currents were a better explanation for genetic distance at large spatial extents (sites greater than 150 km apart), while geographic distance remained the best explanation for spatial extents less than 150 km. Our study demonstrates the utility of combining IBD patterns with oceanographic simulations to understand connectivity in marine environments and to guide marine conservation strategies.
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Affiliation(s)
- Kyra S. Fitz
- Department of Ecology, Evolution and Natural ResourcesRutgers UniversityNew BrunswickNew JerseyUSA
| | - Humberto R. Montes
- Institute of Tropical Ecology and Environmental ManagementVisayas State UniversityBaybay CityPhilippines
| | | | - Malin L. Pinsky
- Department of Ecology, Evolution and Natural ResourcesRutgers UniversityNew BrunswickNew JerseyUSA
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LeBlanc NM, Pavey SA. Comparing mixed models and Random Forest association tests using naturalGWAS and a Striped Bass SNP dataset. Mol Ecol Resour 2022; 23:145-158. [PMID: 35980658 DOI: 10.1111/1755-0998.13701] [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: 11/27/2020] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022]
Abstract
In this study, we used the phenotype simulation package naturalGWAS to test the performance of Zhao's Random Forest method in comparison to an uncorrected Random Forest test, latent factor mixed models (LFMM), genome-wide efficient mixed models (GEMMA), and confounder adjusted linear regression (CATE). We created 400 sets of phenotypes, corresponding to five effect sizes and 2, 5, 15, or 30 causal loci, simulated from two empirical datasets containing SNPs from Striped Bass representing three and 13 populations. All association methods were evaluated for their ability to detect genotype-phenotype associations based on power, false discovery rates, and number of false positives. Genomic inflation was highest for uncorrected Random Forest and LFMM tests and lowest for Gemma and Zhao's Random Forest. All association tests had similar power to detect causal loci, and Zhao's Random Forest had the lowest false discovery rate in all scenarios. To measure the performance of association tests in small datasets with few loci surrounding a causal gene we also ran analyses again after removing causal loci from each dataset. All association tests were only able to find true positives, defined as loci located within 30k bp of a causal locus, in 3%-18% of simulations. In contrast, at least one false positive was found in 17%-44% of simulations. Zhao's Random Forest again identified the fewest false positives of all association tests studied. The ability to test the power of association tests for individual empirical datasets can be an extremely useful first step when designing a GWAS study.
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Affiliation(s)
- Nathalie M LeBlanc
- Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, NB, Canada
| | - Scott A Pavey
- Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, NB, Canada
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10
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Wang G, Lai H, Bi S, Guo D, Zhao X, Chen X, Liu S, Liu X, Su Y, Yi H, Li G. ddRAD-Seq reveals evolutionary insights into population differentiation and the cryptic phylogeography of Hyporhamphus intermedius in Mainland China. Ecol Evol 2022; 12:e9053. [PMID: 35813915 PMCID: PMC9251877 DOI: 10.1002/ece3.9053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 05/28/2022] [Accepted: 06/08/2022] [Indexed: 11/12/2022] Open
Abstract
Species differentiation and local adaptation in heterogeneous environments have attracted much attention, although little is known about the mechanisms involved. Hyporhamphus intermedius is an anadromous, brackish-water halfbeak that is widely distributed in coastal areas and hyperdiverse freshwater systems in China, making it an interesting model for research on phylogeography and local adaptation. Here, 156 individuals were sampled at eight sites from heterogeneous aquatic habitats to examine environmental and genetic contributions to phenotypic divergence. Using double-digest restriction-site-associated DNA sequencing (ddRAD-Seq) in the specimens from the different watersheds, 5498 single nucleotide polymorphisms (SNPs) were found among populations, with obvious population differentiation. We find that present-day Mainland China populations are structured into distinct genetic clusters stretching from southern and northern ancestries, mirroring geography. Following a transplant event in Plateau Lakes, there were virtually no variations of genetic diversity occurred in two populations, despite the fact two main splits were unveiled in the demographic history. Additionally, dorsal, and anal fin traits varied widely between the southern group and the others, which highlighted previously unrecognized lineages. We then explore genotype-phenotype-environment associations and predict candidate loci. Subgroup ranges appeared to correspond to geographic regions with heterogeneous hydrological factors, indicating that these features are likely important drivers of diversification. Accordingly, we conclude that genetic and phenotypic polymorphism and a moderate amount of genetic differentiation occurred, which might be ascribed to population subdivision, and the impact of abiotic factors.
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Affiliation(s)
- Gongpei Wang
- Guangdong Province Key Laboratory for Aquatic Economic AnimalsState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐Sen UniversitySouthern Marine Science and Engineering Guangdong Laboratory (Zhuhai)GuangzhouChina
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic FishGuangzhouChina
| | - Han Lai
- Guangdong Province Key Laboratory for Aquatic Economic AnimalsState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐Sen UniversitySouthern Marine Science and Engineering Guangdong Laboratory (Zhuhai)GuangzhouChina
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic FishGuangzhouChina
| | - Sheng Bi
- Guangdong Province Key Laboratory for Aquatic Economic AnimalsState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐Sen UniversitySouthern Marine Science and Engineering Guangdong Laboratory (Zhuhai)GuangzhouChina
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic FishGuangzhouChina
| | - Dingli Guo
- Guangdong Province Key Laboratory for Aquatic Economic AnimalsState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐Sen UniversitySouthern Marine Science and Engineering Guangdong Laboratory (Zhuhai)GuangzhouChina
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic FishGuangzhouChina
| | - Xiaopin Zhao
- Guangdong Province Key Laboratory for Aquatic Economic AnimalsState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐Sen UniversitySouthern Marine Science and Engineering Guangdong Laboratory (Zhuhai)GuangzhouChina
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic FishGuangzhouChina
| | - Xiaoli Chen
- Guangdong Province Key Laboratory for Aquatic Economic AnimalsState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐Sen UniversitySouthern Marine Science and Engineering Guangdong Laboratory (Zhuhai)GuangzhouChina
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic FishGuangzhouChina
| | - Shuang Liu
- Guangdong Province Key Laboratory for Aquatic Economic AnimalsState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐Sen UniversitySouthern Marine Science and Engineering Guangdong Laboratory (Zhuhai)GuangzhouChina
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic FishGuangzhouChina
| | - Xuange Liu
- Guangdong Province Key Laboratory for Aquatic Economic AnimalsState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐Sen UniversitySouthern Marine Science and Engineering Guangdong Laboratory (Zhuhai)GuangzhouChina
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic FishGuangzhouChina
| | - Yuqin Su
- Guangdong Province Key Laboratory for Aquatic Economic AnimalsState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐Sen UniversitySouthern Marine Science and Engineering Guangdong Laboratory (Zhuhai)GuangzhouChina
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic FishGuangzhouChina
| | - Huadong Yi
- Guangdong Province Key Laboratory for Aquatic Economic AnimalsState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐Sen UniversitySouthern Marine Science and Engineering Guangdong Laboratory (Zhuhai)GuangzhouChina
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic FishGuangzhouChina
| | - Guifeng Li
- Guangdong Province Key Laboratory for Aquatic Economic AnimalsState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐Sen UniversitySouthern Marine Science and Engineering Guangdong Laboratory (Zhuhai)GuangzhouChina
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic FishGuangzhouChina
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11
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Biogeography of the coastal fishes of the Socotra Archipelago: Challenging current ecoregional concepts. PLoS One 2022; 17:e0267086. [PMID: 35486578 PMCID: PMC9053782 DOI: 10.1371/journal.pone.0267086] [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: 07/23/2020] [Accepted: 04/03/2022] [Indexed: 11/19/2022] Open
Abstract
The Socotra Archipelago, located in the eastern Gulf of Aden, has a unique marine environment, which combines tropical and ‘pseudo-temperate’ elements. An updated species inventory recently considered its coastal fish diversity the highest among Arabian ecoregions, necessitating to re-assess the ichthyogeographic position of the island group. The main aim of this study is to describe the distributional biogeography of its coastal fish fauna in relation to contemporary ichthyogeographic and ecoregional concepts. Inferences are drawn with regard to the marine biogeographic arrangement and ecoregional partitioning of the Arabian region. The main datasets comprise eight and twenty selected families including 404 and 898 species, respectively, from Arabian ecoregions. The Socotra Archipelago has close affinities to a putative ecoregion in the eastern Gulf of Aden that extends to southern Oman. It is more closely related to the Arabian Sea coast of Oman than to ecoregions in the Red Sea and a putative ecoregion in the western Gulf of Aden. The Gulf of Aden does not represent a consistent ecoregion in ichthyogeographic terms, because its eastern and western parts are less closely related to one another than to other ecoregions. The Socotra Archipelago and the eastern Gulf of Aden should therefore not be assigned to a joined province with Red Sea ecoregions. The coastal fish faunas of the southern Red Sea have close affinities with those of the western Gulf of Aden. The Arabian/Persian Gulf is least related to the other Arabian ecoregions. The authors posit the Socotra Archipelago as a distinct ecoregion, either on its own or in combination with affiliated mainland areas. This best reflects the ichthyogeographic data and the exceptionally high levels of fish and overall marine diversity. Two alternative ecoregional delineations are proposed, serving as working hypotheses for onward research.
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12
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Abstract
The Stylasteridae, commonly known as lace corals, is a family of colonial calcifying hydrozoans mostly inhabiting deep waters. Stylasterids show a cosmopolitan distribution but, in some areas, they are characterized by low species diversity, such as in the Red Sea, where only a shallow-water species has been reported so far. With this work, we provide the first evidence of a deep-sea stylasterid inhabiting the NEOM region in the northern Saudi Arabian Red Sea, at depths ranging between 166 and 492 m. Morphological examinations revealed that this species was previously unknown and belonging to the genus Stylaster. We, therefore, describe Stylaster tritoni sp. nov., representing the first record of the genus in the Red Sea. Lastly, the phylogenetic position of the species within the Stylasteridae was evaluated, revealing a close relationship with shallow-water Indo-Pacific and Western Atlantic Stylaster species and confirming the polyphyletic nature of the genus Stylaster.
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13
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Smith EG, Hazzouri KM, Choi JY, Delaney P, Al-Kharafi M, Howells EJ, Aranda M, Burt JA. Signatures of selection underpinning rapid coral adaptation to the world's warmest reefs. SCIENCE ADVANCES 2022; 8:eabl7287. [PMID: 35020424 PMCID: PMC10954036 DOI: 10.1126/sciadv.abl7287] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
Coral populations in the world’s warmest reefs, the Persian/Arabian Gulf (PAG), represent an ideal model system to understand the evolutionary response of coral populations to past and present environmental change and to identify genomic loci that contribute to elevated thermal tolerance. Here, we use population genomics of the brain coral Platygyra daedalea to show that corals in the PAG represent a distinct subpopulation that was established during the Holocene marine transgression, and identify selective sweeps in their genomes associated with thermal adaptation. We demonstrate the presence of positive and disruptive selection and provide evidence for selection of differentially methylated haplotypes. While demographic analyses suggest limited potential for genetic rescue of neighboring Indian Ocean reefs, the presence of putative targets of selection in corals outside of the PAG offers hope that loci associated with thermal tolerance may be present in the standing genetic variation.
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Affiliation(s)
- Edward G. Smith
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Khaled M. Hazzouri
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Abu Dhabi, UAE
| | - Jae Young Choi
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Patrice Delaney
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Mohammed Al-Kharafi
- Department of Fisheries Resource Development, Public Authority of Agriculture and Fisheries Resources, Kuwait City, Kuwait
| | - Emily J. Howells
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | - Manuel Aranda
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - John A. Burt
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
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14
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Lau SCY, Strugnell JM, Sands CJ, Silva CNS, Wilson NG. Evolutionary innovations in Antarctic brittle stars linked to glacial refugia. Ecol Evol 2021; 11:17428-17446. [PMID: 34938519 PMCID: PMC8668817 DOI: 10.1002/ece3.8376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 12/31/2022] Open
Abstract
The drivers behind evolutionary innovations such as contrasting life histories and morphological change are central questions of evolutionary biology. However, the environmental and ecological contexts linked to evolutionary innovations are generally unclear. During the Pleistocene glacial cycles, grounded ice sheets expanded across the Southern Ocean continental shelf. Limited ice-free areas remained, and fauna were isolated from other refugial populations. Survival in Southern Ocean refugia could present opportunities for ecological adaptation and evolutionary innovation. Here, we reconstructed the phylogeographic patterns of circum-Antarctic brittle stars Ophionotus victoriae and O. hexactis with contrasting life histories (broadcasting vs brooding) and morphology (5 vs 6 arms). We examined the evolutionary relationship between the two species using cytochrome c oxidase subunit I (COI) data. COI data suggested that O. victoriae is a single species (rather than a species complex) and is closely related to O. hexactis (a separate species). Since their recent divergence in the mid-Pleistocene, O. victoriae and O. hexactis likely persisted differently throughout glacial maxima, in deep-sea and Antarctic island refugia, respectively. Genetic connectivity, within and between the Antarctic continental shelf and islands, was also observed and could be linked to the Antarctic Circumpolar Current and local oceanographic regimes. Signatures of a probable seascape corridor linking connectivity between the Scotia Sea and Prydz Bay are also highlighted. We suggest that survival in Antarctic island refugia was associated with increase in arm number and a switch from broadcast spawning to brooding in O. hexactis, and propose that it could be linked to environmental changes (such as salinity) associated with intensified interglacial-glacial cycles.
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Affiliation(s)
- Sally C. Y. Lau
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and EngineeringJames Cook UniversityTownsvilleQldAustralia
| | - Jan M. Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and EngineeringJames Cook UniversityTownsvilleQldAustralia
- Department of Ecology, Environment and EvolutionSchool of Life SciencesLa Trobe UniversityMelbourneVicAustralia
- Securing Antarctica's Environmental FutureJames Cook UniversityTownsvilleQldAustralia
| | - Chester J. Sands
- British Antarctic SurveyNatural Environment Research CouncilCambridgeUK
| | - Catarina N. S. Silva
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and EngineeringJames Cook UniversityTownsvilleQldAustralia
| | - Nerida G. Wilson
- Collections & ResearchWestern Australian MuseumWelshpoolWAAustralia
- School of Biological SciencesUniversity of Western AustraliaPerthWAAustralia
- Securing Antarctica's Environmental FutureWestern Australian MuseumWelshpoolWAAustralia
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15
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Palaiokostas C, Anjum A, Jeuthe H, Kurta K, Lopes Pinto F, Koning DJ. A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (
Salvelinus alpinus
). Evol Appl 2021; 15:565-577. [PMID: 35505879 PMCID: PMC9046918 DOI: 10.1111/eva.13261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/19/2021] [Accepted: 05/29/2021] [Indexed: 12/25/2022] Open
Abstract
Routine implementation of genomic information for guiding selection decisions is not yet common in the majority of aquaculture species. Reduced representation sequencing approaches offer a cost‐effective solution for obtaining genome‐wide information in species with a limited availability of genomic resources. In the current study, we implemented double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) on an Arctic charr strain with the longest known history of selection (approximately 40 years) aiming to improve selection decisions. In total, 1730 animals reared at four different farms in Sweden and spanning from year classes 2013–2017 were genotyped using ddRAD‐seq. Approximately 5000 single nucleotide polymorphisms (SNPs) were identified, genetic diversity‐related metrics were estimated, and genome‐wide association studies (GWAS) for body length at different time points and age of sexual maturation were conducted. Low genetic differentiation amongst animals from the different farms was observed based on both the results from pairwise Fst values and principal component analysis (PCA). The existence of associations was investigated between the mean genome‐wide heterozygosity of each full‐sib family (year class 2017) and the corresponding inbreeding coefficient or survival to the eyed stage. A moderate correlation (−0.33) was estimated between the mean observed heterozygosity of each full‐sib family and the corresponding inbreeding coefficient, while no linear association was obtained with the survival to the eyed stage. GWAS did not detect loci with major effect for any of the studied traits. However, genomic regions explaining more than 1% of the additive genetic variance for either studied traits were suggested across 14 different chromosomes. Overall, key insights valuable for future selection decisions of Arctic charr have been obtained, suggesting ddRAD as an attractive genotyping platform for obtaining genome‐wide information in a cost‐effective manner.
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Affiliation(s)
- Christos Palaiokostas
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Anam Anjum
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Henrik Jeuthe
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
- Aquaculture Center North Kälarne Sweden
| | - Khrystyna Kurta
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Fernando Lopes Pinto
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Dirk Jan Koning
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
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16
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Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results? Mol Genet Genomics 2021; 296:457-471. [PMID: 33469716 DOI: 10.1007/s00438-020-01756-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the laboratory and bioinformatic parameters of enzyme-based techniques have been investigated in the literature. However, the impact of those parameters on downstream analyses and biological results remains less documented. In this study, we investigated the effects of sevral pre- and post-sequencing settings on ddRAD-seq results for two biological systems: a complex of butterfly species (Coenonympha sp.) and several populations of common beech (Fagus sylvatica). Our results suggest that pre-sequencing parameters (i.e., DNA quantity, number of PCR cycles during library preparation) have a significant impact on the number of recovered reads and SNPs, on the number of unique alleles and on individual heterozygosity. In the same way, we found that post-sequencing settings (i.e., clustering and minimum coverage thresholds) influenced loci reconstruction (e.g., number of loci, mean coverage) and SNP calling (e.g., number of SNPs; heterozygosity) but had only a marginal impact on downstream analyses (e.g., measure of genetic differentiation, estimation of individual admixture, and demographic inferences). In addition, replication analyses confirmed the reproducibility of the ddRAD-seq procedure. Overall, this study assesses the degree of sensitivity of ddRAD-seq data to pre- and post-sequencing protocols, and illustrates its robustness when studying population genetics.
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17
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Klanten OS, Gaither MR, Greaves S, Mills K, O’Keeffe K, Turnbull J, McKinnon R, Booth DJ. Genomic and morphological evidence of distinct populations in the endemic common (weedy) seadragon Phyllopteryx taeniolatus (Syngnathidae) along the east coast of Australia. PLoS One 2020; 15:e0243446. [PMID: 33362197 PMCID: PMC7757807 DOI: 10.1371/journal.pone.0243446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/22/2020] [Indexed: 11/30/2022] Open
Abstract
The common or weedy seadragon, Phyllopteryx taeniolatus, is an iconic and endemic fish found across temperate reefs of southern Australia. Despite its charismatic nature, few studies have been published, and the extent of population sub-structuring remains poorly resolved. Here we used 7462 single nucleotide polymorphisms (SNPs) to identify the extent of population structure in the weedy seadragon along the temperate southeast coast of Australia. We identified four populations, with strong genetic structure (FST = 0.562) between them. Both Discriminant Analysis of Principle Components (DAPC) and Bayesian clustering analyses support four distinct genetic clusters (north to south: central New South Wales, southern NSW, Victoria and Tasmania). In addition to these genetic differences, geographical variation in external morphology was recorded, with individuals from New South Wales shaped differently for a few measurements to those from the Mornington Peninsula (Victoria). We posit that these genetic and morphological differences suggest that the Victorian population of P. taeniolatus was historically isolated by the Bassian Isthmus during the last glacial maximum and should now be considered at least a distinct population. We also recorded high levels of genetic structure among the other locations. Based on the genomic and to a degree morphological evidence presented in this study, we recommend that the Victorian population be managed separately from the eastern populations (New South Wales and Tasmania).
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Affiliation(s)
- O. Selma Klanten
- Fish Ecology Lab, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
- * E-mail:
| | - Michelle R. Gaither
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, United States of America
| | - Samuel Greaves
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, United States of America
| | - Kade Mills
- Victorian National Parks Association, Carlton Melbourne, VIC, Australia
| | | | - John Turnbull
- Underwater Research Group (URG), Sydney, NSW, Australia
- Centre for Marine Biodiversity and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Rob McKinnon
- New South Wales National Parks and Wildlife Service, Merimbula, NSW, Australia
| | - David J. Booth
- Fish Ecology Lab, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
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18
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Nielsen ES, Henriques R, Beger M, Toonen RJ, von der Heyden S. Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species. BMC Evol Biol 2020; 20:121. [PMID: 32938400 PMCID: PMC7493327 DOI: 10.1186/s12862-020-01679-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species' potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). RESULTS Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus. CONCLUSION The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.
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Affiliation(s)
- Erica S Nielsen
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Romina Henriques
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.,Technical University of Denmark, National Institute of Aquatic Resources, Section for Marine Living Resources, Velsøvej 39, 8600, Silkeborg, Denmark
| | - Maria Beger
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.
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19
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Robitzch V, Saenz‐Agudelo P, Berumen ML. Travel with your kin ship! Insights from genetic sibship among settlers of a coral damselfish. Ecol Evol 2020; 10:8265-8278. [PMID: 32788977 PMCID: PMC7417242 DOI: 10.1002/ece3.6533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 01/06/2023] Open
Abstract
Coral reef fish larvae are tiny, exceedingly numerous, and hard to track. They are also highly capable, equipped with swimming and sensory abilities that may influence their dispersal trajectories. Despite the importance of larval input to the dynamics of a population, we remain reliant on indirect insights to the processes influencing larval behavior and transport. Here, we used genetic data (300 independent single nucleotide polymorphisms) derived from a light trap sample of a single recruitment event of Dascyllus abudafur in the Red Sea (N = 168 settlers). We analyzed the genetic composition of the larvae and assessed whether kinship among these was significantly different from random as evidence for cohesive dispersal during the larval phase. We used Monte Carlo simulations of similar-sized recruitment cohorts to compare the expected kinship composition relative to our empirical data. The high number of siblings within the empirical cohort strongly suggests cohesive dispersal among larvae. This work highlights the utility of kinship analysis as a means of inferring dynamics during the pelagic larval phase.
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Affiliation(s)
- Vanessa Robitzch
- Red Sea Research CenterDivision of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Pablo Saenz‐Agudelo
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Michael L. Berumen
- Red Sea Research CenterDivision of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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20
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DiBattista JD, Saenz‐Agudelo P, Piatek MJ, Cagua EF, Bowen BW, Choat JH, Rocha LA, Gaither MR, Hobbs JA, Sinclair‐Taylor TH, McIlwain JH, Priest MA, Braun CD, Hussey NE, Kessel ST, Berumen ML. Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula. Ecol Evol 2020; 10:4314-4330. [PMID: 32489599 PMCID: PMC7246217 DOI: 10.1002/ece3.6199] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and primary productivity that vary both by latitude and by season. The adjacent Arabian Sea is characterized by a sharper environmental gradient, ranging from extensive coral cover and warm temperatures in the southwest, to sparse coral cover, cooler temperatures, and seasonal upwelling in the northeast. Reef fish, however, are not confined to these seas, with some Red Sea fishes extending varying distances into the northern Arabian Sea, while their pelagic larvae are presumably capable of much greater dispersal. These species must therefore cope with a diversity of conditions that invoke the possibility of steep clines in natural selection. Here, we test for genetic structure in two widespread reef fish species (a butterflyfish and surgeonfish) and eight range-restricted butterflyfishes across the Red Sea and Arabian Sea using genome-wide single nucleotide polymorphisms. We performed multiple matrix regression with randomization analyses on genetic distances for all species, as well as reconstructed scenarios for population subdivision in the species with signatures of isolation. We found that (a) widespread species displayed more genetic subdivision than regional endemics and (b) this genetic structure was not correlated with contemporary environmental parameters but instead may reflect historical events. We propose that the endemic species may be adapted to a diversity of local conditions, but the widespread species are instead subject to ecological filtering where different combinations of genotypes persist under divergent ecological regimes.
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Affiliation(s)
- Joseph D. DiBattista
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- School of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
- Australian Museum Research InstituteAustralian MuseumSydneyNSWAustralia
| | - Pablo Saenz‐Agudelo
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Instituto de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | - Marek J. Piatek
- Computational Bioscience Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Edgar Fernando Cagua
- Centre for Integrative EcologySchool of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | | | - John Howard Choat
- School of Marine and Tropical BiologyJames Cook UniversityTownsvilleQldAustralia
| | - Luiz A. Rocha
- Section of IchthyologyCalifornia Academy of SciencesSan FranciscoCAUSA
| | - Michelle R. Gaither
- Section of IchthyologyCalifornia Academy of SciencesSan FranciscoCAUSA
- Genomics and Bioinformatics ClusterDepartment of BiologyUniversity of Central FloridaOrlandoFLUSA
| | - Jean‐Paul A. Hobbs
- School of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
- School of Biological SciencesUniversity of QueenslandBrisbaneQldAustralia
| | - Tane H. Sinclair‐Taylor
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Australian Institute of Marine ScienceTownsvilleQldAustralia
| | | | - Mark A. Priest
- Marine Spatial Ecology LabSchool of Biological Sciences and ARC Centre of Excellence for Coral Reef StudiesUniversity of QueenslandSt. LuciaQldAustralia
| | - Camrin D. Braun
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | | | - Steven T. Kessel
- Daniel P. Haerther Center for Conservation and ResearchJohn G. Shedd AquariumChicagoILUSA
| | - Michael L. Berumen
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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21
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D’Urban Jackson J, Bruford MW, Székely T, DaCosta JM, Sorenson MD, Russo IRM, Maher KH, Cruz-López M, Galindo-Espinosa D, Palacios E, De Sucre-Medrano AE, Cavitt J, Pruner R, Morales AL, Gonzalez O, Burke T, Küpper C. Population differentiation and historical demography of the threatened snowy plover Charadrius nivosus (Cassin, 1858). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01256-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractDelineating conservation units is a complex and often controversial process that is particularly challenging for highly vagile species. Here, we reassess population genetic structure and identify those populations of highest conservation value in the threatened snowy plover (Charadrius nivosus, Cassin, 1858), a partial migrant shorebird endemic to the Americas. We use four categories of genetic data—mitochondrial DNA (mtDNA), microsatellites, Z-linked and autosomal single nucleotide polymorphisms (SNPs)—to: (1) assess subspecies delineation and examine population structure (2) compare the sensitivity of the different types of genetic data to detect spatial genetic patterns, and (3) reconstruct demographic history of the populations analysed. Delineation of two traditionally recognised subspecies was broadly supported by all data. In addition, microsatellite and SNPs but not mtDNA supported the recognition of Caribbean snowy plovers (C. n. tenuirostris) and Floridian populations (eastern C. n. nivosus) as distinct genetic lineage and deme, respectively. Low migration rates estimated from autosomal SNPs (m < 0.03) reflect a general paucity of exchange between genetic lineages. In contrast, we detected strong unidirectional migration (m = 0.26) from the western into the eastern nivosus deme. Within western nivosus, we found no genetic differentiation between coastal Pacific and inland populations. The correlation between geographic and genetic distances was weak but significant for all genetic data sets. All demes showed signatures of bottlenecks occurring during the past 1000 years. We conclude that at least four snowy plover conservation units are warranted: in addition to subspecies nivosus and occidentalis, a third unit comprises the Caribbean tenuirostris lineage and a fourth unit the distinct eastern nivosus deme.
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Kajungiro RA, Palaiokostas C, Pinto FAL, Mmochi AJ, Mtolera M, Houston RD, de Koning DJ. Population Structure and Genetic Diversity of Nile Tilapia ( Oreochromis niloticus) Strains Cultured in Tanzania. Front Genet 2020. [PMID: 31921307 DOI: 10.3389/fgene.2019.01269.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding population structure and genetic diversity within and between local Nile tilapia lines cultured in Tanzania is important for sustainable aquaculture production. This study investigated the genetic structure and diversity among seven Nile tilapia populations in Tanzania (Karanga, Igunga, Ruhila, Fisheries Education and Training Agency, Tanzania Fisheries Research Institute, Kunduchi, and Lake Victoria). Double-digest restriction site-associated DNA (ddRAD) libraries were prepared from 140 individual fish (20 per population) and sequenced using an Illumina HiSeq 4000 resulting in the identification of 2,180 informative single nucleotide polymorphisms (SNPs). Pairwise Fst values revealed strong genetic differentiation between the closely related populations; FETA, Lake Victoria, and Igunga and those from TAFIRI and Karanga with values ranging between 0.45 and 0.55. Population structure was further evaluated using Bayesian model-based clustering (STRUCTURE) and discriminant analysis of principal components (DAPC). Admixture was detected among Karanga, Kunduchi, and Ruhila populations. A cross-validation approach (25% of individual fish from each population was considered of unknown origin) was conducted in order to test the efficiency of the SNP markers to correctly assign individual fish to the population of origin. The cross-validation procedure was repeated 10 times resulting in 77% of the tested individual fish being allocated to the correct population. Overall our results provide a new database of informative SNP markers for both conservation management and aquaculture activities of Nile tilapia strains in Tanzania.
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Affiliation(s)
- Redempta A Kajungiro
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Aquatic Science and Fisheries, College of Agricultural Sciences and Fisheries Technology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Christos Palaiokostas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Fernando A Lopes Pinto
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Aviti J Mmochi
- Institute of Marine Sciences, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Marten Mtolera
- Institute of Marine Sciences, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Dirk Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Kajungiro RA, Palaiokostas C, Pinto FAL, Mmochi AJ, Mtolera M, Houston RD, de Koning DJ. Population Structure and Genetic Diversity of Nile Tilapia ( Oreochromis niloticus) Strains Cultured in Tanzania. Front Genet 2019; 10:1269. [PMID: 31921307 PMCID: PMC6933018 DOI: 10.3389/fgene.2019.01269] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 11/18/2019] [Indexed: 01/15/2023] Open
Abstract
Understanding population structure and genetic diversity within and between local Nile tilapia lines cultured in Tanzania is important for sustainable aquaculture production. This study investigated the genetic structure and diversity among seven Nile tilapia populations in Tanzania (Karanga, Igunga, Ruhila, Fisheries Education and Training Agency, Tanzania Fisheries Research Institute, Kunduchi, and Lake Victoria). Double-digest restriction site-associated DNA (ddRAD) libraries were prepared from 140 individual fish (20 per population) and sequenced using an Illumina HiSeq 4000 resulting in the identification of 2,180 informative single nucleotide polymorphisms (SNPs). Pairwise Fst values revealed strong genetic differentiation between the closely related populations; FETA, Lake Victoria, and Igunga and those from TAFIRI and Karanga with values ranging between 0.45 and 0.55. Population structure was further evaluated using Bayesian model-based clustering (STRUCTURE) and discriminant analysis of principal components (DAPC). Admixture was detected among Karanga, Kunduchi, and Ruhila populations. A cross-validation approach (25% of individual fish from each population was considered of unknown origin) was conducted in order to test the efficiency of the SNP markers to correctly assign individual fish to the population of origin. The cross-validation procedure was repeated 10 times resulting in 77% of the tested individual fish being allocated to the correct population. Overall our results provide a new database of informative SNP markers for both conservation management and aquaculture activities of Nile tilapia strains in Tanzania.
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Affiliation(s)
- Redempta A. Kajungiro
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Aquatic Science and Fisheries, College of Agricultural Sciences and Fisheries Technology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Christos Palaiokostas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Fernando A. Lopes Pinto
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Aviti J. Mmochi
- Institute of Marine Sciences, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Marten Mtolera
- Institute of Marine Sciences, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Dirk Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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24
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Ballare KM, Pope NS, Castilla AR, Cusser S, Metz RP, Jha S. Utilizing field collected insects for next generation sequencing: Effects of sampling, storage, and DNA extraction methods. Ecol Evol 2019; 9:13690-13705. [PMID: 31938475 PMCID: PMC6953651 DOI: 10.1002/ece3.5756] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 08/20/2019] [Accepted: 09/15/2019] [Indexed: 01/04/2023] Open
Abstract
DNA sequencing technologies continue to advance the biological sciences, expanding opportunities for genomic studies of non-model organisms for basic and applied questions. Despite these opportunities, many next generation sequencing protocols have been developed assuming a substantial quantity of high molecular weight DNA (>100 ng), which can be difficult to obtain for many study systems. In particular, the ability to sequence field-collected specimens that exhibit varying levels of DNA degradation remains largely unexplored. In this study we investigate the influence of five traditional insect capture and curation methods on Double-Digest Restriction Enzyme Associated DNA (ddRAD) sequencing success for three wild bee species. We sequenced a total of 105 specimens (between 7-13 specimens per species and treatment). We additionally investigated how different DNA quality metrics (including pre-sequence concentration and contamination) predicted downstream sequencing success, and also compared two DNA extraction methods. We report successful library preparation for all specimens, with all treatments and extraction methods producing enough highly reliable loci for population genetic analyses. Although results varied between species, we found that specimens collected by net sampling directly into 100% EtOH, or by passive trapping followed by 100% EtOH storage before pinning tended to produce higher quality ddRAD assemblies, likely as a result of rapid specimen desiccation. Surprisingly, we found that specimens preserved in propylene glycol during field sampling exhibited lower-quality assemblies. We provide recommendations for each treatment, extraction method, and DNA quality assessment, and further encourage researchers to consider utilizing a wider variety of specimens for genomic analyses.
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Affiliation(s)
- Kimberly M. Ballare
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
- Present address:
Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCAUSA
| | - Nathaniel S. Pope
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
- Present address:
Department of EntomologyPennsylvania State UniversityUniversity ParkPAUSA
| | - Antonio R. Castilla
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
- Present address:
Centre for Applied Ecology “Prof. Baeta Neves”/INBIOInstitutoSuperior of AgronomyUniversity of LisbonLisbonPortugal
| | - Sarah Cusser
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
- Present address:
Kellogg Biological StationMichigan State UniversityHickory CornersMIUSA
| | - Richard P. Metz
- Genomics and Bioinformatics ServiceTexas A&M AgriLife ResearchCollege StationTXUSA
| | - Shalene Jha
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
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Wang Y, Raitsos DE, Krokos G, Gittings JA, Zhan P, Hoteit I. Physical connectivity simulations reveal dynamic linkages between coral reefs in the southern Red Sea and the Indian Ocean. Sci Rep 2019; 9:16598. [PMID: 31719628 PMCID: PMC6851178 DOI: 10.1038/s41598-019-53126-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/27/2019] [Indexed: 11/14/2022] Open
Abstract
The southern Red Sea is genetically distinct from the rest of the basin; yet the reasons responsible for this genetic separation remain unclear. Connectivity is a vital process for the exchange of individuals and genes among geographically separated populations, and is necessary for maintaining biodiversity and resilience in coral reef ecosystems. Here, using long-term, high-resolution, 3-D backward particle tracking simulations, we investigate the physical connectivity of coral reefs in the southern Red Sea with neighbouring regions. Overall, the simulation results reveal that the southern Red Sea coral reefs are more physically connected with regions in the Indian Ocean (e.g., the Gulf of Aden) than with the northern part of the basin. The identified connectivity exhibits a distinct monsoon-related seasonality. Though beyond the country boundaries, relatively remote regions of the Indian Ocean may have a substantial impact on the southern Red Sea coral reef regions, and this should be taken into consideration when establishing conservation strategies for these vulnerable biodiversity hot-spots.
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Affiliation(s)
- Yixin Wang
- King Abdullah University of Science and Technology (KAUST), Department of Earth Science and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Dionysios E Raitsos
- National and Kapodistrian University of Athens, Department of Biology, Athens, Greece.,Plymouth Marine Laboratory (PML), Remote Sensing Group, The Hoe, Plymouth, PL1 3DH, United Kingdom
| | - George Krokos
- King Abdullah University of Science and Technology (KAUST), Department of Earth Science and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - John A Gittings
- King Abdullah University of Science and Technology (KAUST), Department of Earth Science and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Peng Zhan
- King Abdullah University of Science and Technology (KAUST), Department of Earth Science and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ibrahim Hoteit
- King Abdullah University of Science and Technology (KAUST), Department of Earth Science and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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Torquato F, Range P, Ben‐Hamadou R, Sigsgaard EE, Thomsen PF, Riera R, Berumen ML, Burt JA, Feary DA, Marshell A, D'Agostino D, DiBattista JD, Møller PR. Consequences of marine barriers for genetic diversity of the coral-specialist yellowbar angelfish from the Northwestern Indian Ocean. Ecol Evol 2019; 9:11215-11226. [PMID: 31641466 PMCID: PMC6802022 DOI: 10.1002/ece3.5622] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
Ocean circulation, geological history, geographic distance, and seascape heterogeneity play an important role in phylogeography of coral-dependent fishes. Here, we investigate potential genetic population structure within the yellowbar angelfish (Pomacanthus maculosus) across the Northwestern Indian Ocean (NIO). We then discuss our results with respect to the above abiotic features in order to understand the contemporary distribution of genetic diversity of the species. To do so, restriction site-associated DNA sequencing (RAD-seq) was utilized to carry out population genetic analyses on P. maculosus sampled throughout the species' distributional range. First, genetic data were correlated to geographic and environmental distances, and tested for isolation-by-distance and isolation-by-environment, respectively, by applying the Mantel test. Secondly, we used distance-based and model-based methods for clustering genetic data. Our results suggest the presence of two putative barriers to dispersal; one off the southern coast of the Arabian Peninsula and the other off northern Somalia, which together create three genetic subdivisions of P. maculosus within the NIO. Around the Arabian Peninsula, one genetic cluster was associated with the Red Sea and the adjacent Gulf of Aden in the west, and another cluster was associated with the Arabian Gulf and the Sea of Oman in the east. Individuals sampled in Kenya represented a third genetic cluster. The geographic locations of genetic discontinuities observed between genetic subdivisions coincide with the presence of substantial upwelling systems, as well as habitat discontinuity. Our findings shed light on the origin and maintenance of genetic patterns in a common coral reef fish inhabiting the NIO, and reinforce the hypothesis that the evolution of marine fish species in this region has likely been shaped by multiple vicariance events.
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Affiliation(s)
- Felipe Torquato
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Pedro Range
- Environmental Science CenterQatar UniversityDohaQatar
| | - Radhouane Ben‐Hamadou
- Department Biological and Environmental ScienceCollege of Arts and SciencesQatar UniversityDohaQatar
| | - Eva E. Sigsgaard
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Department of BioscienceUniversity of AarhusAarhusDenmark
| | | | - Rodrigo Riera
- Departamento de EcologíaFacultad de CienciasUniversidad Católica de la Santísima ConcepciónConcepciónChile
| | - Michael L. Berumen
- Division of Biological and Environmental Sciences and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - John A. Burt
- Center for Genomics and Systems BiologyNew York University Abu DhabiAbu DhabiUAE
| | | | - Alyssa Marshell
- Marine Ecology Lab OmanDepartment of Marine Science and FisheriesCollege of Agriculture and Marine ScienceSultan Qaboos UniversityMuscatOman
| | | | - Joseph D. DiBattista
- Division of Biological and Environmental Sciences and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- School of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
- Australian Museum Research InstituteAustralian MuseumSydneyNSWAustralia
| | - Peter R. Møller
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
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Gamboa M, Watanabe K. Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan. BMC Genomics 2019; 20:84. [PMID: 30678640 PMCID: PMC6346529 DOI: 10.1186/s12864-019-5453-3] [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: 09/12/2018] [Accepted: 01/14/2019] [Indexed: 11/16/2022] Open
Abstract
Background Environmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. Here, we evaluated the degree of genome-environmental association of seven stonefly species across a wide geographic area in Japan and additionally identified putative environmental drivers and their effect on co-existing multiple stonefly species. Double-digest restriction-associated DNA (ddRAD) libraries were independently sequenced for 219 individuals from 23 sites across four geographical regions along a nationwide latitudinal gradient in Japan. Results A total of 4251 candidate single nucleotide polymorphisms (SNPs) strongly associated with local adaptation were discovered using Latent mixed models; of these, 294 SNPs showed strong correlation with environmental variables, specifically precipitation and altitude, using distance-based redundancy analysis. Genome–genome comparison among the seven species revealed a high sequence similarity of candidate SNPs within a geographical region, suggesting the occurrence of a parallel evolution process. Conclusions Our results revealed genomic signatures of local adaptation and their influence on multiple, co-occurring species. These results can be potentially applied for future studies on river management and climatic stressor impacts. Electronic supplementary material The online version of this article (10.1186/s12864-019-5453-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maribet Gamboa
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, 790-0871, Japan.
| | - Kozo Watanabe
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, 790-0871, Japan
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28
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Berumen ML, Roberts MB, Sinclair-Taylor TH, DiBattista JD, Saenz-Agudelo P, Isari S, He S, Khalil MT, Hardenstine RS, Tietbohl MD, Priest MA, Kattan A, Coker DJ. Fishes and Connectivity of Red Sea Coral Reefs. CORAL REEFS OF THE RED SEA 2019. [DOI: 10.1007/978-3-030-05802-9_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Chen Y, Shenkar N, Ni P, Lin Y, Li S, Zhan A. Rapid microevolution during recent range expansion to harsh environments. BMC Evol Biol 2018; 18:187. [PMID: 30526493 PMCID: PMC6286502 DOI: 10.1186/s12862-018-1311-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/27/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Adaptive evolution is one of the crucial mechanisms for organisms to survive and thrive in new environments. Recent studies suggest that adaptive evolution could rapidly occur in species to respond to novel environments or environmental challenges during range expansion. However, for environmental adaptation, many studies successfully detected phenotypic features associated with local environments, but did not provide ample genetic evidence on microevolutionary dynamics. It is therefore crucial to thoroughly investigate the genetic basis of rapid microevolution in response to environmental changes, in particular on what genes and associated variation are responsible for environmental challenges. Here, we genotyped genome-wide gene-associated microsatellites to detect genetic signatures of rapid microevolution of a marine tunicate invader, Ciona robusta, during recent range expansion to the harsh environment in the Red Sea. RESULTS The Red Sea population was significantly differentiated from the other global populations. The genome-wide scan, as well as multiple analytical methods, successfully identified a set of adaptive genes. Interestingly, the allele frequency largely varied at several adaptive loci in the Red Sea population, and we found significant correlations between allele frequency and local environmental factors at these adaptive loci. Furthermore, a set of genes were annotated to get involved in local temperature and salinity adaptation, and the identified adaptive genes may largely contribute to the invasion success to harsh environments. CONCLUSIONS All the evidence obtained in this study clearly showed that environment-driven selection had left detectable signatures in the genome of Ciona robusta within a few generations. Such a rapid microevolutionary process is largely responsible for the harsh environmental adaptation and therefore contributes to invasion success in different aquatic ecosystems with largely varied environmental factors.
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Affiliation(s)
- Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Noa Shenkar
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 6997801, Tel-Aviv, Israel
- The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel-Aviv, Israel
| | - Ping Ni
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Yaping Lin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China.
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China.
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30
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Binks RM, Byrne M, McMahon K, Pitt G, Murray K, Evans RD. Habitat discontinuities form strong barriers to gene flow among mangrove populations, despite the capacity for long-distance dispersal. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12851] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Rachel M. Binks
- Biodiversity and Conservation Science; Department of Biodiversity, Conservation and Attractions; Kensington Western Australia Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science; Department of Biodiversity, Conservation and Attractions; Kensington Western Australia Australia
| | - Kathryn McMahon
- School of Sciences and Centre for Marine Ecosystems Research; Edith Cowan University; Joondalup Western Australia Australia
| | - Georgina Pitt
- Biodiversity and Conservation Science; Department of Biodiversity, Conservation and Attractions; Kensington Western Australia Australia
| | - Kathy Murray
- Biodiversity and Conservation Science; Department of Biodiversity, Conservation and Attractions; Kensington Western Australia Australia
| | - Richard D. Evans
- Biodiversity and Conservation Science; Department of Biodiversity, Conservation and Attractions; Kensington Western Australia Australia
- School of Biological Sciences and Oceans Institute; University of Western Australia; Crawley Western Australia Australia
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31
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Jeffery NW, Bradbury IR, Stanley RRE, Wringe BF, Van Wyngaarden M, Lowen JB, McKenzie CH, Matheson K, Sargent PS, DiBacco C. Genomewide evidence of environmentally mediated secondary contact of European green crab ( Carcinus maenas) lineages in eastern North America. Evol Appl 2018; 11:869-882. [PMID: 29928296 PMCID: PMC5999199 DOI: 10.1111/eva.12601] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 01/16/2018] [Indexed: 01/01/2023] Open
Abstract
Genetic-environment associations are increasingly revealed through population genomic data and can occur through a number of processes, including secondary contact, divergent natural selection, or isolation by distance. Here, we investigate the influence of the environment, including seasonal temperature and salinity, on the population structure of the invasive European green crab (Carcinus maenas) in eastern North America. Green crab populations in eastern North America are associated with two independent invasions, previously shown to consist of distinct northern and southern ecotypes, with a contact zone in southern Nova Scotia, Canada. Using a RAD-seq panel of 9,137 genomewide SNPs, we detected 41 SNPs (0.49%) whose allele frequencies were highly correlated with environmental data. A principal components analysis of 25 environmental variables differentiated populations into northern, southern, and admixed sites in concordance with the observed genomic spatial structure. Furthermore, a spatial principal components analysis conducted on genomic and geographic data revealed a high degree of global structure (p < .0001) partitioning a northern and southern ecotype. Redundancy and partial redundancy analyses revealed that among the environmental variables tested, winter sea surface temperature had the strongest association with spatial structuring, suggesting that it is an important factor defining range and expansion limits of each ecotype. Understanding environmental thresholds associated with intraspecific diversity will facilitate the ability to manage current and predict future distributions of this aquatic invasive species.
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Affiliation(s)
- Nicholas W. Jeffery
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Faculty of Computer ScienceDalhousie UniversityHalifaxNSCanada
| | - Ian R. Bradbury
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Faculty of Computer ScienceDalhousie UniversityHalifaxNSCanada
- Department of Ocean SciencesMemorial University of NewfoundlandSt. John’sNLCanada
| | - Ryan R. E. Stanley
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
| | - Brendan F. Wringe
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | | | - J. Ben Lowen
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
| | - Cynthia H. McKenzie
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Kyle Matheson
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Philip S. Sargent
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Claudio DiBacco
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
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32
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Crane NL, Tariel J, Caselle JE, Friedlander AM, Robertson DR, Bernardi G. Clipperton Atoll as a model to study small marine populations: Endemism and the genomic consequences of small population size. PLoS One 2018; 13:e0198901. [PMID: 29949612 PMCID: PMC6021044 DOI: 10.1371/journal.pone.0198901] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/29/2018] [Indexed: 01/05/2023] Open
Abstract
Estimating population sizes and genetic diversity are key factors to understand and predict population dynamics. Marine species have been a difficult challenge in that respect, due to the difficulty in assessing population sizes and the open nature of such populations. Small, isolated islands with endemic species offer an opportunity to groundtruth population size estimates with empirical data and investigate the genetic consequences of such small populations. Here we focus on two endemic species of reef fish, the Clipperton damselfish, Stegastes baldwini, and the Clipperton angelfish, Holacanthus limbaughi, on Clipperton Atoll, tropical eastern Pacific. Visual surveys, performed over almost two decades and four expeditions, and genetic surveys based on genomic RAD sequences, allowed us to estimate kinship and genetic diversity, as well as to compare population size estimates based on visual surveys with effective population sizes based on genetics. We found that genetic and visual estimates of population numbers were remarkably similar. S. baldwini and H. limbaughi had population sizes of approximately 800,000 and 60,000, respectively. Relatively small population sizes resulted in low genetic diversity and the presence of apparent kinship. This study emphasizes the importance of small isolated islands as models to study population dynamics of marine organisms.
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Affiliation(s)
- Nicole L. Crane
- Department of Biology, Cabrillo College, Aptos, CA, United States of America
| | - Juliette Tariel
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jennifer E. Caselle
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, United States of America
| | - Alan M. Friedlander
- Pristine Seas, National Geographic Society, Washington, DC, United States of America
- Fisheries Ecology Research Lab, Department of Biology, University of Hawaii, Honolulu, HI, United States of America
| | | | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
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33
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Ivanov V, Lee KM, Mutanen M. Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression. Mol Ecol 2018; 27:1681-1695. [PMID: 29575366 DOI: 10.1111/mec.14564] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 02/23/2018] [Accepted: 03/01/2018] [Indexed: 12/31/2022]
Abstract
Systematists and taxonomists have benefited greatly from the emergence of molecular methods. Species identification has become straightforward through DNA barcoding and the rapid build-up of massive DNA barcode reference libraries. In animals, mitonuclear discordance can significantly complicate the process of species identification and delimitation. The causes of mitonuclear discordance are either biological (e.g., introgression, incomplete lineage sorting, horizontal gene transfer androgenesis) or induced by operational factors (e.g., human error with specimen misidentification or incorrect species delimitation). Moreover, endosymbionts may play an important role in promoting fixation of mitochondrial genomes. Here, we study the mitonuclear discordance of wolf spiders species (Lycosidae) (independent cases from Alopecosa aculeata and Pardosa pullata groups) that share identical COI DNA barcodes. We approached the case utilizing double-digest restriction site-associated DNA sequencing (ddRADseq) to obtain and analyse genomic-scale data. Our results suggest that the observed cases of mitonuclear discordance are not due to operational reasons but result from biological processes. Further analysis indicated introgression and that incomplete lineage sorting is unlikely to have been responsible for the observed discrepancy. Additional survey of endosymbionts provided ideas on further research and their role in shaping mitochondrial DNA distribution patterns. Thus, ddRADseq grants an efficient way to study the taxonomy of problematic groups with insight into underlying evolutionary processes.
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Affiliation(s)
- Vladislav Ivanov
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Kyung Min Lee
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Marko Mutanen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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Abstract
Coral reefs rely on inter-habitat connectivity to maintain gene flow, biodiversity and ecosystem resilience. Coral reef communities of the Red Sea exhibit remarkable genetic homogeneity across most of the Arabian Peninsula coastline, with a genetic break towards the southern part of the basin. While previous studies have attributed these patterns to environmental heterogeneity, we hypothesize that they may also emerge as a result of dynamic circulation flow; yet, such linkages remain undemonstrated. Here, we integrate satellite-derived biophysical observations, particle dispersion model simulations, genetic population data and ship-borne in situ profiles to assess reef connectivity in the Red Sea. We simulated long-term (>20 yrs.) connectivity patterns driven by remotely-sensed sea surface height and evaluated results against estimates of genetic distance among populations of anemonefish, Amphiprion bicinctus, along the eastern Red Sea coastline. Predicted connectivity was remarkably consistent with genetic population data, demonstrating that circulation features (eddies, surface currents) formulate physical pathways for gene flow. The southern basin has lower physical connectivity than elsewhere, agreeing with known genetic structure of coral reef organisms. The central Red Sea provides key source regions, meriting conservation priority. Our analysis demonstrates a cost-effective tool to estimate biophysical connectivity remotely, supporting coastal management in data-limited regions.
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35
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Gould AL, Dunlap PV. Genomic analysis of a cardinalfish with larval homing potential reveals genetic admixture in the Okinawa Islands. Mol Ecol 2017; 26:3870-3882. [DOI: 10.1111/mec.14169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 04/05/2017] [Accepted: 04/25/2017] [Indexed: 01/12/2023]
Affiliation(s)
- A. L. Gould
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI USA
| | - P. V. Dunlap
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI USA
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36
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Affiliation(s)
- Josephine R. Paris
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Jamie R. Stevens
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Julian M. Catchen
- Department of Animal Biology University of Illinois at Urbana–Champaign Urbana IL 61801 USA
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37
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DiBattista JD, Saenz-Agudelo P, Piatek MJ, Wang X, Aranda M, Berumen ML. Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish. Mol Ecol Resour 2017; 17:1330-1341. [PMID: 28236665 DOI: 10.1111/1755-0998.12662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 02/11/2017] [Accepted: 02/16/2017] [Indexed: 01/07/2023]
Abstract
Data from a large-scale restriction site-associated DNA sequencing (RAD-Seq) study of nine butterflyfish species in the Red Sea and Arabian Sea provided a means to test the utility of a recently published draft genome (Chaetodon austriacus) and assess apparent bias in this method of isolating nuclear loci. We here processed double-digest restriction site-associated DNA (ddRAD) sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to see whether it improves the quality of RAD-Seq. Our analyses indicate (i) a modest gap between the number of nonannotated versus annotated SNPs across all species, (ii) an advantage of using genomic resources for closely related but not distantly related butterflyfish species based on the ability to assign putative gene function to SNPs and (iii) an enrichment of genes among sister butterflyfish taxa related to calcium transmembrane transport and binding. The latter result highlights the potential for this approach to reveal insights into adaptive mechanisms in populations inhabiting challenging coral reef environments such as the Red Sea, Arabian Sea and Arabian Gulf with further study.
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Affiliation(s)
- Joseph D DiBattista
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Department of Environment and Agriculture, Curtin University, PO Box U1987, Perth, WA, 6845, Australia
| | - Pablo Saenz-Agudelo
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Marek J Piatek
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xin Wang
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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38
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Franchini P, Monné Parera D, Kautt AF, Meyer A. quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage. Mol Ecol 2017; 26:2783-2795. [PMID: 28247584 DOI: 10.1111/mec.14077] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Paolo Franchini
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Daniel Monné Parera
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Andreas F. Kautt
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
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McKinney GJ, Larson WA, Seeb LW, Seeb JE. RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al
. (2016). Mol Ecol Resour 2017; 17:356-361. [DOI: 10.1111/1755-0998.12649] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/20/2016] [Accepted: 12/20/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Garrett J. McKinney
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
| | - Wesley A. Larson
- U.S. Geological Survey; Wisconsin Cooperative Fishery Research Unit; College of Natural Resources; University of Wisconsin-Stevens Point; 800 Reserve St. Stevens Point WI 54481 USA
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
| | - James E. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
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40
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Riginos C, Crandall ED, Liggins L, Bongaerts P, Treml EA. Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies. Curr Zool 2016; 62:581-601. [PMID: 29491947 PMCID: PMC5804261 DOI: 10.1093/cz/zow067] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 05/25/2016] [Indexed: 11/21/2022] Open
Abstract
Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region (e.g., geographical distance, average sea surface temperature, average salinity). We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water (experienced by most marine taxa at some point in their life cycle), require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for landscape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations.
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Affiliation(s)
- Cynthia Riginos
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Eric D. Crandall
- Division of Science and Environmental Policy, California State University, Seaside, CA 93955, USA
| | - Libby Liggins
- Institute of Natural and Mathematical Sciences, Massey University, Auckland 0745, New Zealand
| | - Pim Bongaerts
- Global Change Institute, The University of Queensland, QLD 4072, St Lucia, Australia
| | - Eric A. Treml
- School of BioSciences, The University of Melbourne, VIC, 3010, Australia
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41
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D’Aloia CC, Bogdanowicz SM, Harrison RG, Buston PM. Cryptic genetic diversity and spatial patterns of admixture within Belizean marine reserves. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0895-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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42
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DiBattista JD, Wang X, Saenz-Agudelo P, Piatek MJ, Aranda M, Berumen ML. Draft genome of an iconic Red Sea reef fish, the blacktail butterflyfish (Chaetodon austriacus): current status and its characteristics. Mol Ecol Resour 2016; 18:347-355. [DOI: 10.1111/1755-0998.12588] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 07/05/2016] [Accepted: 07/19/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Joseph D. DiBattista
- Division of Biological and Environmental Sciences and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
- Department of Environment and Agriculture; Curtin University; PO Box U1987 Perth WA 6845 Australia
| | - Xin Wang
- Division of Biological and Environmental Sciences and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
| | - Pablo Saenz-Agudelo
- Division of Biological and Environmental Sciences and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Valdivia 5090000 Chile
| | - Marek J. Piatek
- Computational Bioscience Research Center; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
| | - Manuel Aranda
- Division of Biological and Environmental Sciences and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
| | - Michael L. Berumen
- Division of Biological and Environmental Sciences and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
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