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Wang Q, Liu Y, Yan L, Chen L, Li B. Genome-Wide SNP Discovery and Population Genetic Analysis of Mesocentrotus nudus in China Seas. Front Genet 2021; 12:717764. [PMID: 34490044 PMCID: PMC8416983 DOI: 10.3389/fgene.2021.717764] [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: 05/31/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022] Open
Abstract
Mesocentrotus nudus is an important commercially aquatic species because of its high edible and medicinal values. However, wild stocks have dramatically decreased in recent decades. Understanding the population structure and genetic diversity can provide vital information for genetic conservation and improvement. In the present study, the genotyping-by-sequencing (GBS) approach was adopted to identify the genome-wide single-nucleotide polymorphisms (SNPs) from a collection of 80 individuals consisting of five geographical populations (16 individuals from each population), covering the natural habitats of M. nudus in China seas. An average of 0.96-Gb clean reads per sample were sequenced, and a total of 51,738 biallelic SNPs were identified. Based on these SNPs, diversity index analysis showed that all populations have a similar pattern with positive Fis (0.136) and low Ne (724.3). Low genetic differentiation and high genetic connectivity among five geographical populations were detected by pairwise Fst, principal component analysis (PCA), admixture, and phylogenetic analysis. Besides, two YWL individuals originating from an isolated ancestor may imply that there is a genetically differentiated population in the adjacent sea. Overall, the results showed that GBS is an effective method to detect genome-wide SNPs for M. nudus and suggested that the protective measures and the investigation with larger spatial scale and sample size for M. nudus should be carried out in the future.
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Affiliation(s)
- Quanchao Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ying Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lang Yan
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Linlin Chen
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Baoquan Li
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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2
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Kelson SJ, Miller MR, Thompson TQ, O'Rourke SM, Carlson SM. Temporal dynamics of migration-linked genetic variation are driven by streamflows and riverscape permeability. Mol Ecol 2020; 29:870-885. [PMID: 32012393 PMCID: PMC7078995 DOI: 10.1111/mec.15367] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/17/2020] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Landscape permeability is often explored spatially, but may also vary temporally. Landscape permeability, including partial barriers, influences migratory animals that move across the landscape. Partial barriers are common in rivers where barrier passage varies with streamflow. We explore the influence of partial barriers on the spatial and temporal distribution of migration‐linked genotypes of Oncorhynchus mykiss, a salmonid fish with co‐occurring resident and migratory forms, in tributaries to the South Fork Eel River, California, USA, Elder and Fox Creeks. We genotyped >4,000 individuals using RAD‐capture and classified individuals as resident, heterozygous or migratory genotypes using life history‐associated loci. Across four years of study (2014–2017), the permeability of partial barriers varied across dry and wet years. In Elder Creek, the largest waterfall was passable for adults migrating up‐river 4–39 days each year. In this stream, the overall spatial pattern, with fewer migratory genotypes above the waterfall, remained true across dry and wet years (67%–76% of migratory alleles were downstream of the waterfall). We also observed a strong relationship between distance upstream and proportion of migratory alleles. In Fox Creek, the primary barrier is at the mouth, and we found that the migratory allele frequency varied with the annual timing of high flow events. In years when rain events occurred during the peak breeding season, migratory allele frequency was high (60%–68%), but otherwise it was low (30% in two years). We highlight that partial barriers and landscape permeability can be temporally dynamic, and this effect can be observed through changing genotype frequencies in migratory animals.
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Affiliation(s)
- Suzanne J Kelson
- Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Michael R Miller
- Department of Animal Science, University of California, Davis, CA, USA
| | - Tasha Q Thompson
- Department of Animal Science, University of California, Davis, CA, USA
| | - Sean M O'Rourke
- Department of Animal Science, University of California, Davis, CA, USA
| | - Stephanie M Carlson
- Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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Abstract
Salmon were among the first nonmodel species for which systematic population genetic studies of natural populations were conducted, often to support management and conservation. The genomics revolution has improved our understanding of the evolutionary ecology of salmon in two major ways: (a) Large increases in the numbers of genetic markers (from dozens to 104-106) provide greater power for traditional analyses, such as the delineation of population structure, hybridization, and population assignment, and (b) qualitatively new insights that were not possible with traditional genetic methods can be achieved by leveraging detailed information about the structure and function of the genome. Studies of the first type have been more common to date, largely because it has taken time for the necessary tools to be developed to fully understand the complex salmon genome. We expect that the next decade will witness many new studies that take full advantage of salmonid genomic resources.
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington 98112, USA;
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195-5020, USA;
| | - Craig R Primmer
- Organismal & Evolutionary Biology Research Program and Biotechnology Institute, University of Helsinki, 00014 Helsinki, Finland;
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McCartney‐Melstad E, Gidiş M, Shaffer HB. An empirical pipeline for choosing the optimal clustering threshold in RADseq studies. Mol Ecol Resour 2019; 19:1195-1204. [DOI: 10.1111/1755-0998.13029] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 04/18/2019] [Accepted: 04/22/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Evan McCartney‐Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability University of California Los Angeles California
| | - Müge Gidiş
- Faculty of Arts and Science, Department of Biochemistry Kütahya Dumlupınar University Kutahya Turkey
| | - H. Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability University of California Los Angeles California
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Larson WA, Dann TH, Limborg MT, McKinney GJ, Seeb JE, Seeb LW. Parallel signatures of selection at genomic islands of divergence and the major histocompatibility complex in ecotypes of sockeye salmon across Alaska. Mol Ecol 2019; 28:2254-2271. [DOI: 10.1111/mec.15082] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/21/2019] [Accepted: 03/20/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Wesley A. Larson
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Tyler H. Dann
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
- Gene Conservation Laboratory Alaska Department of Fish and Game Anchorage Alaska
| | - Morten T. Limborg
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Garrett J. McKinney
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - James E. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
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6
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Narum SR, Di Genova A, Micheletti SJ, Maass A. Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon. Proc Biol Sci 2018; 285:rspb.2018.0935. [PMID: 30051839 DOI: 10.1098/rspb.2018.0935] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/27/2018] [Indexed: 12/12/2022] Open
Abstract
A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present a chromosome-level reference genome assembly for Chinook salmon (Oncorhynchus tshawytscha; 2.36 Gb) that enabled association mapping of life-history variation and phenotypic traits for this species. Whole-genome re-sequencing of populations with distinct life-history traits provided evidence that divergent selection was extensive throughout the genome within and among phylogenetic lineages, indicating that a broad portfolio of phenotypic diversity exists in this species that is related to local adaptation and life-history variation. Association mapping with millions of genome-wide SNPs revealed that a genomic region of major effect on chromosome 28 was associated with phenotypes for premature and mature arrival to spawning grounds and was consistent across three distinct phylogenetic lineages. Our results demonstrate how genomic resources can enlighten the genetic basis of known phenotypes in exploited species and assist in clarifying phenotypic variation that may be difficult to observe in naturally occurring organisms.
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Affiliation(s)
- Shawn R Narum
- Columbia River Inter-Tribal Fish Commission, Hagerman Genetics Laboratory, Hagerman, ID, USA .,Department of Fisheries and Wildlife, University of Idaho, Moscow, ID, USA
| | - Alex Di Genova
- Mathomics Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Santiago 8370456, Chile.,Faculty of Engineering and Science, Universidad Adolfo Ibáñez, Santiago, Chile
| | | | - Alejandro Maass
- Mathomics Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Santiago 8370456, Chile
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McKinney GJ, Waples RK, Pascal CE, Seeb LW, Seeb JE. Resolving allele dosage in duplicated loci using genotyping-by-sequencing data: A path forward for population genetic analysis. Mol Ecol Resour 2018; 18:570-579. [DOI: 10.1111/1755-0998.12763] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Garrett J. McKinney
- School of Aquatic and Fishery Sciences; University of Washington; Seattle WA USA
| | - Ryan K. Waples
- School of Aquatic and Fishery Sciences; University of Washington; Seattle WA USA
| | - Carita E. Pascal
- School of Aquatic and Fishery Sciences; University of Washington; Seattle WA USA
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; Seattle WA USA
| | - James E. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; Seattle WA USA
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8
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Meirmans PG, Liu S, van Tienderen PH. The Analysis of Polyploid Genetic Data. J Hered 2018; 109:283-296. [DOI: 10.1093/jhered/esy006] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/20/2018] [Indexed: 12/14/2022] Open
Affiliation(s)
- Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Shenglin Liu
- Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Peter H van Tienderen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
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