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Volkova NA, Romanov MN, Abdelmanova AS, Larionova PV, German NY, Vetokh AN, Shakhin AV, Volkova LA, Anshakov DV, Fisinin VI, Narushin VG, Griffin DK, Sölkner J, Brem G, McEwan JC, Brauning R, Zinovieva NA. Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail ( Coturnix japonica) Breeds. Animals (Basel) 2023; 13:3439. [PMID: 38003057 PMCID: PMC10668688 DOI: 10.3390/ani13223439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/23/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Traces of long-term artificial selection can be detected in genomes of domesticated birds via whole-genome screening using single-nucleotide polymorphism (SNP) markers. This study thus examined putative genomic regions under selection that are relevant to the development history, divergence and phylogeny among Japanese quails of various breeds and utility types. We sampled 99 birds from eight breeds (11% of the global gene pool) of egg (Japanese, English White, English Black, Tuxedo and Manchurian Golden), meat (Texas White and Pharaoh) and dual-purpose (Estonian) types. The genotyping-by-sequencing analysis was performed for the first time in domestic quails, providing 62,935 SNPs. Using principal component analysis, Neighbor-Net and Admixture algorithms, the studied breeds were characterized according to their genomic architecture, ancestry and direction of selective breeding. Japanese and Pharaoh breeds had the smallest number and length of homozygous segments indicating a lower selective pressure. Tuxedo and Texas White breeds showed the highest values of these indicators and genomic inbreeding suggesting a greater homozygosity. We revealed evidence for the integration of genomic and performance data, and our findings are applicable for elucidating the history of creation and genomic variability in quail breeds that, in turn, will be useful for future breeding improvement strategies.
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Affiliation(s)
- Natalia A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Michael N. Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Alexandra S. Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Polina V. Larionova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Nadezhda Yu. German
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Anastasia N. Vetokh
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Alexey V. Shakhin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Ludmila A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Dmitry V. Anshakov
- Breeding and Genetic Center Zagorsk Experimental Breeding Farm—Branch of the Federal Research Centre, All-Russian Poultry Research and Technological Institute, Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Vladimir I. Fisinin
- Federal Research Center “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Valeriy G. Narushin
- Research Institute for Environment Treatment, 69032 Zaporizhya, Ukraine;
- Vita-Market Co., Ltd., 69032 Zaporizhya, Ukraine
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Johann Sölkner
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences Vienna, 1180 Vienna, Austria;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - John C. McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
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Karunarathne P, Zhou Q, Schliep K, Milesi P. A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: 'rCNV', a versatile r package for paralogue and CNV detection. Mol Ecol Resour 2023; 23:1772-1789. [PMID: 37515483 DOI: 10.1111/1755-0998.13843] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023]
Abstract
Recent studies have highlighted the significant role of copy number variants (CNVs) in phenotypic diversity, environmental adaptation and species divergence across eukaryotes. The presence of CNVs also has the potential to introduce genotyping biases, which can pose challenges to accurate population and quantitative genetic analyses. However, detecting CNVs in genomes, particularly in non-model organisms, presents a formidable challenge. To address this issue, we have developed a statistical framework and an accompanying r software package that leverage allelic-read depth from single nucleotide polymorphism (SNP) data for accurate CNV detection. Our framework capitalises on two key principles. First, it exploits the distribution of allelic-read depth ratios in heterozygotes for individual SNPs by comparing it against an expected distribution based on binomial sampling. Second, it identifies SNPs exhibiting an apparent excess of heterozygotes under Hardy-Weinberg equilibrium. By employing multiple statistical tests, our method not only enhances sensitivity to sampling effects but also effectively addresses reference biases, resulting in optimised SNP classification. Our framework is compatible with various NGS technologies (e.g. RADseq, Exome-capture). This versatility enables CNV calling from genomes of diverse complexities. To streamline the analysis process, we have implemented our framework in the user-friendly r package 'rCNV', which automates the entire workflow seamlessly. We trained our models using simulated data and validated their performance on four datasets derived from different sequencing technologies, including RADseq (Chinook salmon-Oncorhynchus tshawytscha), Rapture (American lobster-Homarus americanus), Exome-capture (Norway spruce-Picea abies) and WGS (Malaria mosquito-Anopheles gambiae).
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Affiliation(s)
- Piyal Karunarathne
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala, Sweden
- Institute of Population Genetics, Heinrich Heine University, Düsseldorf, Germany
| | - Qiujie Zhou
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala, Sweden
| | - Klaus Schliep
- Institute of Computational Biotechnology, Graz University of Technology, Graz, Austria
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala, Sweden
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Najafikhah A, Zeinalabedini M, Arefnezhad B, Mardi M, Nafari M, Nasrolahpourmoghadam M, Jafari O. Genome-wide data suggest a revision in management of the Caspian Sea trout Salmo caspius. PLoS One 2023; 18:e0287777. [PMID: 37471390 PMCID: PMC10358921 DOI: 10.1371/journal.pone.0287777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/13/2023] [Indexed: 07/22/2023] Open
Abstract
Salmo caspius Kessler, 1877 is one of the most commercially important species of Salmonidae in the southern basin of the Caspian Sea. The occurrence of its wild populations has undergone sever reduction during the last years. In spite of the yearly restocking activity, still no progress on the recovery of its wild population has been observed. Hence, the present study was done in order to assess the efficiency of the current restocking activity in the southern Caspian basin in term of genetic diversity. DNA extracts of 32 S. caspius from four different groups were screened using 62621 genome-wide single nucleotide polymorphisms (SNP). The overal genetic diversity and Fst values were 0.18 and 0.08, respectively. Considering the observed admixture pattern and the positive values for inbreeding coeficient it seems that S. caspius suffers from its small effective population size. In order to obtain the maximum performance, alonside with expanding the size of brood stocks, rehabilitation of the habitats and spawning rivers of this nationally endangered species is of great importance.
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Affiliation(s)
- Arezo Najafikhah
- Department of Biotechnology, Payame Noor University, Tehran, Iran
| | - Mehrshad Zeinalabedini
- Department of Genomics, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
| | | | - Mohsen Mardi
- Seed and Plant Certification and Registration Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | | | | | - Omid Jafari
- International Sturgeon Research Institute, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization, Rasht, Iran
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Lowell N, Suhrbier A, Tarpey C, May S, Carson H, Hauser L. Population structure and adaptive differentiation in the sea cucumber Apostichopus californicus and implications for spatial resource management. PLoS One 2023; 18:e0280500. [PMID: 36928497 PMCID: PMC10019739 DOI: 10.1371/journal.pone.0280500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/03/2023] [Indexed: 03/18/2023] Open
Abstract
A growing body of evidence suggests that spatial population structure can develop in marine species despite large population sizes and high gene flow. Characterizing population structure is important for the effective management of exploited species, as it can be used to identify appropriate scales of management in fishery and aquaculture contexts. The California sea cucumber, Apostichopus californicus, is one such exploited species whose management could benefit from further characterization of population structure. Using restriction site-associated DNA (RAD) sequencing, we developed 2075 single nucleotide polymorphisms (SNPs) to quantify genetic structure over a broad section of the species' range along the North American west coast and within the Salish Sea, a region supporting the Washington State A. californicus fishery and developing aquaculture production of the species. We found evidence for population structure (global fixation index (FST) = 0.0068) with limited dispersal driving two patterns of differentiation: isolation-by-distance and a latitudinal gradient of differentiation. Notably, we found detectable population differences among collection sites within the Salish Sea (pairwise FST = 0.001-0.006). Using FST outlier detection and gene-environment association, we identified 10.2% of total SNPs as putatively adaptive. Environmental variables (e.g., temperature, salinity) from the sea surface were more correlated with genetic variation than those same variables measured near the benthos, suggesting that selection on pelagic larvae may drive adaptive differentiation to a greater degree than selection on adults. Our results were consistent with previous estimates of and patterns in population structure for this species in other extents of the range. Additionally, we found that patterns of neutral and adaptive differentiation co-varied, suggesting that adaptive barriers may limit dispersal. Our study provides guidance to decision-makers regarding the designation of management units for A. californicus and adds to the growing body of literature identifying genetic population differentiation in marine species despite large, nominally connected populations.
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Affiliation(s)
- Natalie Lowell
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Andy Suhrbier
- Pacific Shellfish Institute, Olympia, Washington, United States of America
| | - Carolyn Tarpey
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Samuel May
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Henry Carson
- Washington Department of Fish and Wildlife, Olympia, Washington, United States of America
| | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
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Canales‐Aguirre CB, Larson WA, McKinney GJ, Claure CE, Rocha JD, Ceballos SG, Cádiz MI, Yáñez JM, Gomez‐Uchida D. Neutral and adaptive loci reveal fine‐scale population structure in Eleginops maclovinus from north Patagonia. Ecol Evol 2022; 12:e9343. [PMID: 36225825 PMCID: PMC9530513 DOI: 10.1002/ece3.9343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor an important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently investigated species. Eleginops maclovinus is a protandrous hermaphrodite species with economic importance for local communities that are currently managed as a single genetic unit. In this study, we sampled five locations distributed across a salinity cline from Northern Patagonia to investigate the genetic population structure of E. maclovinus. We used restriction site‐associated DNA (RAD) sequencing and outlier tests to obtain neutral and adaptive loci, using FST and GEA approaches. We identified a spatial pattern of structuration with gene flow and spatial selection by environmental association. Neutral and adaptive loci showed two and three genetic groups, respectively. The effective population sizes estimated ranged from 572 (Chepu) to 14,454 (Chaitén) and were influenced more by locality than by salinity cline. We found loci putatively associated with salinity suggesting that salinity may act as a selective driver in E. maclovinus populations. These results suggest a complex interaction between genetic drift, gene flow, and natural selection in this area. Our findings also suggest several evolutionary significant units in this area, and the information should be integrated into the management of this species. We discussed the significance of these results for fishery management and suggest future directions to improve our understanding of how E. maclovinus has adapted to the dynamic waters of Northern Patagonia.
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Affiliation(s)
| | - Wesley A. Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science CenterAuke Bay LaboratoriesJuneauAlaskaUSA
| | | | - C. Eliza Claure
- Centro i~mar, Universidad de Los LagosPuerto MonttChile,Núcleo Milenio INVASALConcepciónChile
| | - J. Dellis Rocha
- Centro i~mar, Universidad de Los LagosPuerto MonttChile,Núcleo Milenio INVASALConcepciónChile
| | - Santiago G. Ceballos
- Centro Austral de Investigaciones Científicas (CADIC‐CONICET)UshuaiaTierra del FuegoArgentina,Universidad Nacional de Tierra del Fuego (ICPA‐UNTDF)UshuaiaArgentina
| | - María I. Cádiz
- Núcleo Milenio INVASALConcepciónChile,Department of BiologyAarhus UniversityAarhus CDenmark
| | - José M. Yáñez
- Núcleo Milenio INVASALConcepciónChile,Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileLa PintanaSantiagoChile
| | - Daniel Gomez‐Uchida
- Núcleo Milenio INVASALConcepciónChile,Genomics in Ecology, Evolution & Conservation Lab (GEECLAB), Departamento de Zoología. Facultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
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Campbell DC, Camak DT, Piller KR. Islands in the desert: assessing fine scale population genomic variation of a group of imperiled desert fishes. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01457-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Jafari O, Ebrahimi M, Hedayati SAA, Zeinalabedini M, Poorbagher H, Nasrolahpourmoghadam M, Fernandes JMO. Integration of Morphometrics and Machine Learning Enables Accurate Distinction between Wild and Farmed Common Carp. LIFE (BASEL, SWITZERLAND) 2022; 12:life12070957. [PMID: 35888047 PMCID: PMC9315565 DOI: 10.3390/life12070957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022]
Abstract
Morphology and feature selection are key approaches to address several issues in fisheries science and stock management, such as the hypothesis of admixture of Caspian common carp (Cyprinus carpio) and farmed carp stocks in Iran. The present study was performed to investigate the population classification of common carp in the southern Caspian basin using data mining algorithms to find the most important characteristic(s) differing between Iranian and farmed common carp. A total of 74 individuals were collected from three locations within the southern Caspian basin and from one farm between November 2015 and April 2016. A dataset of 26 traditional morphometric (TMM) attributes and a dataset of 14 geometric landmark points were constructed and then subjected to various machine learning methods. In general, the machine learning methods had a higher prediction rate with TMM datasets. The highest decision tree accuracy of 77% was obtained by rule and decision tree parallel algorithms, and “head height on eye area” was selected as the best marker to distinguish between wild and farmed common carp. Various machine learning algorithms were evaluated, and we found that the linear discriminant was the best method, with 81.1% accuracy. The results obtained from this novel approach indicate that Darwin’s domestication syndrome is observed in common carp. Moreover, they pave the way for automated detection of farmed fish, which will be most beneficial to detect escapees and improve restocking programs.
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Affiliation(s)
- Omid Jafari
- International Sturgeon Research Institute, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization, Rasht 416353464, Iran
- Correspondence: (O.J.); (J.M.O.F.)
| | - Mansour Ebrahimi
- Department of Biology, School of Basic Science, University of Qom, Qom 3716146611, Iran;
| | - Seyed Ali-Akbar Hedayati
- Department of Fisheries, Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan 4913815739, Iran;
| | - Mehrshad Zeinalabedini
- Department of Genomics, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj 3135933151, Iran;
| | - Hadi Poorbagher
- Department of Fisheries Sciences, Faculty of Natural Resources, University of Tehran, Karaj 3158777871, Iran; (H.P.); (M.N.)
| | - Maryam Nasrolahpourmoghadam
- Department of Fisheries Sciences, Faculty of Natural Resources, University of Tehran, Karaj 3158777871, Iran; (H.P.); (M.N.)
| | - Jorge M. O. Fernandes
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
- Correspondence: (O.J.); (J.M.O.F.)
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Jafari O, Zeinalabedini M, Robledo D, Fernandes JMO, Hedayati AA, Arefnezhad B. Genotyping-by-Sequencing Reveals the Impact of Restocking on Wild Common Carp Populations of the Southern Caspian Basin. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.872176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Understanding the population structure and level of genetic diversity of wild populations is fundamental for appropriate stock management and species conservation. The common carp (Cyprinus carpio) is one of the most important bony fish throughout the Southern coastline of the Caspian Sea, but captures of this species have seen a dramatic reduction during the last decade. As a consequence, a restocking program has been put in place to maintain C. carpio populations, but its impact is not clear. In the present study, the population structure and genetic diversity of C. carpio in the Southern Caspian basin was determined using 17,828 single-nucleotide polymorphism (SNP) markers. A total of 117 individuals collected from four different locations in the southern Caspian basin and a farm were genotyped by genotyping-by-sequencing. The overall Fst obtained was 0.04, indicating a low level of differentiation between populations, and most genetic diversity was attributed to within population variation (97%). The low Fst values suggest that frequent migration events between different locations occur, and three migration events were inferred in the present study. However, each population still showed a distinct genetic profile, which allowed distinguishing the origin of the fish. This indicates that the ongoing restocking program is maintaining the differences between populations to some extent. Nonetheless, high inbreeding and low heterozygosity were detected in all populations, suggesting that additional conservation efforts are required to protect C. carpio populations in the Southern coast of the Caspian Sea.
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Koot E, Wu C, Ruza I, Hilario E, Storey R, Wells R, Chagné D, Wellenreuther M. Genome-wide analysis reveals the genetic stock structure of hoki ( Macruronus novaezelandiae). Evol Appl 2021; 14:2848-2863. [PMID: 34950233 PMCID: PMC8674887 DOI: 10.1111/eva.13317] [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: 08/16/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 12/23/2022] Open
Abstract
The assessment of the genetic structuring of biodiversity is crucial for management and conservation. This is particularly critical for widely distributed and highly mobile deep-water teleosts, such as hoki (Macruronus novaezelandiae). This species is significant to Māori people and supports the largest commercial fishery in New Zealand, but uncertainty about its stock structure presents a challenge for management. Here, we apply a comprehensive genomic analysis to shed light on the demographic structure of this species by (1) assembling the genome, (2) generating a catalogue of genome-wide SNPs to infer the stock structure and (3) identifying regions of the genome under selection. The final genome assembly used short and long reads and is near complete, representing 93.8% of BUSCO genes, and consisting of 566 contigs totalling 501 Mb. Whole-genome re-sequencing of 510 hoki sampled from 14 locations around New Zealand and Australia, at a read depth greater than 10×, produced 227,490 filtered SNPs. Analyses of these SNPs were able to resolve the stock structure of hoki into two genetically and geographically distinct clusters, one including the Australian and the other one all New Zealand locations, indicating genetic exchange between these regions is limited. Location differences within New Zealand samples were much more subtle (global F ST = 0.0006), and while small and significant differences could be detected, they did not conclusively identify additional substructures. Ten putative adaptive SNPs were detected within the New Zealand samples, but these also did not geographically partition the dataset further. Contemporary and historical N e estimation suggest the current New Zealand population of hoki is large yet declining. Overall, our study provides the first genomic resources for hoki and provides detailed insights into the fine-scale population genetic structure to inform the management of this species.
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Affiliation(s)
- Emily Koot
- The New Zealand Institute for Plant and Food Research LtdPalmerston NorthNew Zealand
| | - Chen Wu
- The New Zealand Institute for Plant and Food Research LtdAucklandNew Zealand
| | - Igor Ruza
- The New Zealand Institute for Plant and Food Research LtdNelsonNew Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research LtdAucklandNew Zealand
| | - Roy Storey
- The New Zealand Institute for Plant and Food Research LtdTe PukeNew Zealand
| | | | - David Chagné
- The New Zealand Institute for Plant and Food Research LtdPalmerston NorthNew Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research LtdNelsonNew Zealand
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
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Hierarchical genetic structure and implications for conservation of the world's largest salmonid, Hucho taimen. Sci Rep 2021; 11:20508. [PMID: 34654859 PMCID: PMC8520000 DOI: 10.1038/s41598-021-99530-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/20/2021] [Indexed: 11/09/2022] Open
Abstract
Population genetic analyses can evaluate how evolutionary processes shape diversity and inform conservation and management of imperiled species. Taimen (Hucho taimen), the world’s largest freshwater salmonid, is threatened, endangered, or extirpated across much of its range due to anthropogenic activity including overfishing and habitat degradation. We generated genetic data using high throughput sequencing of reduced representation libraries for taimen from multiple drainages in Mongolia and Russia. Nucleotide diversity estimates were within the range documented in other salmonids, suggesting moderate diversity despite widespread population declines. Similar to other recent studies, our analyses revealed pronounced differentiation among the Arctic (Selenge) and Pacific (Amur and Tugur) drainages, suggesting historical isolation among these systems. However, we found evidence for finer-scale structure within the Pacific drainages, including unexpected differentiation between tributaries and the mainstem of the Tugur River. Differentiation across the Amur and Tugur basins together with coalescent-based demographic modeling suggests the ancestors of Tugur tributary taimen likely diverged in the eastern Amur basin, prior to eventual colonization of the Tugur basin. Our results suggest the potential for differentiation of taimen at different geographic scales, and suggest more thorough geographic and genomic sampling may be needed to inform conservation and management of this iconic salmonid.
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Longo GC, Harms J, Hyde JR, Craig MT, Ramón-Laca A, Nichols KM. Genome-wide markers reveal differentiation between and within the cryptic sister species, sunset and vermilion rockfish. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01397-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThe vermilion rockfish complex, which consists of the cryptic sister species vermilion and sunset rockfish, is one of the most valuable recreational fisheries on the U.S. West Coast. These species are currently managed as a single complex, and because of uncertainty surrounding the relative contribution of each species within existing data sources, the stock status of each species is not fully known. A reliable and cost-effective method is needed to disentangle these species that will allow for the development of abundance indices, life history profiles, and catch histories that may potentially support species-specific stock assessments. Using restriction-site associated DNA sequence (RADseq) markers we generated 10,003 polymorphic loci to characterize the vermilion rockfish complex. PCA and Bayesian clustering approaches based on these loci clearly distinguished between sunset and vermilion rockfishes and identified hybrid individuals. These loci included 203 highly differentiated (FST ≥ 0.99) single nucleotide polymorphisms, which we consider candidates in the planned development of a diagnostic assay capable of distinguishing between these cryptic species. In addition to clearly delineating to species, subsets of the interspecific markers allowed for insight into intraspecific differentiation in both species. Population genetic analyses for sunset rockfish identified two weakly divergent genetic groups with similar levels of genetic diversity. Vermilion rockfish, however, were characterized by three distinct genetic groups with much stronger signals of differentiation and significantly different genetic diversities. Collectively, these data will contribute to well-informed, species-specific management strategies to protect this valuable species complex.
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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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13
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Hirota SK, Yasumoto AA, Nitta K, Tagane M, Miki N, Suyama Y, Yahara T. Evolutionary history of Hemerocallis in Japan inferred from chloroplast and nuclear phylogenies and levels of interspecific gene flow. Mol Phylogenet Evol 2021; 164:107264. [PMID: 34273506 DOI: 10.1016/j.ympev.2021.107264] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/22/2021] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
The perennial herb genus Hemerocallis (Asphodelaceae) shows four flowering types: diurnal half-day, diurnal one-day, nocturnal half-day, and nocturnal one-day flowering. These flowering types are corresponding to their main pollinators, and probably act as a primary mechanism of reproductive isolation. To examine how the four flowering types diverged, we reconstructed the phylogeny of the Japanese species of Hemerocallis using 1615 loci of nuclear genome-wide SNPs and 2078 bp sequences of four cpDNA regions. We also examined interspecific gene flows among taxa by an Isolation-with-Migration model and a population structure analysis. Our study revealed an inconsistency between chloroplast and nuclear genome phylogenies, which may have resulted from chloroplast capture. Each of the following five clusters is monophyletic and clearly separated on the nuclear genome-wide phylogenetic tree: (I) two nocturnal flowering species with lemon-yellow flowers, H. citrina (half-day flowering) and H. lilioasphodelus (one-day flowering); (II) a diurnal one-day flowering species with yellow-orange flowers, H. middendorffii; (III) a variety of a diurnal half-day flowering species with reddish orange flowers, H. fulva var. disticha; (IV) another variety of a diurnal half-day flowering species with reddish orange flowers, H. fulva var. aurantiaca, and a diurnal one-day flowering species with yellow-orange flowers, H. major; (V) a diurnal half-day flowering species with yellow-orange flowers, H. hakuunensis. The five clusters are consistent with traditional phenotype-based taxonomy (cluster I, cluster II, and clusters III-V correspond to Hemerocallis sect. Hemerocallis, Capitatae, and Fulvae, respectively). These findings could indicate that three flowering types (nocturnal flowering, diurnal one-day flowering, and diurnal half-day flowering) diverged in early evolutionary stages of Hemerocallis and subsequently a change from diurnal half-day flowering to diurnal one-day flowering occurred in a lineage of H. major. While genetic differentiation among the five clusters was well maintained, significant gene flow was detected between most pairs of taxa, suggesting that repeated hybridization played a role in the evolution of those taxa.
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Affiliation(s)
- Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Aza-yomogida, Naruko Onsen, Osaki, Miyagi 989-6711, Japan.
| | - Akiko A Yasumoto
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kozue Nitta
- Department of Environmental Science, School of Life and Environmental Science, Azabu University, 1-17-71 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5201, Japan
| | - Misa Tagane
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Nozomu Miki
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Aza-yomogida, Naruko Onsen, Osaki, Miyagi 989-6711, Japan
| | - Tetsukazu Yahara
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
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14
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Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America. Sci Rep 2021; 11:10752. [PMID: 34031525 PMCID: PMC8144384 DOI: 10.1038/s41598-021-90325-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/10/2021] [Indexed: 11/08/2022] Open
Abstract
Detailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.
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15
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Euclide PT, MacDougall T, Robinson JM, Faust MD, Wilson CC, Chen K, Marschall EA, Larson W, Ludsin S. Mixed-stock analysis using Rapture genotyping to evaluate stock-specific exploitation of a walleye population despite weak genetic structure. Evol Appl 2021; 14:1403-1420. [PMID: 34025775 PMCID: PMC8127713 DOI: 10.1111/eva.13209] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/31/2022] Open
Abstract
Mixed-stock analyses using genetic markers have informed fisheries management in cases where strong genetic differentiation occurs among local spawning populations, yet many fisheries are supported by multiple, weakly differentiated stocks. Freshwater fisheries exemplify this problem, with many populations supported by multiple stocks of young evolutionary age and isolated across small spatial scales. Consequently, attempts to conduct genetic mixed-stock analyses of inland fisheries have often been unsuccessful. Advances in genomic sequencing offer the ability to discriminate among populations with weak population structure, providing the necessary resolution to conduct mixed-stock assignment among previously indistinguishable stocks. We used genomic data to conduct a mixed-stock analysis of eastern Lake Erie's commercial and recreational walleye (Sander vitreus) fisheries and estimate the relative harvest of weakly differentiated stocks (pairwise F ST < 0.01). Using RAD-capture (Rapture), we sequenced and genotyped individuals from western and eastern basin local spawning stocks at 12,081 loci with 95% reassignment accuracy, which was not possible in the past using microsatellite markers. A baseline assessment of 395 walleye from 11 spawning stocks identified three reporting groups and refined previous assessments of gene flow among walleye stocks. Genetic assignment of 1,075 walleye harvested in eastern Lake Erie's recreational and commercial fisheries indicated that western basin stocks constituted the majority of harvest during the peak walleye fishing season (July-September), whereas eastern basin individuals comprised much of the early season harvest (May-June). Clear spatial structure in harvest composition existed; catches in more easterly sites contained more individuals of eastern basin origin than did more westerly sites. Our study provides important stock contribution estimates for Lake Erie fishery management and demonstrates the utility of genomic data to facilitate mixed-stock analysis in exploited fish populations having weak population structure or limited existing genetic resources.
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Affiliation(s)
- Peter T. Euclide
- Wisconsin Cooperative Fishery Research Unit, College of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Tom MacDougall
- Lake Erie Management UnitOntario Ministry of Natural Resources and ForestryPort DoverONCanada
| | - Jason M. Robinson
- Lake Erie Fisheries Research UnitNew York State Department of Environmental ConservationDunkirkNYUSA
| | - Matthew D. Faust
- Division of Wildlife, Sandusky Fisheries Research StationOhio Department of Natural ResourcesSanduskyOHUSA
| | - Chris C. Wilson
- Aquatic Research and Monitoring SectionOntario Ministry of Natural Resources and ForestryPeterboroughONCanada
| | - Kuan‐Yu Chen
- Aquatic Ecology Laboratory, Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOHUSA
| | - Elizabeth A. Marschall
- Aquatic Ecology Laboratory, Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOHUSA
| | - Wesley Larson
- U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
- Present address:
National Oceanic and Atmospheric AdministrationTed Stevens Marine Research InstituteJuneauAKUSA
| | - Stuart Ludsin
- Aquatic Ecology Laboratory, Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOHUSA
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16
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Camak DT, Osborne MJ, Turner TF. Population genomics and conservation of Gila Trout (Oncorhynchus gilae). CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01355-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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17
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Robalo JI, Farias I, Francisco SM, Avellaneda K, Castilho R, Figueiredo I. Genetic population structure of the Blackspot seabream ( Pagellus bogaraveo): contribution of mtDNA control region to fisheries management. Mitochondrial DNA A DNA Mapp Seq Anal 2021; 32:115-119. [PMID: 33576693 DOI: 10.1080/24701394.2021.1882445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Marine fisheries management models have traditionally considered biological parameters and geopolitical boundaries. The result is the existence of fisheries management units that do not match genetic populations. However, this panorama is changing with the contribution of genetic and genomic data. Pagellus bogaraveo is a commercially important sparid in the northeast Atlantic, with three stock components being considered by ICES: the Celtic Sea and Bay of Biscay, Atlantic Iberian waters and the Azores. The northern stock collapsed (1975-1985) and is essential to characterize the genetic makeup of the species, particularly in the Iberian Peninsula, where it is managed as a single stock. The mitochondrial control region was used to screen the intraspecific diversity and population structure of individuals from six locations across the species range. The genetic diversity found is similar among sites, and there is differentiation between the Azores and the remaining locations.
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Affiliation(s)
- Joana I Robalo
- MARE - Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Lisboa, Portugal
| | - Inês Farias
- Portuguese Institute for Sea and Atmosphere (IPMA), Algés, Portugal
| | - Sara M Francisco
- MARE - Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Lisboa, Portugal
| | - Karen Avellaneda
- MARE - Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Lisboa, Portugal
| | - Rita Castilho
- University of the Algarve, Faro, Portugal.,Faculty of Science and Technology, Centre of Marine Sciences (CCMAR), Faro, Portugal
| | - Ivone Figueiredo
- Portuguese Institute for Sea and Atmosphere (IPMA), Algés, Portugal
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18
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Imai R, Tsuda Y, Ebihara A, Matsumoto S, Tezuka A, Nagano AJ, Ootsuki R, Watano Y. Mating system evolution and genetic structure of diploid sexual populations of Cyrtomium falcatum in Japan. Sci Rep 2021; 11:3124. [PMID: 33542454 PMCID: PMC7862634 DOI: 10.1038/s41598-021-82731-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 01/12/2021] [Indexed: 11/09/2022] Open
Abstract
Evolution of mating systems has become one of the most important research areas in evolutionary biology. Cyrtomium falcatum is a homosporous fern species native to eastern Asia. Two subspecies belonging to a sexual diploid race of C. falcatum are recognized: subsp. littorale and subsp. australe. Subspecies littorale shows intermediate selfing rates, while subsp. australe is an obligate outcrosser. We aimed to evaluate the process of mating system evolution and divergence for the two subspecies using restriction site associated DNA sequencing (RAD-seq). The results showed that subsp. littorale had lower genetic diversity and stronger genetic drift than subsp. australe. Fluctuations in the effective population size over time were evaluated by extended Bayesian skyline plot and Stairway plot analyses, both of which revealed a severe population bottleneck about 20,000 years ago in subsp. littorale. This bottleneck and the subsequent range expansion after the LGM appear to have played an important role in the divergence of the two subspecies and the evolution of selfing in subsp. littorale. These results shed new light on the relationship between mating system evolution and past demographic change in fern species.
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Affiliation(s)
- Ryosuke Imai
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda , Nagano, 386-2204, Japan.
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda , Nagano, 386-2204, Japan
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Sadamu Matsumoto
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Ayumi Tezuka
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Ryo Ootsuki
- Department of Natural Sciences, Faculty of Arts and Sciences, Komazawa University, 1-23-1 Komazawa, Setagaya-ku, Tokyo, 154-8525, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Inage, Chiba, Chiba, 263-8522, Japan
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19
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Luikart G, Antao T, Hand BK, Muhlfeld CC, Boyer MC, Cosart T, Trethewey B, Al-Chockhachy R, Waples RS. Detecting population declines via monitoring the effective number of breeders (N b ). Mol Ecol Resour 2020; 21:379-393. [PMID: 32881365 DOI: 10.1111/1755-0998.13251] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/16/2022]
Abstract
Estimating the effective population size and effective number of breeders per year (Nb ) can facilitate early detection of population declines. We used computer simulations to quantify bias and precision of the one-sample LDNe estimator of Nb in age-structured populations using a range of published species life history types, sample sizes, and DNA markers. Nb estimates were biased by ~5%-10% when using SNPs or microsatellites in species ranging from fishes to mosquitoes, frogs, and seaweed. The bias (high or low) was similar for different life history types within a species suggesting that life history variation in populations will not influence Nb estimation. Precision was higher for 100 SNPs (H ≈ 0.30) than for 15 microsatellites (H ≈ 0.70). Confidence intervals (CIs) were occasionally too narrow, and biased high when Nb was small (Nb < 50); however, the magnitude of bias would unlikely influence management decisions. The CIs (from LDNe) were sufficiently narrow to achieve high statistical power (≥0.80) to reject the null hypothesis that Nb = 50 when the true Nb = 30 and when sampling 50 individuals and 200 SNPs. Similarly, CIs were sufficiently narrow to reject Nb = 500 when the true Nb = 400 and when sampling 200 individuals and 5,000 loci. Finally, we present a linear regression method that provides high power to detect a decline in Nb when sampling at least five consecutive cohorts. This study provides guidelines and tools to simulate and estimate Nb for age structured populations (https://github.com/popgengui/agestrucnb/), which should help biologists develop sensitive monitoring programmes for early detection of changes in Nb and population declines.
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Affiliation(s)
- Gordon Luikart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Tiago Antao
- The Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Brian K Hand
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Clint C Muhlfeld
- Northern Rocky Mountain Science Center, U.S. Geological Survey, Glacier National Park, Northern Rocky Mountain Science Center, West Glacier, MT, USA
| | | | - Ted Cosart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Brian Trethewey
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Robert Al-Chockhachy
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT, USA
| | - Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
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20
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Genome-wide SNPs reveal complex fine scale population structure in the California market squid fishery (Doryteuthis opalescens). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01321-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Hohenlohe PA, Funk WC, Rajora OP. Population genomics for wildlife conservation and management. Mol Ecol 2020; 30:62-82. [PMID: 33145846 PMCID: PMC7894518 DOI: 10.1111/mec.15720] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 10/02/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.
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Affiliation(s)
- Paul A Hohenlohe
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
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22
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Zielinski DP, McLaughlin RL, Pratt TC, Goodwin RA, Muir AM. Single-Stream Recycling Inspires Selective Fish Passage Solutions for the Connectivity Conundrum in Aquatic Ecosystems. Bioscience 2020; 70:871-886. [PMID: 33093814 PMCID: PMC7567676 DOI: 10.1093/biosci/biaa090] [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] [Indexed: 11/24/2022] Open
Abstract
Barrier removal is a recognized solution for reversing river fragmentation, but restoring connectivity can have consequences for both desirable and undesirable species, resulting in a connectivity conundrum. Selectively passing desirable taxa while restricting the dispersal of undesirable taxa (selective connectivity) would solve many aspects of the connectivity conundrum. Selective connectivity is a technical challenge of sorting an assortment of things. Multiattribute sorting systems exist in other fields, although none have yet been devised for freely moving organisms within a river. We describe an approach to selective fish passage that integrates ecology and biology with engineering designs modeled after material recycling processes that mirror the stages of fish passage: approach, entry, passage, and fate. A key feature of this concept is the integration of multiple sorting processes each targeting a specific attribute. Leveraging concepts from other sectors to improve river ecosystem function may yield fast, reliable solutions to the connectivity conundrum.
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Affiliation(s)
| | | | - Thomas C Pratt
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, Sault Ste Marie, Ontario, Canada
| | - R Andrew Goodwin
- Environmental Laboratory, US Army Engineer Research and Development Center, Portland, Oregon
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23
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Zhang B, Jia L, He X, Chen C, Liu H, Liu K, Zhao N, Bao B. Large scale SNP unearthing and genetic architecture analysis in sea-captured and cultured populations of Cynoglossus semilaevis. Genomics 2020; 112:3238-3246. [PMID: 32531446 DOI: 10.1016/j.ygeno.2020.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/09/2020] [Accepted: 06/06/2020] [Indexed: 01/07/2023]
Abstract
Knowledge on population structure and genetic diversity is a focal point for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Here we used the GBS approach for the genome-wide identification of SNPs in a collection of Cynoglossus semilaevis and for the assessment of the level of genetic diversity in C. semilaevis genotypes. GBS analysis generated a total of 55.12 Gb high-quality sequence data, with an average of 0.63 Gb per sample. The total number of SNP markers was 563, 109. In order to explore the genetic diversity of C. semilaevis and to select a minimal core set representing most of the total genetic variation with minimum redundancy, C. semilaevis sequences were analyzed using high quality SNPs. Based on hierarchical clustering, it was possible to divide the collection into 2 clusters. The marine fishing populations were clustered and clearly separated from the cultured populations, and the cultured populations from Hebei was also distinct from the other two local populations. These analyses showed that genotypes were clustered based on species-related features. Differential significant SNPs were also captured and validated by GBS and SNaPshot, with linkage disequilibrium and haplotype analysis, seven SNPs have been confirmed to have obvious differentiation in two populations, which may be used as the characteristic evaluation sites of sea-captured and cultured Cynoglossus semilaevis populations. And SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs. These differential SNPs could be also employed as the characteristic evaluation sites of sea-captured and cultured Cynoglossus semilaevis populations in future.
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China;International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Lei Jia
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Xiaoxu He
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Chunxiu Chen
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Hao Liu
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Kefeng Liu
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Na Zhao
- Tianjin Haolinsaiao Biotechnology Co, Ltd, Tianjin, China.
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China;International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
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24
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McKinney G, McPhee MV, Pascal C, Seeb JE, Seeb LW. Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon. G3 (BETHESDA, MD.) 2020; 10:1553-1561. [PMID: 32165371 PMCID: PMC7202013 DOI: 10.1534/g3.119.400972] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/28/2020] [Indexed: 11/26/2022]
Abstract
Many studies exclude loci that exhibit linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of excluding or ignoring loci exhibiting LD. Blindly excluding loci in LD would have prevented detection of the sex-determining region and chromosome inversion while failing to understand the genomic features leading to high-LD could have resulted in false interpretations of population structure.
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Affiliation(s)
- Garrett McKinney
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, AK, 99801
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
| | - Megan V McPhee
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, AK, 99801
| | - Carita Pascal
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
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25
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Ackiss AS, Larson WA, Stott W. Genotyping-by-sequencing illuminates high levels of divergence among sympatric forms of coregonines in the Laurentian Great Lakes. Evol Appl 2020; 13:1037-1054. [PMID: 32431751 PMCID: PMC7232772 DOI: 10.1111/eva.12919] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/05/2020] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
Effective resource management depends on our ability to partition diversity into biologically meaningful units. Recent evolutionary divergence, however, can often lead to ambiguity in morphological and genetic differentiation, complicating the delineation of valid conservation units. Such is the case with the "coregonine problem," where recent postglacial radiations of coregonines into lacustrine habitats resulted in the evolution of numerous species flocks, often with ambiguous taxonomy. The application of genomics methods is beginning to shed light on this problem and the evolutionary mechanisms underlying divergence in these ecologically and economically important fishes. Here, we used restriction site-associated DNA (RAD) sequencing to examine genetic diversity and differentiation among sympatric forms in the Coregonus artedi complex in the Apostle Islands of Lake Superior, the largest lake in the Laurentian Great Lakes. Using 29,068 SNPs, we were able to clearly distinguish among the three most common forms for the first time, as well as identify putative hybrids and potentially misidentified specimens. Population assignment rates for these forms using our RAD data were 93%-100% with the only mis-assignments arising from putative hybrids, an improvement from 62% to 77% using microsatellites. Estimates of pairwise differentiation (F ST: 0.045-0.056) were large given the detection of hybrids, suggesting that reduced fitness of hybrid individuals may be a potential mechanism for the maintenance of differentiation. We also used a newly built C. artedi linkage map to look for islands of genetic divergence among forms and found widespread differentiation across the genome, a pattern indicative of long-term drift, suggesting that these forms have been reproductively isolated for a substantial amount of time. The results of this study provide valuable information that can be applied to develop well-informed management strategies and stress the importance of re-evaluating conservation units with genomic tools to ensure they accurately reflect species diversity.
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Affiliation(s)
- Amanda S. Ackiss
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsin
| | - Wesley A. Larson
- U.S. Geological SurveyWisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsin
| | - Wendylee Stott
- U.S. Geological SurveyGreat Lakes Science CenterAnn ArborMichigan
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26
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Genetic structure and diversity of Australian freshwater crocodiles (Crocodylus johnstoni) from the Kimberley, Western Australia. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01259-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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Novak BJ, Fraser D, Maloney TH. Transforming Ocean Conservation: Applying the Genetic Rescue Toolkit. Genes (Basel) 2020; 11:E209. [PMID: 32085502 PMCID: PMC7074136 DOI: 10.3390/genes11020209] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/25/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023] Open
Abstract
Although oceans provide critical ecosystem services and support the most abundant populations on earth, the extent of damage impacting oceans and the diversity of strategies to protect them is disconcertingly, and disproportionately, understudied. While conventional modes of conservation have made strides in mitigating impacts of human activities on ocean ecosystems, those strategies alone cannot completely stem the tide of mounting threats. Biotechnology and genomic research should be harnessed and developed within conservation frameworks to foster the persistence of viable ocean ecosystems. This document distills the results of a targeted survey, the Ocean Genomics Horizon Scan, which assessed opportunities to bring novel genetic rescue tools to marine conservation. From this Horizon Scan, we have identified how novel approaches from synthetic biology and genomics can alleviate major marine threats. While ethical frameworks for biotechnological interventions are necessary for effective and responsible practice, here we primarily assessed technological and social factors directly affecting technical development and deployment of biotechnology interventions for marine conservation. Genetic insight can greatly enhance established conservation methods, but the severity of many threats may demand genomic intervention. While intervention is controversial, for many marine areas the cost of inaction is too high to allow controversy to be a barrier to conserving viable ecosystems. Here, we offer a set of recommendations for engagement and program development to deploy genetic rescue safely and responsibly.
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Affiliation(s)
- Ben J. Novak
- Revive & Restore, 1505 Bridgeway #203, Sausalito, CA 94965, USA;
| | - Devaughn Fraser
- Genetics Research Lab, California Department of Fish and Wildlife, Sacramento, CA 95834, USA;
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28
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Graham CF, Boreham DR, Manzon RG, Stott W, Wilson JY, Somers CM. How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: A case study using the lake whitefish. PLoS One 2020; 15:e0226608. [PMID: 31978053 PMCID: PMC6980518 DOI: 10.1371/journal.pone.0226608] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 12/01/2019] [Indexed: 12/30/2022] Open
Abstract
Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth, as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these “simple” methodological decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) a larger number of loci at low sequencing depth based on a 9mer (library A); and (2) fewer loci at higher sequencing depth based on a 10mer (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (FST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters, largely due to retention of more loci in analyses. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for FST and ADMIXTURE, but not DAPC. When detecting fine population differentiation, the population map influenced the number of loci and missing data, which generated artefacts in all downstream analyses tested. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library construction and bioinformatics parameters can have important impacts on the interpretation of population subdivision. Although potentially more costly on a per-locus basis, early investment in striking a balance between the number of loci and sequencing effort is well worth the reduced genomic coverage for population genetics studies. More conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation. Overall, we recommend that researchers approach “simple” methodological decisions with caution, especially when working on non-model species for the first time.
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Affiliation(s)
- Carly F. Graham
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Douglas R. Boreham
- Medical Sciences, Northern Ontario School of Medicine, Greater Sudbury, Ontario, Canada
| | - Richard G. Manzon
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Wendylee Stott
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA
| | - Joanna Y. Wilson
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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29
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Fuller J, Ferchaud A, Laporte M, Le Luyer J, Davis TB, Côté SD, Bernatchez L. Absence of founder effect and evidence for adaptive divergence in a recently introduced insular population of white‐tailed deer (
Odocoileus virginianus
). Mol Ecol 2019; 29:86-104. [DOI: 10.1111/mec.15317] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Jérémie Fuller
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Anne‐Laure Ferchaud
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Jérémy Le Luyer
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | | | - Steeve D. Côté
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
| | - Louis Bernatchez
- Département de Biologie Université Laval Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
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30
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Kuismin M, Saatoglu D, Niskanen AK, Jensen H, Sillanpää MJ. Genetic assignment of individuals to source populations using network estimation tools. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Markku Kuismin
- Research Unit of Mathematical Sciences University of Oulu Oulu Finland
- Biocenter Oulu University of Oulu Oulu Finland
| | - Dilan Saatoglu
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Alina K. Niskanen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
| | - Henrik Jensen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Mikko J. Sillanpää
- Research Unit of Mathematical Sciences University of Oulu Oulu Finland
- Biocenter Oulu University of Oulu Oulu Finland
- Infotech Oulu University of Oulu Oulu Finland
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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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32
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Schmidt DJ, Huey JA, Hughes JM. Genome-Wide SNPs Identify Limits to Connectivity in the Extreme Freshwater Disperser, Spangled Perch Leiopotherapon unicolor (Terapontidae). J Hered 2019; 109:320-325. [PMID: 29228349 DOI: 10.1093/jhered/esx101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/10/2017] [Indexed: 12/31/2022] Open
Abstract
The utility of restriction-site associated DNA sequencing (RADseq) to resolve fine-scale population structure was tested on an abundant and vagile fish species in a tropical river. Australia's most widespread freshwater fish, the "extreme disperser" Leiopotherapon unicolor was sampled from 6 locations in an unregulated system, the Daly River in Australia's Northern Territory. Despite an expectation of high connectivity based on life history knowledge of this species derived from arid zone habitats, L. unicolor was not a panmictic population in the tropical lower Daly. Using ~14000 polymorphic RADseq loci, we found a pattern of upstream versus downstream population subdivision and evidence for differentiation among tributary populations. The magnitude of population structure was low with narrow confidence intervals (global FST = 0.014; 95% CI = 0.012-0.016). Confidence intervals around pairwise FST estimates were all nonzero and consistent with the results of clustering analyses. This population structure was not explained by spatially heterogeneous selection acting on a subset of loci, or by sampling groups of closely related individuals (average within-site relatedness ≈ 0). One implication of the low but significant structure observed in the tropics is the possibility that L. unicolor may exhibit contrasting patterns of migratory biology in tropical versus arid zone habitats. We conclude that the RADseq revolution holds promise for delineating subtle patterns of population subdivision in species characterized by high within-population variation and low among-population differentiation.
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Affiliation(s)
- Daniel J Schmidt
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
| | - Joel A Huey
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia.,Terrestrial Zoology & Molecular Systematics Unit, Western Australian Museum, Welshpool, Western Australia, Australia
| | - Jane M Hughes
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
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33
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Sandoval-Castillo J. Conservation genetics of elasmobranchs of the Mexican Pacific Coast, trends and perspectives. ADVANCES IN MARINE BIOLOGY 2019; 83:115-157. [PMID: 31606069 DOI: 10.1016/bs.amb.2019.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
One of the most critical threats to biodiversity is the high extinction rate driven by human activities. Reducing extinction rates requires the implementation of conservation programmes based on robust scientific data. Elasmobranchs are important ecological components of the ocean, and several species sustain substantial economic activities. Unfortunately, elasmobranchs are one of the most threatened and understudied animal taxa. The Mexican Pacific Coast (MPC) is a region with high elasmobranch diversity and is the seat of major elasmobranch fisheries. But it is also a developing region with several conservation and management challenges which require national and international attention. Here, we review the conservation genetics literature of elasmobranchs from the MPC. We present a synthesis of the works using samples from the region and emphasize the main gaps and biases in these data. In addition, we discuss the benefits and challenges of generating genomic information to improve the management and conservation of an elasmobranch biodiversity hotspot in a developing country. We found 47 elasmobranch genetic articles that cover <30% of the elasmobranch diversity in the region. These studies mainly used mitochondrial DNA sequences to analyse the genetic structure of commercially important and abundant species of the order Carcharhiniformes. Some of these papers also assessed mating systems, demographic parameters, and taxonomic uncertainties, all of which are important topics for efficient management decisions. In terms of conservation genetics, elasmobranchs from the MPC remain understudied. However, high-throughput sequencing technologies have increased the power and accessibility of genomic tools, even in developing countries such as Mexico. The tools described here provide information relevant for biodiversity conservation. Therefore, we strongly suggest that investment in genomic research will assist implementation of efficient management strategies. In time, this will reduce the extinction risk of the unique elasmobranch biodiversity from the MPC.
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Affiliation(s)
- Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.
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34
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Bocek M, Motyka M, Kusy D, Bocak L. Genomic and Mitochondrial Data Identify Different Species Boundaries in Aposematically Polymorphic Eniclases Net-Winged Beetles (Coleoptera: Lycidae). INSECTS 2019; 10:E295. [PMID: 31514482 PMCID: PMC6780303 DOI: 10.3390/insects10090295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/05/2019] [Accepted: 09/07/2019] [Indexed: 12/14/2022]
Abstract
Species delineation is essential for any evolutionary and biodiversity research, and recent advances in genomic sequencing have made it possible to robustly define species boundaries and detect hidden diversity. Here, we studied 14 species of aposematically colored New Guinean Eniclases (Coleoptera: Lycidae) whose conventional morphology- and single-locus mtDNA-based taxonomy has been contentious. We analyzed mitochondrial and restriction site associated DNA fragments to obtain a phylogenetic hypothesis and compared relationships recovered by the RAD analysis with species limits based on other information. The results show the presence of cryptic diversity and common mitonuclear discordance when over 30% of individuals were incorrectly assigned to species if only mitogenomic markers were considered. Nuclear data falsified the species rank of one species and identified one earlier unrecognized lineage deserving species rank. Further, our analyses demonstrate a highly variable phenotypic differentiation, with several pairs of cryptic species standing in contrast with genetically close but phenotypically highly divergent lineages. We show that morphological and mitogenomic analyses produce reliable information for taxonomy in most cases. Nevertheless, the species boundaries among closely related species should be based on all lines of evidence, including nuclear markers.
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Affiliation(s)
- Matej Bocek
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic.
| | - Michal Motyka
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic.
| | - Dominik Kusy
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic.
| | - Ladislav Bocak
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic.
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35
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Fuller N, Ford AT, Lerebours A, Gudkov DI, Nagorskaya LL, Smith JT. Chronic radiation exposure at Chernobyl shows no effect on genetic diversity in the freshwater crustacean, Asellus aquaticus thirty years on. Ecol Evol 2019; 9:10135-10144. [PMID: 31624541 PMCID: PMC6787803 DOI: 10.1002/ece3.5478] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/19/2019] [Accepted: 07/02/2019] [Indexed: 12/17/2022] Open
Abstract
Analysis of genetic diversity represents a fundamental component of ecological risk assessments in contaminated environments. Many studies have assessed the genetic implications of chronic radiation exposure at Chernobyl, generally recording an elevated genetic diversity and mutation rate in rodents, plants, and birds inhabiting contaminated areas. Only limited studies have considered genetic diversity in aquatic biota at Chernobyl, despite the large number of freshwater systems where elevated dose rates will persist for many years. Consequently, the present study aimed to assess the effects of chronic radiation exposure on genetic diversity in the freshwater crustacean, Asellus aquaticus, using a genome-wide SNP approach (Genotyping-by-sequencing). It was hypothesized that genetic diversity in A. aquaticus would be positively correlated with dose rate. A. aquaticus was collected from six lakes in Belarus and the Ukraine ranging in dose rate from 0.064 to 27.1 µGy/hr. Genotyping-by-sequencing analysis was performed on 74 individuals. A significant relationship between geographical distance and genetic differentiation confirmed the Isolation-by-Distance model. Conversely, no significant relationship between dose rate and genetic differentiation suggested no effect of the contamination gradient on genetic differentiation between populations. No significant relationship between five measures of genetic diversity and dose rate was recorded, suggesting that radiation exposure has not significantly influenced genetic diversity in A. aquaticus at Chernobyl. This is the first study to adopt a genome-wide SNP approach to assess the impacts of environmental radiation exposure on biota. These findings are fundamental to understanding the long-term success of aquatic populations in contaminated environments at Chernobyl and Fukushima.
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Affiliation(s)
- Neil Fuller
- Institute of Marine Sciences, School of Biological SciencesUniversity of PortsmouthPortsmouthUK
| | - Alex T. Ford
- Institute of Marine Sciences, School of Biological SciencesUniversity of PortsmouthPortsmouthUK
| | - Adélaïde Lerebours
- Institute of Marine Sciences, School of Biological SciencesUniversity of PortsmouthPortsmouthUK
| | - Dmitri I. Gudkov
- Department of Freshwater RadioecologyInstitute of HydrobiologyKievUkraine
| | - Liubov L. Nagorskaya
- Applied Science Center for Bioresources of the National Academy of Sciences of BelarusMinskBelarus
| | - Jim T. Smith
- School of Earth & Environmental SciencesUniversity of PortsmouthPortsmouthUK
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36
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Dupuis JR, Ruiz‐Arce R, Barr NB, Thomas DB, Geib SM. Range-wide population genomics of the Mexican fruit fly: Toward development of pathway analysis tools. Evol Appl 2019; 12:1641-1660. [PMID: 31462920 PMCID: PMC6708432 DOI: 10.1111/eva.12824] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 11/30/2022] Open
Abstract
Recurrently invading pests provide unique challenges for pest management, but also present opportunities to utilize genomics to understand invasion dynamics and inform regulatory management through pathway analysis. In the southern United States, the Mexican fruit fly Anastrepha ludens is such a pest, and its incursions into Texas and California represent major threats to the agricultural systems of those regions. We developed a draft genome assembly for A. ludens, conducted range-wide population genomics using restriction site-associated DNA sequencing, and then developed and demonstrated a panel of highly differentiated diagnostic SNPs for source determination of intercepted flies in this system. Using 2,081 genomewide SNPs, we identified four populations across the range of A. ludens, corresponding to western Mexico, eastern Mexico/Texas, Guatemala/Belize/Honduras, and Costa Rica/Panama, with some intergradation present between clusters, particularly in Central America. From this population genomics framework, we developed a diagnostic panel of 28 highly differentiated SNPs that were able to recreate the genomewide population structure in this species. We demonstrated this panel on a set of test specimens, including specimens intercepted as part of regular trapping surveillance in Texas and California, and we were able to predict populations of origin for these specimens. This methodology presents a highly applied use of genomic techniques and can be implemented in any group of recurrently invading pests.
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Affiliation(s)
- Julian R. Dupuis
- U.S. Department of Agriculture‐Agricultural Research ServiceDaniel K. Inouye U.S. Pacific Basin Agricultural Research CenterHiloHawaii
- Department of Plant and Environmental Protection SciencesUniversity of Hawai’i at MānoaHonoluluHawaii
| | - Raul Ruiz‐Arce
- U.S. Department of Agriculture‐Animal and Plant Health Inspection Service, Plant Protection & Quarantine, Science and TechnologyMission LaboratoryEdinburgTexas
| | - Norman B. Barr
- U.S. Department of Agriculture‐Animal and Plant Health Inspection Service, Plant Protection & Quarantine, Science and TechnologyMission LaboratoryEdinburgTexas
| | - Donald B. Thomas
- U.S. Department of Agriculture‐Agricultural Research ServiceCattle Fever Tick Research LaboratoryEdinburgTexas
| | - Scott M. Geib
- U.S. Department of Agriculture‐Agricultural Research ServiceDaniel K. Inouye U.S. Pacific Basin Agricultural Research CenterHiloHawaii
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37
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Li YL, Xue DX, Zhang BD, Liu JX. Population Genomic Signatures of Genetic Structure and Environmental Selection in the Catadromous Roughskin Sculpin Trachidermus fasciatus. Genome Biol Evol 2019; 11:1751-1764. [PMID: 31173074 PMCID: PMC6601870 DOI: 10.1093/gbe/evz118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2019] [Indexed: 12/24/2022] Open
Abstract
Understanding the patterns of genetic diversity and adaptation across species' range is crucial to assess its long-term persistence and determine appropriate conservation measures. The impacts of human activities on the genetic diversity and genetic adaptation to heterogeneous environments remain poorly understood in the marine realm. The roughskin sculpin (Trachidermus fasciatus) is a small catadromous fish, and has been listed as a second-class state protected aquatic animal since 1988 in China. To elucidate the underlying mechanism of population genetic structuring and genetic adaptations to local environments, RAD tags were sequenced for 202 individuals in nine populations across the range of T. fasciatus in China. The pairwise FST values over 9,271 filtered SNPs were significant except that between Dongying and Weifang. All the genetic clustering analysis revealed significant population structure with high support for eight distinct genetic clusters. Both the minor allele frequency spectra and Ne estimations suggested extremely small Ne in some populations (e.g., Qinhuangdao, Rongcheng, Wendeng, and Qingdao), which might result from recent population bottleneck. The strong genetic structure can be partly attributed to genetic drift and habitat fragmentation, likely due to the anthropogenic activities. Annotations of candidate adaptive loci suggested that genes involved in metabolism, development, and osmoregulation were critical for adaptation to spatially heterogenous environment of local populations. In the context of anthropogenic activities and environmental change, results of the present population genomic work provided important contributions to the understanding of genetic differentiation and adaptation to changing environments.
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Affiliation(s)
- Yu-Long Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Dong-Xiu Xue
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Bai-Dong Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jin-Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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38
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Introgressive hybridisation between two widespread sharks in the east Pacific region. Mol Phylogenet Evol 2019; 136:119-127. [DOI: 10.1016/j.ympev.2019.04.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 03/27/2019] [Accepted: 04/10/2019] [Indexed: 11/21/2022]
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Lou F, Han Z, Gao T. Transcriptomic Responses of Two Ecologically Divergent Populations of Japanese Mantis Shrimp ( Oratosquilla oratoria) under Thermal Stress. Animals (Basel) 2019; 9:ani9070399. [PMID: 31262058 PMCID: PMC6680513 DOI: 10.3390/ani9070399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/28/2019] [Indexed: 01/12/2023] Open
Abstract
Simple Summary Rising ocean temperature would change the seawater chemistry and affect the external and internal physiology of crustaceans due to their lack of certain efficient temperature regulators. In addition, the infraspecific populations of crustaceans might also have different response strategies to the rising of temperature. Therefore, we identified the transcriptomic variations to the same thermal stress between ecologically divergent populations of Oratosquilla oratoria. The aim of this study was to investigate the population-specific function genes and relevant pathways in response to thermal stress in O. oratoria. The results showed that gene-expressed variation was in a population-specific pattern, which indicated that the local environment could lead to the evolvement of changes in gene regulation, ultimately leading to adaptive divergences. Additionally, we found several genes with large pleiotropic effects in the Zhoushan population, which might indicate that the regulation mechanisms of the Zhoushan population were more efficient than those of the Qingdao population under same thermal stress. The results provided some novel insights into the local adaptive differences of the infraspecific populations of O. oratoria and other crustaceans. Abstract Crustaceans are generally considered more sensitive to ocean warming due to their lack of certain efficient regulators. However, the alterations in the physiology and behavior of crustaceans in response to thermal stress differ vastly even among the infraspecific populations of heterogeneous landscapes. Consequently, understanding the impact of temperature fluctuation on crustacean infraspecific populations might be essential for maintaining a sustainable persistence of populations at existing locations. In the present study, we chose the Japanese mantis shrimp (Oratosquilla oratoria) as the representative crustacean population, and conducted transcriptome analyses in two divergent O. oratoria populations (the Zhoushan and Qingdao populations) under same thermal stress (20–28 °C) to identify the population-specific expression response to thermal stress. The results showed significant differences in gene expressions, GO terms and metabolic pathways between the two populations. We hypothesized that intraspecific mutations in the same or different genes might lead to thermal adaptive divergences. Temperature increases from 20–28 °C produced significant enrichment in GO terms and altered the metabolic pathways in the Zhoushan population despite the lack of differentially expressed unigenes. Therefore, several functional genes with large pleiotropic effects may underlie the response to thermal stress in the Zhoushan population. Furthermore, the most significantly enriched biological processes of the Qingdao population were associated with the state or activity of cells and its significant enriched pathways with genetic information processing as well as immune and environmental information processing. In contrast, the differentially regulated unigenes of the Zhoushan population were primarily involved in the regulatory cellular and transcription processes and the most significant pathways found were metabolic and digestive. Consequently, the regulatory mechanisms of the Zhoushan population are probably more efficient than those of the Qingdao population under the same thermal stress.
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Affiliation(s)
- Fangrui Lou
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China
- Fishery College, Ocean University of China, Qingdao 266003, China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China.
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China.
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Shen Y, Wang L, Fu J, Xu X, Yue GH, Li J. Population structure, demographic history and local adaptation of the grass carp. BMC Genomics 2019; 20:467. [PMID: 31174480 PMCID: PMC6555922 DOI: 10.1186/s12864-019-5872-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/31/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture. RESULTS We used 43,310 SNPs to infer the population structure, evidence of local adaptation and sources of introduction. The overall genetic differentiation of this species was low. The native populations were differentiated into three genetic clusters, corresponding to the Yangtze, Pearl and Heilongjiang River Systems, respectively. The populations in Malaysia, India and Nepal were introduced from both the Yangtze and Pearl River Systems. Loci and genes involved in putative local selection for native locations were identified. Evidence of both positive and balancing selection was found in the introduced locations. Genes associated with loci under putative selection were involved in many biological functions. Outlier loci were grouped into clusters as genomic islands within some specific genomic regions, which likely agrees with the divergence hitchhiking scenario of divergence-with-gene-flow. CONCLUSIONS This study, for the first time, sheds novel insights on the population differentiation of the grass carp, genetics of its strong ability in adaption to diverse environments and sources of some introduced grass carp populations. Our data also suggests that the natural populations of the grass carp have been affected by the aquaculture besides neutral and adaptive forces.
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Affiliation(s)
- Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China.,Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Le Wang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Gen Hua Yue
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore. .,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Republic of Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China. .,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
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Xuereb A, Benestan L, Normandeau É, Daigle RM, Curtis JMR, Bernatchez L, Fortin MJ. Asymmetric oceanographic processes mediate connectivity and population genetic structure, as revealed by RADseq, in a highly dispersive marine invertebrate (Parastichopus californicus). Mol Ecol 2019; 27:2347-2364. [PMID: 29654703 DOI: 10.1111/mec.14589] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 01/02/2023]
Abstract
Marine populations are typically characterized by weak genetic differentiation due to the potential for long-distance dispersal favouring high levels of gene flow. However, strong directional advection of water masses or retentive hydrodynamic forces can influence the degree of genetic exchange among marine populations. To determine the oceanographic drivers of genetic structure in a highly dispersive marine invertebrate, the giant California sea cucumber (Parastichopus californicus), we first tested for the presence of genetic discontinuities along the coast of North America in the northeastern Pacific Ocean. Then, we tested two hypotheses regarding spatial processes influencing population structure: (i) isolation by distance (IBD: genetic structure is explained by geographic distance) and (ii) isolation by resistance (IBR: genetic structure is driven by ocean circulation). Using RADseq, we genotyped 717 individuals from 24 sampling locations across 2,719 neutral SNPs to assess the degree of population differentiation and integrated estimates of genetic variation with inferred connectivity probabilities from a biophysical model of larval dispersal mediated by ocean currents. We identified two clusters separating north and south regions, as well as significant, albeit weak, substructure within regions (FST = 0.002, p = .001). After modelling the asymmetric nature of ocean currents, we demonstrated that local oceanography (IBR) was a better predictor of genetic variation (R2 = .49) than geographic distance (IBD) (R2 = .18), and directional processes played an important role in shaping fine-scale structure. Our study contributes to the growing body of literature identifying significant population structure in marine systems and has important implications for the spatial management of P. californicus and other exploited marine species.
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Affiliation(s)
- Amanda Xuereb
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Laura Benestan
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Éric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Rémi M Daigle
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Janelle M R Curtis
- Pacific Biological Station, Ecosystem Sciences Division, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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Silliman K. Population structure, genetic connectivity, and adaptation in the Olympia oyster ( Ostrea lurida) along the west coast of North America. Evol Appl 2019; 12:923-939. [PMID: 31080505 PMCID: PMC6503834 DOI: 10.1111/eva.12766] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/28/2018] [Accepted: 12/02/2018] [Indexed: 01/02/2023] Open
Abstract
Effective management of threatened and exploited species requires an understanding of both the genetic connectivity among populations and local adaptation. The Olympia oyster (Ostrea lurida), patchily distributed from Baja California to the central coast of Canada, has a long history of population declines due to anthropogenic stressors. For such coastal marine species, population structure could follow a continuous isolation-by-distance model, contain regional blocks of genetic similarity separated by barriers to gene flow, or be consistent with a null model of no population structure. To distinguish between these hypotheses in O. lurida, 13,424 single nucleotide polymorphisms (SNPs) were used to characterize rangewide population structure, genetic connectivity, and adaptive divergence. Samples were collected across the species range on the west coast of North America, from southern California to Vancouver Island. A conservative approach for detecting putative loci under selection identified 235 SNPs across 129 GBS loci, which were functionally annotated and analyzed separately from the remaining neutral loci. While strong population structure was observed on a regional scale in both neutral and outlier markers, neutral markers had greater power to detect fine-scale structure. Geographic regions of reduced gene flow aligned with known marine biogeographic barriers, such as Cape Mendocino, Monterey Bay, and the currents around Cape Flattery. The outlier loci identified as under putative selection included genes involved in developmental regulation, sensory information processing, energy metabolism, immune response, and muscle contraction. These loci are excellent candidates for future research and may provide targets for genetic monitoring programs. Beyond specific applications for restoration and management of the Olympia oyster, this study lends to the growing body of evidence for both population structure and adaptive differentiation across a range of marine species exhibiting the potential for panmixia. Computational notebooks are available to facilitate reproducibility and future open-sourced research on the population structure of O. lurida.
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Smith CT, Von Bargen J, DeHaan PW, Scheerer P, Meeuwig MH. Genetic structure and the history of chub in the Alvord Basin. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01148-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Xuereb A, D’Aloia CC, Daigle RM, Andrello M, Dalongeville A, Manel S, Mouillot D, Guichard F, Côté IM, Curtis JMR, Bernatchez L, Fortin MJ. Marine Conservation and Marine Protected Areas. POPULATION GENOMICS 2019. [DOI: 10.1007/13836_2018_63] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Population Genomics Applied to Fishery Management and Conservation. POPULATION GENOMICS 2019. [DOI: 10.1007/13836_2019_66] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Kardos M, Shafer AB. The Peril of Gene-Targeted Conservation. Trends Ecol Evol 2018; 33:827-839. [DOI: 10.1016/j.tree.2018.08.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 01/01/2023]
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Al-Breiki RD, Kjeldsen SR, Afzal H, Al Hinai MS, Zenger KR, Jerry DR, Al-Abri MA, Delghandi M. Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline. BMC Genomics 2018; 19:690. [PMID: 30231936 PMCID: PMC6146514 DOI: 10.1186/s12864-018-5044-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species. RESULTS After stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise FST estimates revealed low differentiation among populations (pairwise FST range = - 0.0008 - 0.0021). Analysis of genetic variation using putatively directional FST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range = 0.0288-0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus. CONCLUSIONS Findings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes.
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Affiliation(s)
- Rufaida Dhuhai Al-Breiki
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
- College of Agriculture and Marine Sciences, Department of Marine Sciences and Fisheries, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Shannon R. Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Hasifa Afzal
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Manal Saif Al Hinai
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Mohammed Ali Al-Abri
- College of Agriculture and Marine Sciences, Department of Animal and Veterinary Sciences and Technology, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Madjid Delghandi
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
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Development of genome-wide SNPs for population genetics and population assignment of Sebastiscus marmoratus. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0868-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Hendricks S, Anderson EC, Antao T, Bernatchez L, Forester BR, Garner B, Hand BK, Hohenlohe PA, Kardos M, Koop B, Sethuraman A, Waples RS, Luikart G. Recent advances in conservation and population genomics data analysis. Evol Appl 2018. [PMCID: PMC6099823 DOI: 10.1111/eva.12659] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
New computational methods and next‐generation sequencing (NGS) approaches have enabled the use of thousands or hundreds of thousands of genetic markers to address previously intractable questions. The methods and massive marker sets present both new data analysis challenges and opportunities to visualize, understand, and apply population and conservation genomic data in novel ways. The large scale and complexity of NGS data also increases the expertise and effort required to thoroughly and thoughtfully analyze and interpret data. To aid in this endeavor, a recent workshop entitled “Population Genomic Data Analysis,” also known as “ConGen 2017,” was held at the University of Montana. The ConGen workshop brought 15 instructors together with knowledge in a wide range of topics including NGS data filtering, genome assembly, genomic monitoring of effective population size, migration modeling, detecting adaptive genomic variation, genomewide association analysis, inbreeding depression, and landscape genomics. Here, we summarize the major themes of the workshop and the important take‐home points that were offered to students throughout. We emphasize increasing participation by women in population and conservation genomics as a vital step for the advancement of science. Some important themes that emerged during the workshop included the need for data visualization and its importance in finding problematic data, the effects of data filtering choices on downstream population genomic analyses, the increasing availability of whole‐genome sequencing, and the new challenges it presents. Our goal here is to help motivate and educate a worldwide audience to improve population genomic data analysis and interpretation, and thereby advance the contribution of genomics to molecular ecology, evolutionary biology, and especially to the conservation of biodiversity.
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Affiliation(s)
- Sarah Hendricks
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Eric C. Anderson
- Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Santa Cruz California
- University of California Santa Cruz California
| | - Tiago Antao
- Division of Biological Sciences University of Montana Missoula Montana
| | - Louis Bernatchez
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | | | - Brittany Garner
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
- Wildlife Program Fish and Wildlife Genomics Group College of Forestry and Conservation University of Montana Missoula Montana
| | - Brian K. Hand
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
| | - Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Martin Kardos
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
| | - Ben Koop
- Department of Biology Centre for Biomedical Research University of Victoria Victoria British Columbia Canada
| | - Arun Sethuraman
- Department of Biological Sciences California State University San Marcos San Marcos California
| | - Robin S. Waples
- NOAA Fisheries Northwest Fisheries Science Center Seattle Washington
| | - Gordon Luikart
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
- Wildlife Program Fish and Wildlife Genomics Group College of Forestry and Conservation University of Montana Missoula Montana
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Gaughran SJ, Quinzin MC, Miller JM, Garrick RC, Edwards DL, Russello MA, Poulakakis N, Ciofi C, Beheregaray LB, Caccone A. Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study. Evol Appl 2018; 11:1084-1093. [PMID: 30026799 PMCID: PMC6050186 DOI: 10.1111/eva.12551] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/31/2017] [Indexed: 12/25/2022] Open
Abstract
High-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in nonmodel species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that represent three species of Galápagos giant tortoises (Chelonoidis spp.). Though microsatellite and mitochondrial DNA analyses have supported the distinctiveness of these species, a recent study called into question how well these markers matched with data from genomic SNPs, thereby questioning decades of studies in nonmodel organisms. Using >20,000 genomewide SNPs from 30 individuals from three Galápagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNPs and 2-5 individuals, or hundreds of SNPs and 10 individuals, but only if the units of analysis are delineated in a way that is consistent with evolutionary history. We show that the lack of structure in the recent SNP-based study was likely due to unnatural grouping of individuals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few samples per population, and underscores the importance of sampling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions.
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Affiliation(s)
| | - Maud C. Quinzin
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Joshua M. Miller
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | | | | | - Michael A. Russello
- Department of BiologyUniversity of British Columbia, Okanagan CampusKelownaBCCanada
| | - Nikos Poulakakis
- Department of BiologySchool of Sciences and EngineeringUniversity of CreteHeraklion, CreteGreece
- Natural History Museum of CreteSchool of Sciences and EngineeringUniversity of CreteHeraklion, CreteGreece
| | - Claudio Ciofi
- Department of BiologyUniversity of FlorenceSesto Fiorentino (FI)Italy
| | - Luciano B. Beheregaray
- Molecular Ecology LabSchool of Biological SciencesFlinders UniversityAdelaideSAAustralia
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
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