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Pearce DL, Edson JE, Jennelle CS, Walter WD. Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels. Sci Rep 2024; 14:11340. [PMID: 38760358 PMCID: PMC11101418 DOI: 10.1038/s41598-024-56128-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/01/2024] [Indexed: 05/19/2024] Open
Abstract
Genetics studies are used by wildlife managers and researchers to gain inference into a population of a species of interest. To gain these insights, microsatellites have been the primary method; however, there currently is a shift from microsatellites to single nucleotide polymorphisms (SNPs). With the different DNA requirements between microsatellites and SNPs, an investigation into which samples can provide adequate DNA yield is warranted. Using samples that were collected from previous genetic projects from regions in the USA from 2014 to 2021, we investigated the DNA yield of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed high- or medium-density SNP panels. We found seven sample categories that met the DNA requirements for use in all three panels, and one sample category that did not meet any of the three panels requirements; however, DNA integrity was highly variable and not all sample categories that met panel DNA requirements could be considered high quality DNA. Additionally, we used linear random-effects models to determine which covariates would have the greatest influence on DNA yield. We determined that all covariates (tissue type, storage method, preservative, DNA quality, time until DNA extraction and time after DNA extraction) could influence DNA yield.
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Affiliation(s)
- David L Pearce
- Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 413 Forest Resources Building, University Park, PA, 16802, USA
- Department of Rangeland, Wildlife and Fisheries Management, Texas A&M University, College Station, TX, 77843, USA
| | - Jessie E Edson
- Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 413 Forest Resources Building, University Park, PA, 16802, USA
| | - Chris S Jennelle
- Minnesota Department of Natural Resources, 5463 West Broadway Ave., Forest Lake, MN, 55025, USA
- Minnesota Department of Natural Resources, Division of Ecological and Water Resources, Nongame Wildlife Program, St Paul, MN, 55155, USA
| | - W David Walter
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 403 Forest Resources Building, University Park, PA, 16802, USA.
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2
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Pepke ML. Telomere length is not a useful tool for chronological age estimation in animals. Bioessays 2024; 46:e2300187. [PMID: 38047504 DOI: 10.1002/bies.202300187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
Telomeres are short repetitive DNA sequences capping the ends of chromosomes. Telomere shortening occurs during cell division and may be accelerated by oxidative damage or ameliorated by telomere maintenance mechanisms. Consequently, telomere length changes with age, which was recently confirmed in a large meta-analysis across vertebrates. However, based on the correlation between telomere length and age, it was concluded that telomere length can be used as a tool for chronological age estimation in animals. Correlation should not be confused with predictability, and the current data and studies suggest that telomeres cannot be used to reliably predict individual chronological age. There are biological reasons for why there is large individual variation in telomere dynamics, which is mainly due to high susceptibility to a wide range of environmental, but also genetic factors, rendering telomeres unfeasible as a tool for age estimation. The use of telomeres for chronological age estimation is largely a misguided effort, but its occasional reappearance in the literature raises concerns that it will mislead resources in wildlife conservation.
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Affiliation(s)
- Michael L Pepke
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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3
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Omondi SF, Githae EW, Khasa DP. Long-distance gene flow in Acacia senegal: Hope for disturbed and fragmented populations. Ecol Evol 2023; 13:e10292. [PMID: 37449018 PMCID: PMC10337015 DOI: 10.1002/ece3.10292] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Even though pollen and seed dispersals are some of the important factors that determine tree species survival across landscapes, gene dispersal data of important tropical dryland tree species such as Acacia senegal that are undergoing various population disturbances remain scarce. Understanding patterns of gene dispersal in these ecosystems is important for conservation, landscape restoration and tree improvement. We investigated pollen and seed mediated gene flow in two A. senegal populations of contrasting state (less disturbed and heavily undisturbed) using nine microsatellites and 128 genotyping-by-sequencing single nucleotide polymorphism (SNPs) multilocus genotypes of two growth stages (juvenile and adult trees) and their spatial locations. We performed parentage assignments using likelihood approach and undertook spatial genetic structure (SGS) analyses for the two growth stages through correlation among kinship coefficients and geographical distances between pair of individuals. The SNPs showed higher resolving power and assignment rates than microsatellites; however, a combination of the two marker-types improved the assignment rate and provided robust parentage assessments. We found evidence of long-distance (up to 210 m) pollination events for both populations; however, the majority of seed dispersal was found closer to the putative maternal parent. On average, parentage analysis showed high amounts of pollen (40%) and seed (20%) immigration in both populations. Significant positive SGS was found only for the adult cohorts in the less disturbed population for distance classes 20 and 40 m, indicating historical short-distance seed dispersals. Our results suggest long-distance gene flow within the species and we recommend conservation of remnant and isolated populations or individual trees to promote genetic connectivity.
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Affiliation(s)
- Stephen F. Omondi
- Department of Forest Genetics and Tree ImprovementKenya Forestry Research InstituteNairobiKenya
| | | | - Damase P. Khasa
- Centre for Forest Research and Institute for Systems and Integrative BiologyUniversité LavalSainte‐FoyQuébecCanada
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4
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Wenne R. Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations. Genes (Basel) 2023; 14:genes14040808. [PMID: 37107566 PMCID: PMC10138012 DOI: 10.3390/genes14040808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/28/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.
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Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
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5
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Coleman RR, Kraft DW, Hoban ML, Toonen RJ, Bowen BW. Genomic assessment of larval odyssey: self-recruitment and biased settlement in the Hawaiian surgeonfish Acanthurus triostegus sandvicensis. JOURNAL OF FISH BIOLOGY 2023; 102:581-595. [PMID: 36564830 DOI: 10.1111/jfb.15294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
The gap between spawning and settlement location of marine fishes, where the larvae occupy an oceanic phase, is a great mystery in both natural history and conservation. Recent genomic approaches provide some resolution, especially in linking parent to offspring with assays of nucleotide polymorphisms. Here, the authors applied this method to the endemic Hawaiian convict tang (Acanthurus triostegus sandvicensis), a surgeonfish with a long pelagic larval stage of c. 54-77 days. They collected 606 adults and 607 juveniles from 23 locations around the island of O'ahu, Hawai'i. Based on 399 single nucleotide polymorphisms, the authors assigned 68 of these juveniles back to a parent (11.2% assignment rate). Each side of the island showed significant population differentiation, with higher levels in the west and north. The west and north sides of the island also had little evidence of recruitment, which may be due to westerly currents in the region or an artefact of uneven sampling. In contrast, the majority of juveniles (94%) sampled along the eastern shore originated on that side of the island, primarily within semi-enclosed Kāne'ohe Bay. Nearly half of the juveniles assigned to parents were found in the southern part of Kāne'ohe Bay, with local settlement likely facilitated by extended water residence time. Several instances of self-recruitment, when juveniles return to their natal location, were observed along the eastern and southern shores. Cumulatively, these findings indicate that most dispersal is between adjacent regions on the eastern and southern shores. Regional management efforts for Acanthurus triostegus and possibly other reef fishes will be effective only with collaboration among adjacent coastal communities, consistent with the traditional moku system of native Hawaiian resource management.
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Affiliation(s)
- Richard R Coleman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA
- Department of Integrative Biology, University of Texas, Austin, Texas, USA
| | - Derek W Kraft
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, USA
| | - Mykle L Hoban
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, USA
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, USA
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Osmond DR, King RA, Stockley B, Launey S, Stevens JR. A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales. JOURNAL OF FISH BIOLOGY 2023; 102:258-270. [PMID: 36281821 DOI: 10.1111/jfb.15258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The rivers of southern England and northern France which drain into the English Channel contain several genetically unique groups of trout (Salmo trutta L.) that have suffered dramatic declines in numbers over the past 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 95 single nucleotide polymorphism (SNP) loci for trout from this region and investigate their applicability and variability in both target (i.e., southern English) and non-target trout populations from northern Britain and Ireland. In addition, we present three case studies which demonstrate the utility and resolution of these genetic markers at three levels of spatial separation:(a) between closely related populations in nearby rivers, (b) within a catchment and (c) when determining parentage and familial relationships between fish sampled from a single site, using both empirical and simulated data. The SNP loci will be useful for population genetic and assignment studies on brown trout within the UK and beyond.
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Affiliation(s)
- Daniel R Osmond
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
| | - R Andrew King
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
| | - Bruce Stockley
- Westcountry Rivers Trust, Rain-Charm House, Cornwall, UK
| | - Sophie Launey
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest INRAe, Rennes, France
| | - Jamie R Stevens
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
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Muller-Girard M, Fowles G, Duchamp J, Kouneski S, Mollohan C, Smyser TJ, Turner GG, Westrich B, Doyle JM. A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population. BMC Ecol Evol 2022; 22:137. [PMID: 36418951 PMCID: PMC9686018 DOI: 10.1186/s12862-022-02083-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 10/19/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, the abundance of Allegheny woodrats has declined throughout the species' range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small, genetically depauperate subpopulation in New Jersey, woodrats were translocated from a genetically robust population in Pennsylvania (PA) in 2015, 2016 and 2017. Herein, we assess the efficacy of these translocations to restore genetic diversity within the recipient population. RESULTS We designed a novel 134 single nucleotide polymorphism panel, which was used to genotype the six woodrats translocated from PA and 82 individuals from the NJ population captured before and after the translocation events. These data indicated that a minimum of two translocated individuals successfully produced at least 13 offspring, who reproduced as well. Further, population-wide observed heterozygosity rose substantially following the first set of translocations, reached levels comparable to that of populations in Indiana and Ohio, and remained elevated over the subsequent years. Abundance also increased during the monitoring period, suggesting Pennsylvania translocations initiated genetic rescue of the New Jersey population. CONCLUSIONS Our results indicate, encouragingly, that very small numbers of translocated individuals can successfully restore the genetic diversity of a threatened population. Our work also highlights the challenges of managing very small populations, such as when translocated individuals have greater reproductive success relative to residents. Finally, we note that ongoing work with Allegheny woodrats may broadly shape our understanding of genetic rescue within metapopulations and across heterogeneous landscapes.
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Affiliation(s)
- Megan Muller-Girard
- grid.265122.00000 0001 0719 7561Department of Environmental Science and Studies, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
| | - Gretchen Fowles
- Endangered and Nongame Species Program, New Jersey DEP Fish and Wildlife, 1255 County Rd 629, Lebanon, NJ 08833 USA
| | - Joseph Duchamp
- grid.257427.10000000088740847Department of Biology, Indiana University of Pennsylvania, 975 Oakland Avenue, Indiana, PA 15705-1081 USA
| | - Samantha Kouneski
- grid.265122.00000 0001 0719 7561Department of Biological Sciences, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
| | | | - Timothy J. Smyser
- grid.413759.d0000 0001 0725 8379USDA-APHIS-WS National Wildlife Research Center, Fort Collins, CO USA
| | - Gregory G. Turner
- Pennsylvania Game Commission, 2001 Elmerton Avenue, Harrisburg, PA 17110 USA
| | - Bradford Westrich
- grid.448453.a0000 0004 1130 5264Indiana Department of Natural Resources, 5596 East State Road 46, Bloomington, IN 47401 USA
| | - Jacqueline M. Doyle
- grid.265122.00000 0001 0719 7561Department of Biological Sciences, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
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Revealing Genetic Diversity and Population Structure of Endangered Altay White-Headed Cattle Population Using 100 k SNP Markers. Animals (Basel) 2022; 12:ani12223214. [PMID: 36428441 PMCID: PMC9686749 DOI: 10.3390/ani12223214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/17/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
Understanding the genetic basis of native cattle populations that have adapted to the local environment is of great significance for formulating appropriate strategies and programs for genetic improvement and protection. Therefore, it is necessary to understand the genetic diversity and population structure of Altay white-headed cattle so as to meet the current production needs under various environments, carry out continuous genetic improvement, and promote rapid adaptation to changing environments and breeding objectives. A total of 46 individual samples of endangered Xinjiang Altay white-headed cattle were collected in this study, including nine bulls and 37 cows. To collect genotype data, 100 k SNP markers were used, and then studies of genetic diversity, genetic structure, inbreeding degree, and family analysis were carried out. A total of 101,220 SNP loci were detected, and the genotype detection rate for individuals was ≥90%. There were 85,993 SNP loci that passed quality control, of which 93.5% were polymorphic. The average effective allele number was 0.036, the Polymorphism Information Content was 0.304 and the minimum allele frequency was 0.309, the average observed heterozygosity was 0.413, and the average expected heterozygosity was 0.403. The average genetic distance of Idengtical By State (IBS) was 0.3090, there were 461 ROH (genome-length homozygous fragments), 76.1% of which were between 1 and 5 MB in length, and the average inbreeding coefficient was 0.016. The 46 Altay white-headed cattle were divided into their families, and the individual numbers of each family were obviously different. To sum up, the Altay white-headed cattle conservation population had low heterozygosity, a high inbreeding degree, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the follow-up seed conservation process, seed selection and matching should be carried out according to the divided families to ensure the long-term protection of Altay white-headed cattle genetic resources.
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Venditti DA, Steele CA, Ayers BS, McCormick JL. How Long Can Dead Fish Tell Tales? Effects of Time, Tissue, Preservation, and Handling on Genotyping Success. NORTHWEST SCIENCE 2022. [DOI: 10.3955/046.095.0309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- David A. Venditti
- Idaho Department of Fish and Game, 1414 East Locust Lane, Nampa, Idaho 83686
| | - Craig A. Steele
- Pacific States Marine Fisheries Commission, 1800 Trout Road, Eagle, Idaho 83616
| | - Brian S. Ayers
- Pacific States Marine Fisheries Commission, 1800 Trout Road, Eagle, Idaho 83616
| | - Joshua L. McCormick
- Idaho Department of Fish and Game, 1414 East Locust Lane, Nampa, Idaho 83686
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Lv W, Yuan Q, Huang W, Sun X, Lv W, Zhou W. Asian Swamp eel Monopterus albus Population Structure and Genetic Diversity in China. Front Genet 2022; 13:898958. [PMID: 35719368 PMCID: PMC9198659 DOI: 10.3389/fgene.2022.898958] [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: 03/18/2022] [Accepted: 05/09/2022] [Indexed: 11/23/2022] Open
Abstract
The Asian swamp eel (Monopterus albus) is one of the most widely distributed freshwater fish in China. In this study, we identified the single nucleotide polymorphisms (SNPs) of M. albus from 19 wild populations in China using restriction-site associated DNA sequencing (RAD-seq), and used SNP markers to investigate the swamp eel the genetic diversity and population genetic structure. A total of 8941794 SNPs were identified. Phylogenetic and principal component analysis suggested that the 19 populations were clustered into four groups: The Jiaoling County (JL) and Poyang Lake (PYH)populations in Group Ⅰ; the Chengdu City (CD), Dali City (YN), Eli Village (EL), Dongting Lake (DTH), Huoqiu County (HQ), and Chaohu Lake (CH) populations in Group Ⅱ; the Puyang City (PY), Chongming Island (CM), Tai Lake (TH), Gaoyou Lake (GYH), Weishan Lake (WSH), Haimen City (HM), Hongze Lake (HZH), Baiyangdian Lake (BYD), Dagushan (DGS), and Pinghu City (PH) populations in group Ⅲ; and the Lingshui County (LS) populations in Group Ⅳ. All 19 populations may have evolved from four ancestors. The genetic diversity was relatively high in CM, GYH, and HM; and low in LS, EL, and JL. The LS, and CM populations had the highest and lowest differentiation from the other populations, respectively. These findings provide new insights for germplasm resources protection and artificial breeding of M. albus.
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Affiliation(s)
- Weiwei Lv
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Quan Yuan
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Weiwei Huang
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xiaolin Sun
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Weiguang Lv
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wenzong Zhou
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Ganbold O, Purevee E, Khorloo M, Jargalsaikhan A, Khayankhyarvaa T, Ochirbat A, Purevdorj Z, Munkhbayar M. Strong Population Genetic Structure of Phrynocephalus versicolor in Mongolia. HERPETOLOGICA 2022. [DOI: 10.1655/herpetologica-d-21-00012.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Onolragchaa Ganbold
- Department of Biology, Mongolian National University of Education, Ulaanbaatar 14191, Mongolia
| | - Erdenetushig Purevee
- Department of Biology, Mongolian National University of Education, Ulaanbaatar 14191, Mongolia
| | - Munkhbayar Khorloo
- Department of Biology, Mongolian National University of Education, Ulaanbaatar 14191, Mongolia
| | - Ariunbold Jargalsaikhan
- Department of Biology, Mongolian National University of Education, Ulaanbaatar 14191, Mongolia
| | - Terbish Khayankhyarvaa
- Department of Biology, School of Science, Mongolian National University, Ulaanbaatar 14200, Mongolia
| | - Altangoo Ochirbat
- School of Mathematics and Natural Science, Mongolian National University of Education, Ulaanbaatar 14191, Mongolia
| | - Zoljargal Purevdorj
- Department of Forest Resource, Chungnam National University, Daejeon 34134, Korea
| | - Munkhbaatar Munkhbayar
- Department of Biology, Mongolian National University of Education, Ulaanbaatar 14191, Mongolia
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12
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Shedd KR, Lescak EA, Habicht C, Knudsen EE, Dann TH, Hoyt HA, Prince DJ, Templin WD. Reduced relative fitness in hatchery-origin Pink Salmon in two streams in Prince William Sound, Alaska. Evol Appl 2022; 15:429-446. [PMID: 35386398 PMCID: PMC8965367 DOI: 10.1111/eva.13356] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 01/21/2022] [Accepted: 02/03/2022] [Indexed: 12/02/2022] Open
Abstract
Previous studies generally report that hatchery-origin Pacific Salmon (Oncorhynchus spp.) have lower relative reproductive success (RRS) than their natural-origin counterparts. We estimated the RRS of Pink Salmon (O. gorbuscha) in Prince William Sound (PWS), Alaska using incomplete pedigrees. In contrast to other RRS studies, Pink Salmon have a short freshwater life history, freshwater habitats in PWS are largely unaltered by development, and sampling was conducted without the aid of dams or weirs resulting in incomplete sampling of spawning individuals. Pink Salmon released from large-scale hatchery programs in PWS have interacted with wild populations for more than 15 generations. Hatchery populations were established from PWS populations but have subsequently been managed as separate broodstocks. Gene flow is primarily directional, from hatchery strays to wild populations. We used genetic-based parentage analysis to estimate the RRS of a single generation of stray hatchery-origin Pink Salmon in two streams, and across the odd- and even-year lineages. Despite incomplete sampling, we assigned 1745 offspring to at least one parent. Reproductive success (RS), measured as sampled adult offspring that returned to their natal stream, was significantly lower for hatchery- vs. natural-origin parents in both lineages, with RRS ranging from 0.03 to 0.47 for females and 0.05 to 0.86 for males. Generalized linear modeling for the even-year lineage indicated that RRS was lower for hatchery-origin fish, ranging from 0.42 to 0.60, after accounting for sample date (run timing), sample location within the stream, and fish length. Our results strongly suggest that hatchery-origin strays have lower fitness in the wild. The consequences of reduced RRS on wild productivity depend on whether the mechanisms underlying reduced RRS are environmentally driven, and likely ephemeral, or genetically driven, and likely persistent across generations.
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Riley JL, Noble DWA, Stow AJ, Bolton PE, While GM, Dennison S, Byrne RW, Whiting MJ. Socioecology of the Australian Tree Skink (Egernia striolata). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.722455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is great diversity in social behavior across the animal kingdom. Understanding the factors responsible for this diversity can help inform theory about how sociality evolves and is maintained. The Australian Tree Skink (Egernia striolata) exhibits inter- and intra-population variability in sociality and is therefore a good system for informing models of social evolution. Here, we conducted a multi-year study of a Tree Skink population to describe intra-population variation in the social organization and mating system of this species. Skinks aggregated in small groups of 2–5 individuals, and these aggregations were typically associated with shared shelter sites (crevices and hollows within rocks and trees). Aggregations were typically made up of one or more adult females and, often, one male and/or juvenile(s). Social network and spatial overlap analyses showed that social associations were strongly biased toward kin. Tree skinks also exhibited high site fidelity regardless of age or sex. There were high levels of genetic monogamy observed with most females (87%) and males (68%) only breeding with a single partner. Our results indicate that Tree Skinks reside in small family groups and are monogamous, which corresponds with existing research across populations. Similar to previous work, our study area consisted of discrete habitat patches (i.e., rock outcrops, trees, or both), which likely limits offspring dispersal and promotes social tolerance between parents and their offspring. Our study clearly demonstrates that there is intra-population variability in Tree Skink social behavior, but it also provides evidence that there is a high degree of inter-population consistency in sociality across their geographic range. We also highlight promising possible avenues for future research, specifically discussing the importance of studying the nature and extent of Tree Skink parental care and quantifying the fitness outcomes of kin-based sociality in this species, which are topics that will further our understanding of the mechanisms underlying variation in vertebrate social behavior.
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Hauser SS, Athrey G, Leberg PL. Waste not, want not: Microsatellites remain an economical and informative technology for conservation genetics. Ecol Evol 2021; 11:15800-15814. [PMID: 34824791 PMCID: PMC8601879 DOI: 10.1002/ece3.8250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/07/2021] [Accepted: 09/16/2021] [Indexed: 11/07/2022] Open
Abstract
Comparisons of microsatellites and single-nucleotide polymorphisms (SNPs) have found that SNPs outperform microsatellites in population genetic analyses, questioning the continued utility of microsatellites in population and landscape genetics. Yet, highly polymorphic markers may be of value in species that have reduced genetic variation. This study repeated previous analyses that used microsatellites with SNPs developed from ddRAD sequencing in the black-capped vireo source-sink system. SNPs provided greater resolution of genetic diversity, population differentiation, and migrant detection but could not reconstruct parentage relationships due to insufficient heterozygosities. The biological inferences made by both sets of markers were similar: asymmetrical gene flow from source sites to the remaining sink sites. With the landscape genetic analyses, we found different results between the two molecular markers, but associations of the top environmental features (riparian, open habitat, agriculture, and human development) with dispersal estimates were shared between marker types. Despite the higher precision of SNPs, we find that microsatellites effectively uncover population processes and patterns and are superior for parentage analyses in this species with reduced genetic diversity. This study illustrates the continued applicability and relevance of microsatellites in population genetic research.
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Affiliation(s)
- Samantha S. Hauser
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisianaUSA
| | - Giridhar Athrey
- Faculty of Ecology and Evolutionary BiologyTexas A&M UniversityCollege StationTexasUSA
| | - Paul L. Leberg
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisianaUSA
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15
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Forsdick NJ, Martini D, Brown L, Cross HB, Maloney RF, Steeves TE, Knapp M. Genomic sequencing confirms absence of introgression despite past hybridisation between a critically endangered bird and its common congener. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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16
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Weng Z, Yang Y, Wang X, Wu L, Hua S, Zhang H, Meng Z. Parentage Analysis in Giant Grouper ( Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data. Genes (Basel) 2021; 12:genes12071042. [PMID: 34356058 PMCID: PMC8304347 DOI: 10.3390/genes12071042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/18/2022] Open
Abstract
Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.
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Affiliation(s)
- Zhuoying Weng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Yang Yang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Xi Wang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Lina Wu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Sijie Hua
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Hanfei Zhang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Zining Meng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
- Southern Laboratory of Ocean Science and Engineering, Zhuhai 519000, China
- Correspondence:
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17
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Byer NW, Holding ML, Crowell MM, Pierson TW, Dilts TE, Larrucea ES, Shoemaker KT, Matocq MD. Adaptive divergence despite low effective population size in a peripherally isolated population of the pygmy rabbit, Brachylagus idahoensis. Mol Ecol 2021; 30:4173-4188. [PMID: 34166550 DOI: 10.1111/mec.16040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 06/01/2021] [Accepted: 06/18/2021] [Indexed: 11/30/2022]
Abstract
Local adaptation can occur when spatially separated populations are subjected to contrasting environmental conditions. Historically, understanding the genetic basis of adaptation has been difficult, but increased availability of genome-wide markers facilitates studies of local adaptation in non-model organisms of conservation concern. The pygmy rabbit (Brachylagus idahoensis) is an imperiled lagomorph that relies on sagebrush for forage and cover. This reliance has led to widespread population declines following reductions in the distribution of sagebrush, leading to geographic separation between populations. In this study, we used >20,000 single nucleotide polymorphisms, genotype-environment association methods, and demographic modeling to examine neutral genetic variation and local adaptation in the pygmy rabbit in Nevada and California. We identified 308 loci as outliers, many of which had functional annotations related to metabolism of plant secondary compounds. Likewise, patterns of spatial variation in outlier loci were correlated with landscape and climatic variables including proximity to streams, sagebrush cover, and precipitation. We found that populations in the Mono Basin of California probably diverged from other Great Basin populations during late Pleistocene climate oscillations, and that this region is adaptively differentiated from other regions in the southern Great Basin despite limited gene flow and low effective population size. Our results demonstrate that peripherally isolated populations can maintain adaptive divergence.
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Affiliation(s)
- Nathan W Byer
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Matthew L Holding
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Miranda M Crowell
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Todd W Pierson
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Kennesaw, Georgia, USA
| | - Thomas E Dilts
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | | | - Kevin T Shoemaker
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
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18
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Blanco G, Morinha F. Genetic signatures of population bottlenecks, relatedness, and inbreeding highlight recent and novel conservation concerns in the Egyptian vulture. PeerJ 2021; 9:e11139. [PMID: 33828925 PMCID: PMC8005290 DOI: 10.7717/peerj.11139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/01/2021] [Indexed: 11/20/2022] Open
Abstract
The assessment of temporal variation in genetic features can be particularly informative on the factors behind demography and viability of wildlife populations and species. We used molecular methods to evaluate neutral genetic variation, relatedness, bottlenecks, and inbreeding in a declining population of Egyptian vulture (Neophron percnopterus) in central Spain. The results show that the genetic diversity remained relatively stable over a period of twelve years despite the decline in census and effective population sizes in the last decades. A relatively high proportion of nestlings from different and distant territories showed high relatedness in each study year. We also found support for an increasing impact of severe recent (contemporary) rather than distant (historical) past demographic bottlenecks, and the first evidence of inbred mating between full siblings coinciding with lethal malformations in offspring. The inbred nestling with feather malformations was positive to beak and feather disease virus recorded for the first time in this species. These results alert on recent and novel threats potentially affecting health and reducing the adaptive potential of individuals in this threatened species.
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Affiliation(s)
- Guillermo Blanco
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
| | - Francisco Morinha
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
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19
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Maximum likelihood parentage assignment using quantitative genotypes. Heredity (Edinb) 2021; 126:884-895. [PMID: 33692533 DOI: 10.1038/s41437-021-00421-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/09/2022] Open
Abstract
The cost of parentage assignment precludes its application in many selective breeding programmes and molecular ecology studies, and/or limits the circumstances or number of individuals to which it is applied. Pooling samples from more than one individual, and using appropriate genetic markers and algorithms to determine parental contributions to pools, is one means of reducing the cost of parentage assignment. This paper describes and validates a novel maximum likelihood (ML) parentage-assignment method, that can be used to accurately assign parentage to pooled samples of multiple individuals-previously published ML methods are applicable to samples of single individuals only-using low-density single nucleotide polymorphism (SNP) 'quantitative' (also referred to as 'continuous') genotype data. It is demonstrated with simulated data that, when applied to pools, this 'quantitative maximum likelihood' method assigns parentage with greater accuracy than established maximum likelihood parentage-assignment approaches, which rely on accurate discrete genotype calls; exclusion methods; and estimating parental contributions to pools by solving the weighted least squares problem. Quantitative maximum likelihood can be applied to pools generated using either a 'pooling-for-individual-parentage-assignment' approach, whereby each individual in a pool is tagged or traceable and from a known and mutually exclusive set of possible parents; or a 'pooling-by-phenotype' approach, whereby individuals of the same, or similar, phenotype/s are pooled. Although computationally intensive when applied to large pools, quantitative maximum likelihood has the potential to substantially reduce the cost of parentage assignment, even if applied to pools comprised of few individuals.
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20
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Ding ZF, Zhang CL, Zhang WS, Yuan QM, Wang LW, Ren G, Li E, Hu HJ, Liang W. Determining the level of extra-pair paternity in yellow-bellied prinias, a socially monogamous passerine. Zool Res 2021; 42:108-115. [PMID: 32987453 PMCID: PMC7840452 DOI: 10.24272/j.issn.2095-8137.2020.079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Previous work based on molecular evidence has shown that most socially monogamous birds follow a genetic polyandrous mating system. However, our knowledge about avian mating systems is heavily biased toward the north temperate zone, with data on tropical birds remaining relatively scarce. This uneven distribution of both phylogenetic and spatial sampling has hampered our understanding and interpretation of results. In this study, we investigated the frequency of extra-pair paternity (EPP) in a tropical population of yellow-bellied prinias (Prinia flaviventris) in Guangxi, southern China. A total of 129 individuals belonging to 24 nests were sampled, among which 12 out of 83 chicks (14.46%) in seven nests were found to be EPP offspring. In nests in which all nestlings were sampled, only five out of 56 chicks were EPP offspring, accounting for an unbiased EPP rate of 8.93%. This rate is below the average rate of EPP in the family Sylviidae. The possible causes of EPP in prinias and the occurrence of EPP in birds with high resource investment and intensive parental care are discussed. This study highlights the value of genome-wide markers in determining relatedness in a wild bird species without a reference genome.
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Affiliation(s)
- Zhi-Feng Ding
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510260, China
| | - Chun-Lan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510260, China
| | - Wen-Sui Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510260, China
| | - Qian-Min Yuan
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510260, China
| | - Long-Wu Wang
- State Forestry Administration of China Key Laboratory for Biodiversity Conservation in Mountainous Areas of Southwest Karst, School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 550001, China
| | - Gang Ren
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510260, China.,College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - En Li
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Hui-Jian Hu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510260, China. E-mail:
| | - Wei Liang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, Hainan 571158, China. E-mail:
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21
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Brown TA, Tsurusaki N, Burns M. Genomic Determination of Reproductive Mode in Facultatively Parthenogenetic Opiliones. J Hered 2021; 112:34-44. [PMID: 33448304 DOI: 10.1093/jhered/esaa045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 11/03/2020] [Indexed: 01/15/2023] Open
Abstract
Sexual reproduction may pose myriad short-term costs to females. Despite these costs, sexual reproduction is near ubiquitous. Facultative parthenogenesis is theorized to mitigate some of the costs of sex, as individuals can participate in occasional sex to limit costs while obtaining many benefits. However, most theoretical models assume sexual reproduction is fixed following mating, with no possibility of clutches of mixed reproductive ontogeny. Therefore, we asked: if coercive males are present at high frequency in a population of facultative parthenogens, will their clutches be solely sexually produced, or will there be evidence of sexually and asexually-produced offspring? How will their offspring production compare to conspecifics in low-frequency male populations? We addressed our questions by collecting females and egg clutches of the facultatively parthenogenetic Opiliones species Leiobunum manubriatum and L. globosum. In L. manubriatum, females from populations with few males were not significantly more fecund than females from populations with higher male relative frequency, despite the potential release of the former from sexual conflict. We used 3 genotyping methods along with a custom set of DNA capture probes to reveal that offspring of L. manubriatum from these high male populations were primarily produced via asexual reproduction. This is surprising because sex ratios in these southern populations approach equality, increasing the probability for females to encounter mates and produce offspring sexually. We additionally found evidence for reproductive polymorphisms within populations. Rapid and accurate SNP genotyping data will continue to allow us to address broader evolutionary questions regarding the role of facultative reproductive modes in the maintenance of sex.
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Affiliation(s)
- Tyler A Brown
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
| | - Nobuo Tsurusaki
- Laboratory of Biodiversity and Taxonomy, Department of Agricultural, Life, and Environmental Sciences, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Mercedes Burns
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
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22
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Nazari S, Pourkazmi M. Isolation and characterization of SNP markers of rainbow trout (Onchorhynchus mykiss Walbaum, 1792) from transcriptomic sequences. Mol Biol Rep 2021; 48:989-995. [PMID: 33393004 DOI: 10.1007/s11033-020-06088-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/12/2020] [Indexed: 11/30/2022]
Abstract
Rainbow trout (Onchorhynchus mykiss) is one of the most important freshwater aquaculture fish in Iran. It is necessary to develop available molecular marker such as SNPs, which represent a useful tool in detecting adaptive signals in populations and also parentage assignment for O. mykiss. Genetic architecture of broodstock populations is important for breeding programs, as it enables decisions on broodstock screening and genomic selection. In this study, 52 novel single nucleotide polymorphism (SNP) markers for O. mykiss were discovered and validated based on transcriptome sequencing, by means of paired-end sequencing in an Illumina HiSeq 2500 platform. The SNPs were identified through liver transcriptome sequencing from fifteen samples. The observed and expected heterozygosities ranged from 0.177 to 1.000 and 0.239 to 0.638, respectively. The minimum allele frequency (MAF) ranged from 0.166 to 0.489. Among these SNP loci, twenty-two loci showed significant departures from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.05) and significant linkage disequilibrium was found. The SNP markers identified in this research could be useful for novel studies, such as those related to associations between high-resolution molecular markers and quantitative traits studies. Moreover, these SNP markers would be used in genetic studies helping economic performance improvement and management of this species.
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Affiliation(s)
- Sajad Nazari
- Shahid Motahary Cold-Water Fishes Genetic and Breeding Research Center, Iranian Fisheries Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Yasouj, Iran.
| | - Mohammad Pourkazmi
- Iranian Fisheries Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Teharn, Iran
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23
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Magliolo M, Prost S, Orozco-terWengel P, Burger P, Kropff AS, Kotze A, Grobler JP, Dalton DL. Unlocking the potential of a validated single nucleotide polymorphism array for genomic monitoring of trade in cheetahs (Acinonyx jubatus). Mol Biol Rep 2020; 48:171-181. [PMID: 33275194 DOI: 10.1007/s11033-020-06030-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 11/24/2020] [Indexed: 10/22/2022]
Abstract
Cheetahs (Acinonyx jubatus) are listed as vulnerable on the International Union for Conservation of Nature Red List of Threatened Species. Threats include loss of habitat, human-wildlife conflict and illegal wildlife trade. In South Africa, the export of wild cheetah is a restricted activity under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), however, limited legal trade is permitted of animals born to captive parents. To effectively monitor the legal and illegal trade in South Africa, it was thus essential to develop a validated molecular test. Here, we designed a single nucleotide polymorphism (SNP) array for cheetah from Double Digest Restriction Associated DNA sequencing data for individual identification and parentage testing. In order to validate the array, unrelated individuals and 16 family groups consisting of both parents and one to three offspring were genotyped using the Applied Biosystems™ QuantStudio™ 12K Flex Real-Time PCR System. In addition, parentage assignments were compared to microsatellite data. Cross-species amplification was tested in various felids and cheetah sub-species in order to determine the utility of the SNP array in other species. We obtained successful genotyping results for 218 SNPs in cheetah (A. j. jubatus) with an optimal DNA input concentration ranging from 10 to 30 ng/µl. The combination of SNPs had a higher resolving power for individual identification compared to microsatellites and provided high assignment accuracy in known pedigrees. Cross-species amplification in other felids was determined to be limited. However, the SNP array demonstrated a clear genetic discrimination of two cheetah subspecies tested here. We conclude that the described SNP array is suitable for accurate parentage assignment and provides an important traceability tool for forensic investigations of cheetah trade.
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Affiliation(s)
- Michelle Magliolo
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa.,Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Stefan Prost
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa.,LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Nature Research Society, Frankfurt, Germany
| | | | - Pamela Burger
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria
| | - Anna S Kropff
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
| | - Antoinette Kotze
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa.,Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Desire Lee Dalton
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa. .,Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa.
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24
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Maffey L, Garzón MJ, Confalonieri V, Chanampa MM, Hasson E, Schweigmann N. Genome-Wide Screening of Aedes aegypti (Culicidae: Diptera) Populations From Northwestern Argentina: Active and Passive Dispersal Shape Genetic Structure. JOURNAL OF MEDICAL ENTOMOLOGY 2020; 57:1930-1941. [PMID: 32692366 DOI: 10.1093/jme/tjaa125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 06/11/2023]
Abstract
Aedes aegypti is the primary vector of arboviruses of great impact on human health. Our goal was to assess the spatial genetic structure of Ae. aegypti at the regional and local levels in Northwestern Argentina, an area with high prevalence of dengue fever. We analyzed 59 Ae. aegypti individuals collected from six locations in Northwestern Argentina using nuclear genome-wide Single Nucleotide Polymorphisms (SNPs) generated with double digest Restriction-site Associated DNA Sequencing. We also performed an entomological survey in 70 households in the cities of Orán and Tartagal. An analysis at the regional level indicated that the populations of Ae. aegypti in Northwestern Argentina are spatially structured and present a significant IBD pattern. Our results suggest that passive transport of eggs/immature stages, in both northward and southward directions, plays an important role in structuring Ae. aegypti populations at a regional scale and also as a source for the introduction of novel genetic variants through migration events into established populations. At a local level, we found neither spatial genetic structure nor significant isolation by distance (IBD) in Tartagal, indicating high gene flow within the city and active dispersal. In contrast, samples from Orán formed two clusters with a significant IBD pattern, although weaker than that at a regional level. Both populations showed signs of recent bottleneck events, probably coincident with past eradication campaigns. The entomological survey revealed a high prevalence of Ae. aegypti in both cities, although significantly higher in Tartagal.
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Affiliation(s)
- Lucía Maffey
- Grupo de Estudio de Mosquitos, Departamento de Ecología, Genética y Evolución (DEGE-UBA) / Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA-CONICET), Buenos Aires, Argentina
| | - Maximiliano J Garzón
- Grupo de Estudio de Mosquitos, Departamento de Ecología, Genética y Evolución (DEGE-UBA) / Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA-CONICET), Buenos Aires, Argentina
| | - Viviana Confalonieri
- Grupo de Investigación en Filogenias y Filogeografía, Departamento de Ecología, Genética y Evolución (DEGE-UBA) / Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA-CONICET), Buenos Aires, Argentina
| | - Mariana M Chanampa
- Instituto de Investigación en Energía No Convencional (INENCO/CONICET Unidad Salud y ambiente), Salta, Argentina
| | - Esteban Hasson
- Laboratorio de Evolución, Departamento de Ecología, Genética y Evolución (DEGE-UBA) / Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA-CONICET), Buenos Aires, Argentina
| | - Nicolás Schweigmann
- Grupo de Estudio de Mosquitos, Departamento de Ecología, Genética y Evolución (DEGE-UBA) / Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA-CONICET), Buenos Aires, Argentina
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25
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Pepping MY, O’Rourke SM, Huang C, Katz JVE, Jeffres C, Miller MR. Rapture facilitates inexpensive and high-throughput parent-based tagging in salmonids. PLoS One 2020; 15:e0239221. [PMID: 33175847 PMCID: PMC7657533 DOI: 10.1371/journal.pone.0239221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/01/2020] [Indexed: 11/30/2022] Open
Abstract
Accurate methods for tracking individuals are crucial to the success of fisheries and aquaculture management. Management of migratory salmonid populations, which are important for the health of many economies, ecosystems, and indigenous cultures, is particularly dependent on data gathered from tagged fish. However, the physical tagging methods currently used have many challenges including cost, variable marker retention, and information limited to tagged individuals. Genetic tracking methods combat many of the problems associated with physical tags, but have their own challenges including high cost, potentially difficult marker design, and incompatibility of markers across species. Here we show the feasibility of a new genotyping method for parent-based tagging (PBT), where individuals are tracked through the inherent genetic relationships with their parents. We found that Rapture sequencing, a combination of restriction-site associated DNA and capture sequencing, provides sufficient data for parentage assignment. Additionally, the same capture bait set, which targets specific restriction-site associated DNA loci, can be used for both Rainbow Trout Oncorhynchus mykiss and Chinook Salmon Oncorhynchus tshawytscha. We input 248 single nucleotide polymorphisms from 1,121 samples to parentage assignment software and compared parent-offspring relationships of the spawning pairs recorded in a hatchery. Interestingly, our results suggest sperm contamination during hatchery spawning occurred in the production of 14% of offspring, further confirming the need for genetic tagging in accurately tracking individuals. PBT with Rapture successfully assigned progeny to parents with a 98.86% accuracy with sufficient genetic data. Cost for this pilot study was approximately $3 USD per sample. As costs vary based on the number of markers used and individuals sequenced, we expect that when implemented at a large-scale, per sample costs could be further decreased. We conclude that Rapture PBT provides a cost-effective and accurate alternative to the physical coded wire tags, and other genetic-based methods.
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Affiliation(s)
- Michelle Y. Pepping
- Department of Animal Science, University of California, Davis, California, United States of America
- Center for Watershed Sciences, University of California, Davis, California, United States of America
| | - Sean M. O’Rourke
- Department of Animal Science, University of California, Davis, California, United States of America
| | - Connie Huang
- Department of Animal Science, University of California, Davis, California, United States of America
| | - Jacob V. E. Katz
- California Trout, San Francisco, California, United States of America
| | - Carson Jeffres
- Center for Watershed Sciences, University of California, Davis, California, United States of America
| | - Michael R. Miller
- Department of Animal Science, University of California, Davis, California, United States of America
- Center for Watershed Sciences, University of California, Davis, California, United States of America
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26
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May SA, McKinney GJ, Hilborn R, Hauser L, Naish KA. Power of a dual-use SNP panel for pedigree reconstruction and population assignment. Ecol Evol 2020; 10:9522-9531. [PMID: 32953080 PMCID: PMC7487233 DOI: 10.1002/ece3.6645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 11/28/2022] Open
Abstract
The use of high-throughput, low-density sequencing approaches has dramatically increased in recent years in studies of eco-evolutionary processes in wild populations and domestication in commercial aquaculture. Most of these studies focus on identifying panels of SNP loci for a single downstream application, whereas there have been few studies examining the trade-offs for selecting panels of markers for use in multiple applications. Here, we detail the use of a bioinformatic workflow for the development of a dual-purpose SNP panel for parentage and population assignment, which included identifying putative SNP loci, filtering for the most informative loci for the two tasks, designing effective multiplex PCR primers, optimizing the SNP panel for performance, and performing quality control steps for downstream applications. We applied this workflow to two adjacent Alaskan Sockeye Salmon populations and identified a GTseq panel of 142 SNP loci for parentage and 35 SNP loci for population assignment. Only 50-75 panel loci were necessary for >95% accurate parentage, whereas population assignment success, with all 172 panel loci, ranged from 93.9% to 96.2%. Finally, we discuss the trade-offs and complexities of the decision-making process that drives SNP panel development, optimization, and testing.
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Affiliation(s)
- Samuel A. May
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - Garrett J. McKinney
- NRC Research Associateship ProgramNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Ray Hilborn
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - Lorenz Hauser
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - Kerry A. Naish
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
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Zimmerman SJ, Aldridge CL, Oyler-McCance SJ. An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern. BMC Genomics 2020; 21:382. [PMID: 32487020 PMCID: PMC7268520 DOI: 10.1186/s12864-020-06783-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/14/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Use of genomic tools to characterize wildlife populations has increased in recent years. In the past, genetic characterization has been accomplished with more traditional genetic tools (e.g., microsatellites). The explosion of genomic methods and the subsequent creation of large SNP datasets has led to the promise of increased precision in population genetic parameter estimates and identification of demographically and evolutionarily independent groups, as well as questions about the future usefulness of the more traditional genetic tools. At present, few empirical comparisons of population genetic parameters and clustering analyses performed with microsatellites and SNPs have been conducted. RESULTS Here we used microsatellite and SNP data generated from Gunnison sage-grouse (Centrocercus minimus) samples to evaluate concordance of the results obtained from each dataset for common metrics of genetic diversity (HO, HE, FIS, AR) and differentiation (FST, GST, DJost). Additionally, we evaluated clustering of individuals using putatively neutral (SNPs and microsatellites), putatively adaptive, and a combined dataset of putatively neutral and adaptive loci. We took particular interest in the conservation implications of any differences. Generally, we found high concordance between microsatellites and SNPs for HE, FIS, AR, and all differentiation estimates. Although there was strong correlation between metrics from SNPs and microsatellites, the magnitude of the diversity and differentiation metrics were quite different in some cases. Clustering analyses also showed similar patterns, though SNP data was able to cluster individuals into more distinct groups. Importantly, clustering analyses with SNP data suggest strong demographic independence among the six distinct populations of Gunnison sage-grouse with some indication of evolutionary independence in two or three populations; a finding that was not revealed by microsatellite data. CONCLUSION We demonstrate that SNPs have three main advantages over microsatellites: more precise estimates of population-level diversity, higher power to identify groups in clustering methods, and the ability to consider local adaptation. This study adds to a growing body of work comparing the use of SNPs and microsatellites to evaluate genetic diversity and differentiation for a species of conservation concern with relatively high population structure and using the most common method of obtaining SNP genotypes for non-model organisms.
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Affiliation(s)
- Shawna J Zimmerman
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Bldg. C, Fort Collins, CO, 80526, USA.
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, 80526, USA.
| | - Cameron L Aldridge
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Bldg. C, Fort Collins, CO, 80526, USA
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, 80526, USA
| | - Sara J Oyler-McCance
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Bldg. C, Fort Collins, CO, 80526, USA
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28
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Izumiyama M, Westphal MF, Crow KD. In the surf zone: Reproductive strategy of the calico surfperch (Amphistichus koelzi) in a comparative context. JOURNAL OF FISH BIOLOGY 2020; 96:939-949. [PMID: 32048298 DOI: 10.1111/jfb.14283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/08/2020] [Indexed: 06/10/2023]
Abstract
We examined the reproductive life history of calico surfperch (Amphistichus koelzi), including mating season, pregnancy, gestation and multiple paternity utilizing restriction site-associated DNA sequencing. Furthermore, we compared the mating season of calico with barred (Amphistichus argenteus), walleye (Hyperprosopon argenteum) and silver (Hyperprosopon ellipticum) surfperches to determine if the timing of reproduction is divergent within and between the genera. In calico surfperch, the mating season occurs from October to November, and females gestate from December to May. All broods exhibit multiple paternity with a range of four to seven sires per brood. The mating season of calico overlaps completely with barred surfperch; however, barred surfperches have a protracted mating season which extends until the beginning of December, which may be due to differences in reproductive strategy such as size at first reproduction. In the genus, the Hyperprosopon mating season begins earlier than Amphistichus, with divergence in the onset of mating between Hyperprosopon congeners of approximately 1 month.
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Affiliation(s)
- Michael Izumiyama
- Department of Biology, San Francisco State University, San Francisco, California, USA
| | - Michael F Westphal
- Bureau of Land Management, California Coastal National Monument, Marina, California, USA
| | - Karen D Crow
- Department of Biology, San Francisco State University, San Francisco, California, USA
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29
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Clendenin HR, Adams JR, Ausband DE, Hayden JA, Hohenlohe PA, Waits LP. Combining Harvest and Genetics to Estimate Reproduction in Wolves. J Wildl Manage 2020. [DOI: 10.1002/jwmg.21820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Heather R. Clendenin
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of Idaho 875 Perimeter Drive MS3051 Moscow ID 83844‐3051 USA
| | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences, Laboratory for Ecological, Evolutionary and Conservation GeneticsUniversity of Idaho 875 Perimeter Drive MS1136 Moscow ID 83844‐1136 USA
| | | | - James A. Hayden
- Idaho Department of Fish and Game, P.O. Box 25Boise ID 83814 USA
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of Idaho 875 Perimeter Drive MS3051 Moscow ID 83844‐3051 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of Idaho 875 Perimeter Drive MS1136 Moscow ID 83844‐1136 USA
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30
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Saint-Pé K, Leitwein M, Tissot L, Poulet N, Guinand B, Berrebi P, Marselli G, Lascaux JM, Gagnaire PA, Blanchet S. Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics. BMC Genomics 2019; 20:582. [PMID: 31307373 PMCID: PMC6631668 DOI: 10.1186/s12864-019-5958-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 07/04/2019] [Indexed: 01/04/2023] Open
Abstract
Background The brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. The most commonly used genetic markers for this species are microsatellites and mitochondrial markers that lack replicability among laboratories, and a large genome coverage. An alternative that may be particularly efficient and universal is the development of small to large panels of Single Nucleotide Polymorphism markers (SNPs). Here, we used Restriction site Associated DNA sequences (RADs) markers to identify a set of 12,204 informative SNPs positioned on the brown trout linkage map and suitable for population genetics studies. Then, we used this novel resource to develop a cost-effective array of 192 SNPs (96 × 2) evenly spread on this map. This array was tested for genotyping success in five independent rivers occupied by two main brown trout evolutionary lineages (Atlantic -AT- and Mediterranean -ME-) on a total of 1862 individuals. Moreover, inference of admixture rate with domestic strains and population differentiation were assessed for a small river system (the Taurion River, 190 individuals) and results were compared to a panel of 13 microsatellites. Results A high genotyping success was observed for all rivers (< 1% of non-genotyped loci per individual), although some initially used SNP failed to be amplified, probably because of mutations in primers, and were replaced. These SNPs permitted to identify patterns of isolation-by-distance for some rivers. Finally, we found that microsatellite and SNP markers yielded very similar patterns for population differentiation and admixture assessments, with SNPs having better ability to detect introgression and differentiation. Conclusions The novel resources provided here opens new perspectives for universality and genome-wide studies in brown trout populations. Electronic supplementary material The online version of this article (10.1186/s12864-019-5958-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keoni Saint-Pé
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d'Ecologie Théorique et Expérimentale, SETE, UMR 5321, 2 route du CNRS, 09200, Moulis, France.
| | - Maeva Leitwein
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,ISEM, CNRS, Univ. Montpellier, IRD, EPHE, Montpellier, France
| | - Laurence Tissot
- EDF R and D LNHE - Laboratoire National d'Hydraulique et Environnement, 6 quai Watier, 78401, Chatou Cedex, France
| | - Nicolas Poulet
- Pôle écohydraulique AFB-IMT, allée du Pr Camille Soula, 31400, Toulouse, France
| | - Bruno Guinand
- ISEM, CNRS, Univ. Montpellier, IRD, EPHE, Montpellier, France
| | - Patrick Berrebi
- ISEM, CNRS, Univ. Montpellier, IRD, EPHE, Montpellier, France.,Present address: Genome - Research and Diagnostic, 697 avenue de Lunel, 34400, Saint-Just, France
| | - Geoffrey Marselli
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d'Ecologie Théorique et Expérimentale, SETE, UMR 5321, 2 route du CNRS, 09200, Moulis, France
| | | | | | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d'Ecologie Théorique et Expérimentale, SETE, UMR 5321, 2 route du CNRS, 09200, Moulis, France.,Université de Toulouse, UPS, UMR 5174 (EDB), 118 route de Narbonne, F-31062, Toulouse cedex 4, France
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31
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Jasper M, Schmidt TL, Ahmad NW, Sinkins SP, Hoffmann AA. A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito. Mol Ecol Resour 2019; 19:1254-1264. [PMID: 31125998 PMCID: PMC6790672 DOI: 10.1111/1755-0998.13043] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 12/21/2022]
Abstract
Understanding past dispersal and breeding events can provide insight into ecology and evolution and can help inform strategies for conservation and the control of pest species. However, parent-offspring dispersal can be difficult to investigate in rare species and in small pest species such as mosquitoes. Here, we develop a methodology for estimating parent-offspring dispersal from the spatial distribution of close kin, using pairwise kinship estimates derived from genome-wide single nucleotide polymorphisms (SNPs). SNPs were scored in 162 Aedes aegypti (yellow fever mosquito) collected from eight close-set, high-rise apartment buildings in an area of Malaysia with high dengue incidence. We used the SNPs to reconstruct kinship groups across three orders of kinship. We transformed the geographical distances between all kin pairs within each kinship category into axial standard deviations of these distances, then decomposed these into components representing past dispersal events. From these components, we isolated the axial standard deviation of parent-offspring dispersal and estimated neighbourhood area (129 m), median parent-offspring dispersal distance (75 m) and oviposition dispersal radius within a gonotrophic cycle (36 m). We also analysed genetic structure using distance-based redundancy analysis and linear regression, finding isolation by distance both within and between buildings and estimating neighbourhood size at 268 individuals. These findings indicate the scale required to suppress local outbreaks of arboviral disease and to target releases of modified mosquitoes for mosquito and disease control. Our methodology is readily implementable for studies of other species, including pests and species of conservation significance.
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Affiliation(s)
- Moshe Jasper
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Thomas L Schmidt
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Nazni W Ahmad
- Institute for Medical Research, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | | | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
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32
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Foroughirad V, Levengood AL, Mann J, Frère CH. Quality and quantity of genetic relatedness data affect the analysis of social structure. Mol Ecol Resour 2019; 19:1181-1194. [PMID: 31056823 DOI: 10.1111/1755-0998.13028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023]
Abstract
Kinship plays a fundamental role in the evolution of social systems and is considered a key driver of group living. To understand the role of kinship in the formation and maintenance of social bonds, accurate measures of genetic relatedness are critical. Genotype-by-sequencing technologies are rapidly advancing the accuracy and precision of genetic relatedness estimates for wild populations. The ability to assign kinship from genetic data varies depending on a species' or population's mating system and pattern of dispersal, and empirical data from longitudinal studies are crucial to validate these methods. We use data from a long-term behavioural study of a polygynandrous, bisexually philopatric marine mammal to measure accuracy and precision of parentage and genetic relatedness estimation against a known partial pedigree. We show that with moderate but obtainable sample sizes of approximately 4,235 SNPs and 272 individuals, highly accurate parentage assignments and genetic relatedness coefficients can be obtained. Additionally, we subsample our data to quantify how data availability affects relatedness estimation and kinship assignment. Lastly, we conduct a social network analysis to investigate the extent to which accuracy and precision of relatedness estimation improve statistical power to detect an effect of relatedness on social structure. Our results provide practical guidance for minimum sample sizes and sequencing depth for future studies, as well as thresholds for post hoc interpretation of previous analyses.
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Affiliation(s)
- Vivienne Foroughirad
- Division of Marine Science and Conservation, Duke University Marine Laboratory, Beaufort, North Carolina
| | - Alexis L Levengood
- Global Change Ecology Research Group, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Janet Mann
- Departments of Biology and Psychology, Georgetown University, Washington, District of Columbia
| | - Céline H Frère
- Global Change Ecology Research Group, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
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Development and characterization of polymorphic microsatellite markers in northern fulmar, Fulmarus glacialis (Procellariiformes), and cross-species amplification in eight other seabirds. Genes Genomics 2019; 41:1015-1026. [PMID: 31134591 DOI: 10.1007/s13258-019-00819-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 04/11/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND In the North Pacific, northern fulmar (Fulmarus glacialis) forms extensive colonies in few locales, which may lead to limited gene flow and locale-specific population threats. In the Atlantic, there are thousands of colonies of varying sizes and in Europe the species is considered threatened. Prior screens and classical microsatellite development in fulmar failed to provide a suite of markers adequate for population genetics studies. OBJECTIVES The objective of this study was to isolate a suite of polymorphic microsatellite loci with sufficient variability to quantify levels of gene flow, population affinity, and identify familial relationships in fulmar. We also performed a cross-species screening of these markers in eight other species. METHODS We used shotgun sequencing to isolate 26 novel microsatellite markers in fulmar to screen for variability using individuals from two distinct regions: the Pacific (Chagulak Island, Alaska) and the Atlantic (Hafnarey Island, Iceland). RESULTS Polymorphism was present in 24 loci in Chagulak and 23 in Hafnarey, while one locus failed to amplify in either colony. Polymorphic loci exhibited moderate levels of genetic diversity and this suite of loci uncovered genetic structuring between the regions. Among the other species screened, polymorphism was present in one to seven loci. CONCLUSION The loci yielded sufficient variability for use in population studies and estimation of familial relationships; as few as five loci provide resolution to determine individual identity. These markers will allow further insight into the global population dynamics and phylogeography of fulmars. We also demonstrated some markers are transferable to other species.
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34
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O’Brien DM, Keogh JS, Silla AJ, Byrne PG. Female choice for related males in wild red-backed toadlets (Pseudophryne coriacea). Behav Ecol 2019. [DOI: 10.1093/beheco/arz031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
AbstractMate choice for genetic benefits is assumed to be widespread in nature, yet very few studies have comprehensively examined relationships between female mate choice and male genetic quality in wild populations. Here, we use exhaustive sampling and single nucleotide polymorphisms to provide a partial test of the “good genes as heterozygosity” hypothesis and the “genetic compatibility” hypothesis in an entire population of terrestrial breeding red-backed toadlets, Pseudophryne coriacea. We found that successful males did not display higher heterozygosity, despite a positive relationship between male heterozygosity and offspring heterozygosity. Rather, in the larger of 2 breeding events, we found that successful males were more genetically similar to their mate than expected under random mating, indicating that females can use pre- or post-copulatory mate choice mechanisms to bias paternity toward more related males. These findings provide no support for the good genes as heterozygosity hypothesis but lend support to the genetic compatibility hypothesis. A complete test of this hypothesis will now require evaluating how parental genetic similarity impacts offspring fitness. Terrestrial toadlets show a high degree of site fidelity, high levels of genetic structuring between populations, and frequently hybridize with sister species. As such, female mate choice for related males may be an adaptive strategy to reduce outbreeding depression. Our findings provide the first population-wide evidence for non-random preferential inbreeding in a wild amphibian. We argue that such reproductive patterns may be common in amphibians because extreme genetic differentiation within meta-populations creates an inherently high risk of outbreeding depression.
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Affiliation(s)
- Daniel M O’Brien
- School of Earth, Atmospheric and Lifesciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - J Scott Keogh
- Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - Aimee J Silla
- School of Earth, Atmospheric and Lifesciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Phillip G Byrne
- School of Earth, Atmospheric and Lifesciences, University of Wollongong, Wollongong, New South Wales, Australia
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35
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Flanagan SP, Jones AG. The future of parentage analysis: From microsatellites to SNPs and beyond. Mol Ecol 2019; 28:544-567. [PMID: 30575167 DOI: 10.1111/mec.14988] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/14/2022]
Abstract
Parentage analysis is a cornerstone of molecular ecology that has delivered fundamental insights into behaviour, ecology and evolution. Microsatellite markers have long been the king of parentage, their hypervariable nature conferring sufficient power to correctly assign offspring to parents. However, microsatellite markers have seen a sharp decline in use with the rise of next-generation sequencing technologies, especially in the study of population genetics and local adaptation. The time is ripe to review the current state of parentage analysis and see how it stands to be affected by the emergence of next-generation sequencing approaches. We find that single nucleotide polymorphisms (SNPs), the typical next-generation sequencing marker, remain underutilized in parentage analysis but are gaining momentum, with 58 SNP-based parentage analyses published thus far. Many of these papers, particularly the earlier ones, compare the power of SNPs and microsatellites in a parentage context. In virtually every case, SNPs are at least as powerful as microsatellite markers. As few as 100-500 SNPs are sufficient to resolve parentage completely in most situations. We also provide an overview of the analytical programs that are commonly used and compatible with SNP data. As the next-generation parentage enterprise grows, a reliance on likelihood and Bayesian approaches, as opposed to strict exclusion, will become increasingly important. We discuss some of the caveats surrounding the use of next-generation sequencing data for parentage analysis and conclude that the future is bright for this important realm of molecular ecology.
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Affiliation(s)
- Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, Idaho
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36
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Lemopoulos A, Prokkola JM, Uusi‐Heikkilä S, Vasemägi A, Huusko A, Hyvärinen P, Koljonen M, Koskiniemi J, Vainikka A. Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation. Ecol Evol 2019; 9:2106-2120. [PMID: 30847096 PMCID: PMC6392366 DOI: 10.1002/ece3.4905] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/30/2018] [Accepted: 12/21/2018] [Indexed: 12/24/2022] Open
Abstract
The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.
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Affiliation(s)
- Alexandre Lemopoulos
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Department of BiologyUniversity of TurkuTurkuFinland
| | - Jenni M. Prokkola
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Silva Uusi‐Heikkilä
- Department of BiologyUniversity of TurkuTurkuFinland
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Anti Vasemägi
- Department of BiologyUniversity of TurkuTurkuFinland
- Department of Aquatic Resources, Institute of Freshwater ResearchSwedish University of Agricultural SciencesDrottningholmSweden
- Estonian University of Life SciencesInstitute of Veterinary Medicine and Animal SciencesTartuEstonia
| | - Ari Huusko
- Natural Resources Institute Finland (Luke), Kainuu Fisheries Research StationPaltamoFinland
| | - Pekka Hyvärinen
- Natural Resources Institute Finland (Luke), Kainuu Fisheries Research StationPaltamoFinland
| | | | - Jarmo Koskiniemi
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Anssi Vainikka
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
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Wang J. Pedigree reconstruction from poor quality genotype data. Heredity (Edinb) 2019; 122:719-728. [PMID: 30631146 PMCID: PMC6781133 DOI: 10.1038/s41437-018-0178-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 11/09/2022] Open
Abstract
Marker genotype data could suffer from a high rate of errors such as false alleles and allelic dropouts (null alleles) in situations such as SNPs from low-coverage next-generation sequencing and microsatellites from noninvasive samples. Use of such data without accounting for mistyping properly could lead to inaccurate or incorrect inferences of family relationships such as parentage and sibship. This study shows that markers with a high error rate are still informative. Simply discarding them could cause a substantial loss of precious information, and is impractical in situations where virtually all markers (e.g. SNPs from low-coverage next-generation sequencing, microsatellites from noninvasive samples) suffer from a similarly high error rate. This study also shows that some previous error models are valid for markers of low error rates, but fail for markers of high error rates. It proposes an improved error model and demonstrates, using simulated and empirical data of a high error rate (say, >0.5), that it leads to more accurate sibship and parentage inferences than previous models. It suggests that, in reality, markers of high error rates should be used rather than discarded in pedigree reconstruction, so long as the error rates can be estimated and used properly in the analyses.
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Affiliation(s)
- Jinliang Wang
- Institute of Zoology, Zoological Society of London, London, NW1 4RY, UK.
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38
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Lopez JV, Kamel B, Medina M, Collins T, Baums IB. Multiple Facets of Marine Invertebrate Conservation Genomics. Annu Rev Anim Biosci 2018; 7:473-497. [PMID: 30485758 DOI: 10.1146/annurev-animal-020518-115034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Conservation genomics aims to preserve the viability of populations and the biodiversity of living organisms. Invertebrate organisms represent 95% of animal biodiversity; however, few genomic resources currently exist for the group. The subset of marine invertebrates includes the most ancient metazoan lineages and possesses codes for unique gene products and possible keys to adaptation. The benefits of supporting invertebrate conservation genomics research (e.g., likely discovery of novel genes, protein regulatory mechanisms, genomic innovations, and transposable elements) outweigh the various hurdles (rare, small, or polymorphic starting materials). Here we review best conservation genomics practices in the laboratory and in silico when applied to marine invertebrates and also showcase unique features in several case studies of acroporid corals, crown-of-thorns starfish, apple snails, and abalone. Marine conservation genomics should also address how diversity can lead to unique marine innovations, the impact of deleterious variation, and how genomic monitoring and profiling could positively affect broader conservation goals (e.g., value of baseline data for in situ/ex situ genomic stocks).
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Affiliation(s)
- Jose V Lopez
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida 33004, USA;
| | - Bishoy Kamel
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, New Mexico 87131, USA;
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
| | - Timothy Collins
- Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA;
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
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39
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Andrews KR, Adams JR, Cassirer EF, Plowright RK, Gardner C, Dwire M, Hohenlohe PA, Waits LP. A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data. Mol Ecol Resour 2018; 18:1263-1281. [PMID: 29870119 PMCID: PMC6207459 DOI: 10.1111/1755-0998.12910] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 11/30/2022]
Abstract
The development of high-throughput sequencing technologies is dramatically increasing the use of single nucleotide polymorphisms (SNPs) across the field of genetics, but most parentage studies of wild populations still rely on microsatellites. We developed a bioinformatic pipeline for identifying SNP panels that are informative for parentage analysis from restriction site-associated DNA sequencing (RADseq) data. This pipeline includes options for analysis with or without a reference genome, and provides methods to maximize genotyping accuracy and select sets of unlinked loci that have high statistical power. We test this pipeline on small populations of Mexican gray wolf and bighorn sheep, for which parentage analyses are expected to be challenging due to low genetic diversity and the presence of many closely related individuals. We compare the results of parentage analysis across SNP panels generated with or without the use of a reference genome, and between SNPs and microsatellites. For Mexican gray wolf, we conducted parentage analyses for 30 pups from a single cohort where samples were available from 64% of possible mothers and 53% of possible fathers, and the accuracy of parentage assignments could be estimated because true identities of parents were known a priori based on field data. For bighorn sheep, we conducted maternity analyses for 39 lambs from five cohorts where 77% of possible mothers were sampled, but true identities of parents were unknown. Analyses with and without a reference genome produced SNP panels with ≥95% parentage assignment accuracy for Mexican gray wolf, outperforming microsatellites at 78% accuracy. Maternity assignments were completely consistent across all SNP panels for the bighorn sheep, and were 74.4% consistent with assignments from microsatellites. Accuracy and consistency of parentage analysis were not reduced when using as few as 284 SNPs for Mexican gray wolf and 142 SNPs for bighorn sheep, indicating our pipeline can be used to develop SNP genotyping assays for parentage analysis with relatively small numbers of loci.
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Affiliation(s)
- Kimberly R. Andrews
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844, USA
- Current address: Genetics and Genomics Group, University of Washington JISAO and NOAA Pacific Marine Environmental Lab, Seattle, WA 98115, USA
| | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844, USA
| | - E. Frances Cassirer
- Idaho Department of Fish and Game, 3316 16th Street, Lewiston, ID 83501, USA
| | - Raina K. Plowright
- Department of Microbiology and Immunology, Montana State University, 109 Lewis Hall, Bozeman, MT 59717, USA
| | - Colby Gardner
- U.S. Fish and Wildlife Service, 2105 Osuna Road NE, Albuquerque, NM 87113, USA
| | - Maggie Dwire
- U.S. Fish and Wildlife Service, 2105 Osuna Road NE, Albuquerque, NM 87113, USA
| | - Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844, USA
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40
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Sylvester EVA, Beiko RG, Bentzen P, Paterson I, Horne JB, Watson B, Lehnert S, Duffy S, Clément M, Robertson MJ, Bradbury IR. Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America. Mol Ecol 2018; 27:4026-4040. [PMID: 30152128 DOI: 10.1111/mec.14849] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 08/16/2018] [Accepted: 08/22/2018] [Indexed: 12/18/2022]
Abstract
Conservation of exploited species requires an understanding of both genetic diversity and the dominant structuring forces, particularly near range limits, where climatic variation can drive rapid expansions or contractions of geographic range. Here, we examine population structure and landscape associations in Atlantic salmon (Salmo salar) across a heterogeneous landscape near the northern range limit in Labrador, Canada. Analysis of two amplicon-based data sets containing 101 microsatellites and 376 single nucleotide polymorphisms (SNPs) from 35 locations revealed clear differentiation between populations spawning in rivers flowing into a large marine embayment (Lake Melville) compared to coastal populations. The mechanisms influencing the differentiation of embayment populations were investigated using both multivariate and machine-learning landscape genetic approaches. We identified temperature as the strongest correlate with genetic structure, particularly warm temperature extremes and wider annual temperature ranges. The genomic basis of this divergence was further explored using a subset of locations (n = 17) and a 220K SNP array. SNPs associated with spatial structuring and temperature mapped to a diverse set of genes and molecular pathways, including regulation of gene expression, immune response, and cell development and differentiation. The results spanning molecular marker types and both novel and established methods clearly show climate-associated, fine-scale population structure across an environmental gradient in Atlantic salmon near its range limit in North America, highlighting valuable approaches for predicting population responses to climate change and managing species sustainability.
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Affiliation(s)
- Emma V A Sylvester
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - Paul Bentzen
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Ian Paterson
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - John B Horne
- University of Southern Mississippi Gulf Coast Research Laboratory, Ocean Springs, MS, Canada
| | - Beth Watson
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Sarah Lehnert
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada
| | - Steven Duffy
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute, Memorial University of Newfoundland, St. John's, NL, Canada.,Labrador Institute, Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Martha J Robertson
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada
| | - Ian R Bradbury
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada.,Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada.,Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, NS, Canada
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41
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Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang J. Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl 2018; 11:1094-1119. [PMID: 30026800 PMCID: PMC6050181 DOI: 10.1111/eva.12600] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/02/2018] [Indexed: 12/12/2022] Open
Abstract
The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.
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Affiliation(s)
- Emma L. Carroll
- Scottish Oceans Institute and Sea Mammal Research UnitUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places Research InstituteCardiff UniversityCardiff, WalesUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Gregoire Leroy
- Animal Production and Health DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Alan Strand
- Grice Marine LaboratoryDepartment of BiologyCollege of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
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42
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Förster DW, Bull JK, Lenz D, Autenrieth M, Paijmans JLA, Kraus RHS, Nowak C, Bayerl H, Kuehn R, Saveljev AP, Sindičić M, Hofreiter M, Schmidt K, Fickel J. Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species. Mol Ecol Resour 2018; 18:1356-1373. [PMID: 29978939 DOI: 10.1111/1755-0998.12924] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/28/2018] [Accepted: 06/05/2018] [Indexed: 11/29/2022]
Abstract
Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species' European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.
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Affiliation(s)
- Daniel W Förster
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - James K Bull
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Dorina Lenz
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Marijke Autenrieth
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Robert H S Kraus
- Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Radolfzell, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Helmut Bayerl
- Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technical University of Munich, Freising, Germany
| | - Ralph Kuehn
- Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technical University of Munich, Freising, Germany.,Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, New Mexico
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia
| | - Magda Sindičić
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Krzysztof Schmidt
- Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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43
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Ramírez‐Valiente JA, Deacon NJ, Etterson J, Center A, Sparks JP, Sparks KL, Longwell T, Pilz G, Cavender‐Bares J. Natural selection and neutral evolutionary processes contribute to genetic divergence in leaf traits across a precipitation gradient in the tropical oak
Quercus oleoides. Mol Ecol 2018; 27:2176-2192. [DOI: 10.1111/mec.14566] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/02/2018] [Accepted: 03/12/2018] [Indexed: 01/20/2023]
Affiliation(s)
| | - Nicholas J. Deacon
- Department of Ecology, Evolution and Behavior University of Minnesota Saint Paul MN USA
| | - Julie Etterson
- Department of Biology University of Minnesota Duluth Duluth MN USA
| | - Alyson Center
- Department of Ecology, Evolution and Behavior University of Minnesota Saint Paul MN USA
- Department of Biology Normandale Community College Bloomington MN USA
| | - Jed P. Sparks
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| | - Kimberlee L. Sparks
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| | | | - George Pilz
- Herbarium Paul C. Standley Escuela Agricola Panamericana Tegucigalpa Honduras
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44
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Ford MJ, Parsons KM, Ward EJ, Hempelmann JA, Emmons CK, Bradley Hanson M, Balcomb KC, Park LK. Inbreeding in an endangered killer whale population. Anim Conserv 2018. [DOI: 10.1111/acv.12413] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- M. J. Ford
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
| | - K. M. Parsons
- North Gulf Oceanic Society, under contract to Marine Mammal Laboratory; Alaska Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
| | - E. J. Ward
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
| | - J. A. Hempelmann
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
| | - C. K. Emmons
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
| | - M. Bradley Hanson
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
| | | | - L. K. Park
- Conservation Biology Division; Northwest Fisheries Science Center; National Marine Fisheries Service; NOAA; Seattle WA USA
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45
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Giangregorio P, Norman AJ, Davoli F, Spong G. Testing a new SNP-chip on the Alpine and Apennine brown bear (Ursus arctos) populations using non-invasive samples. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-1017-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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46
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Puncher GN, Cariani A, Maes GE, Van Houdt J, Herten K, Cannas R, Rodriguez-Ezpeleta N, Albaina A, Estonba A, Lutcavage M, Hanke A, Rooker J, Franks JS, Quattro JM, Basilone G, Fraile I, Laconcha U, Goñi N, Kimoto A, Macías D, Alemany F, Deguara S, Zgozi SW, Garibaldi F, Oray IK, Karakulak FS, Abid N, Santos MN, Addis P, Arrizabalaga H, Tinti F. Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next-generation sequencing. Mol Ecol Resour 2018; 18:620-638. [PMID: 29405659 DOI: 10.1111/1755-0998.12764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/06/2018] [Accepted: 01/19/2018] [Indexed: 01/05/2023]
Abstract
The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species' stock dynamics, a genomewide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 SNPs was ultimately developed by selecting loci with the most pronounced differences between western Atlantic and Mediterranean Sea LYOY. The panel was evaluated by genotyping a different set of LYOY (n = 326), and from these, 77.8% and 82.1% were correctly assigned to western Atlantic and Mediterranean Sea origins, respectively. The panel revealed temporally persistent differentiation among LYOY from the western Atlantic and Mediterranean Sea (FST = 0.008, p = .034). The composition of six mixed feeding aggregations in the Atlantic Ocean and Mediterranean Sea was characterized using genotypes from medium (n = 184) and large (n = 48) adults, applying population assignment and mixture analyses. The results provide evidence of persistent population structuring across broad geographic areas and extensive mixing in the Atlantic Ocean, particularly in the mid-Atlantic Bight and Gulf of St. Lawrence. The genomic reference and genotyping tools presented here constitute novel resources useful for future research and conservation efforts.
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Affiliation(s)
- Gregory N Puncher
- Department of Biological, Geological and Environmental Sciences/Laboratory of Genetics and Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy.,Department of Biology, Marine Biology Research Group, Ghent University, Ghent, Belgium.,Department of Biology, University of New Brunswick, Saint John, NB, Canada
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences/Laboratory of Genetics and Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy
| | - Gregory E Maes
- Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Centre for Human Genetics, Genomics Core, KU Leuven - UZ Leuven, Leuven, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven (KU Leuven), Leuven, Belgium
| | - Jeroen Van Houdt
- Centre for Human Genetics, Genomics Core, KU Leuven - UZ Leuven, Leuven, Belgium
| | - Koen Herten
- Centre for Human Genetics, Genomics Core, KU Leuven - UZ Leuven, Leuven, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven (KU Leuven), Leuven, Belgium
| | - Rita Cannas
- Department of Life & Environmental Sciences (DISVA), University of Cagliari, Cagliari, Italy
| | | | - Aitor Albaina
- Laboratory of Genetics Faculty of Science & Technology, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.,Environmental Studies Centre (CEA), Vitoria-Gasteiz City Council, Vitoria-Gasteiz, Spain
| | - Andone Estonba
- Laboratory of Genetics Faculty of Science & Technology, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Molly Lutcavage
- School for the Environment and Large Pelagics Research Center, University of Massachusetts, Boston, Gloucester, MA, USA
| | - Alex Hanke
- Fisheries and Oceans Canada, St. Andrews Biological Station, St. Andrews, NB, Canada
| | - Jay Rooker
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, USA.,Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - James S Franks
- Gulf Coast Research Laboratory, Center for Fisheries Research and Development, University of Southern Mississippi, Ocean Springs, MS, USA
| | - Joseph M Quattro
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Gualtiero Basilone
- National Research Council, Institute for Marine and Coastal Environment, Detached Unit of Capo Granitola, Trapani, Italy
| | - Igaratza Fraile
- Marine Research Division, AZTI Tecnalia, Pasaia, Gipuzkoa, Spain
| | - Urtzi Laconcha
- Marine Research Division, AZTI Tecnalia, Pasaia, Gipuzkoa, Spain.,Laboratory of Genetics Faculty of Science & Technology, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Nicolas Goñi
- Marine Research Division, AZTI Tecnalia, Pasaia, Gipuzkoa, Spain
| | - Ai Kimoto
- National Research Institute of Far Seas Fisheries, Shizuoka, Japan
| | - David Macías
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
| | - Francisco Alemany
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
| | - Simeon Deguara
- Federation of Maltese Aquaculture Producers (FMAP), Valletta, Malta
| | - Salem W Zgozi
- Marine Biology Research Center, Tripoli-Tajura, Libya
| | - Fulvio Garibaldi
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genova, Italy
| | - Isik K Oray
- Faculty of Fisheries, Istanbul University, Laleli-Istanbul, Turkey
| | | | - Noureddine Abid
- National Institute of Fisheries Research, Regional Centre of Tangier, Tanger, Morocco
| | | | - Piero Addis
- Department of Life & Environmental Sciences (DISVA), University of Cagliari, Cagliari, Italy
| | | | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences/Laboratory of Genetics and Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy
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47
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Thrasher DJ, Butcher BG, Campagna L, Webster MS, Lovette IJ. Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: A proof of concept in a highly promiscuous bird. Mol Ecol Resour 2018; 18:953-965. [PMID: 29455472 DOI: 10.1111/1755-0998.12771] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 01/31/2018] [Accepted: 02/04/2018] [Indexed: 12/17/2022]
Abstract
Information on genetic relationships among individuals is essential to many studies of the behaviour and ecology of wild organisms. Parentage and relatedness assays based on large numbers of single nucleotide polymorphism (SNP) loci hold substantial advantages over the microsatellite markers traditionally used for these purposes. We present a double-digest restriction site-associated DNA sequencing (ddRAD-seq) analysis pipeline that, as such, simultaneously achieves the SNP discovery and genotyping steps and which is optimized to return a statistically powerful set of SNP markers (typically 150-600 after stringent filtering) from large numbers of individuals (up to 240 per run). We explore the trade-offs inherent in this approach through a set of experiments in a species with a complex social system, the variegated fairy-wren (Malurus lamberti) and further validate it in a phylogenetically broad set of other bird species. Through direct comparisons with a parallel data set from a robust panel of highly variable microsatellite markers, we show that this ddRAD-seq approach results in substantially improved power to discriminate among potential relatives and considerably more precise estimates of relatedness coefficients. The pipeline is designed to be universally applicable to all bird species (and with minor modifications to many other taxa), to be cost- and time-efficient, and to be replicable across independent runs such that genotype data from different study periods can be combined and analysed as field samples are accumulated.
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Affiliation(s)
- Derrick J Thrasher
- Macaulay Library, Cornell Laboratory of Ornithology, Ithaca, NY, USA
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Bronwyn G Butcher
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, NY, USA
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, NY, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Michael S Webster
- Macaulay Library, Cornell Laboratory of Ornithology, Ithaca, NY, USA
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Irby J Lovette
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, NY, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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48
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Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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49
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Guo B, Guan A, Qi P, Lv Z, Wu C, Xu K, Ping H, Shi H. Parentage determination of cuttlefish (Sepiella japonica) based on microsatellite DNA markers. ANIM BIOL 2018. [DOI: 10.1163/15707563-00002543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Microsatellite markers have been used for more than ten years to elucidate parentage relationships in aquaculture species. This study aimed to assess the feasibility of utilizing microsatellite markers for parentage determination in cuttlefish (Sepiella japonica) using simulations and real data analysis. We developed a panel of eight microsatellite markers in our lab. These markers were highly polymorphic with a mean of 10.1 alleles and an average expected heterozygosity value of 0.809. Using five simple sequence repeat markers, an allele frequency data-based simulation indicated that the combined exclusion probability values would be over 99%, whereas the rate of assignment success for the real data set was 91.8%. Mismatches caused by null alleles and scoring errors at microsatellite loci were the major reasons for the discrepancies between the simulations and real data analysis. We concluded that microsatellite markers can be used as a powerful tool to evaluate the effectiveness of enhancement and release programs for S. japonica.
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Affiliation(s)
- Baoying Guo
- 1National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316004, PR China
| | - Ao Guan
- 1National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316004, PR China
| | - Pengzhi Qi
- 1National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316004, PR China
| | - Zhenming Lv
- 1National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316004, PR China
| | - Changwen Wu
- 1National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316004, PR China
| | - Kaida Xu
- 2Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, MOA, Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhoushan 316021, PR China
| | - Hongling Ping
- 3Zhejiang Province Key Lab of Mariculture and Enhancement, Marine Fisheries Research Institute of Zhejiang, Zhoushan 316021, PR China
| | - Huilai Shi
- 3Zhejiang Province Key Lab of Mariculture and Enhancement, Marine Fisheries Research Institute of Zhejiang, Zhoushan 316021, PR China
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Lin JE, Hard JJ, Hilborn R, Hauser L. Modeling local adaptation and gene flow in sockeye salmon. Ecosphere 2017. [DOI: 10.1002/ecs2.2039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jocelyn E. Lin
- School of Aquatic and Fishery Sciences University of Washington Box 355020 Seattle Washington 98195 USA
| | - Jeffrey J. Hard
- Conservation Biology Division Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration 2725 Montlake Boulevard East Seattle Washington 98112 USA
| | - Ray Hilborn
- School of Aquatic and Fishery Sciences University of Washington Box 355020 Seattle Washington 98195 USA
| | - Lorenz Hauser
- School of Aquatic and Fishery Sciences University of Washington Box 355020 Seattle Washington 98195 USA
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