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Aunins AW, Eackles MS, Kazyak DC, Drummond MR, King TL. Development of microsatellite markers for three at risk tiger beetles Cicindela dorsalis dorsalis, C. d. media, and C. puritana. BMC Res Notes 2020; 13:171. [PMID: 32293541 PMCID: PMC7092472 DOI: 10.1186/s13104-020-04985-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/27/2020] [Indexed: 11/20/2022] Open
Abstract
Objective Tiger beetles inhabiting sandy beaches and cliffs along the east coast of the United States are facing increasing habitat loss due to erosion, urbanization, and sea level rise. The northeastern beach tiger beetle Cicindela dorsalis dorsalis and Puritan tiger beetle Cicindela puritana are both listed as threatened under the Endangered Species Act of 1973, while the white beach tiger beetle Cicindela dorsalis media is not listed but has been declining. Extirpation of these beetles, in some cases from entire states, has isolated many populations reducing gene flow and elevating the risk for the loss of genetic variation. To facilitate investigations of population genetic structure, we developed suites of microsatellite loci for conservation genetic studies. Results Shotgun genomic sequencing of all species identified thousands of candidate microsatellite loci, among which 17 loci were optimized and verified to cross-amplify within C. d. media and C. d. dorsalis, and eight separate loci were optimized for C. puritana. Most loci conformed to Hardy–Weinberg equilibrium, showed no evidence of linkage disequilibrium or null alleles, and revealed population genetic characteristics informative for natural resource managers among the populations tested.
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Affiliation(s)
- Aaron W Aunins
- U.S. Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV, 25430, USA.
| | - Michael S Eackles
- U.S. Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV, 25430, USA
| | - David C Kazyak
- U.S. Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV, 25430, USA
| | - Michael R Drummond
- U.S. Fish and Wildlife Service, Virginia Field Office (Retired), 6669 Short Lane, Gloucester, VA, 23061, USA
| | - Timothy L King
- U.S. Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV, 25430, USA
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Stepien CA, Snyder MR, Elz AE. Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: Differentiation of fronts, introgression, and eDNA metabarcode detection. PLoS One 2019; 14:e0203012. [PMID: 30917127 PMCID: PMC6436794 DOI: 10.1371/journal.pone.0203012] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/05/2019] [Indexed: 11/19/2022] Open
Abstract
In the 1970s, the introduced silver carp Hypophthalmichthys molitrix (which is indigenous to eastern Asia) escaped from southern U.S. aquaculture to spread throughout the Mississippi River basin, and since has steadily moved northward. This large, prolific filter-feeder reduces food availability for other fishes. It now has reached the threshold of the Laurentian Great Lakes, where it likely will significantly impact food chains and fisheries. Our study evaluates population genetic variability and differentiation of the silver carp using 10 nuclear DNA microsatellite loci, and sequences of two mitochondrial genes-cytochrome b and cytochrome c oxidase subunit 1, along with the nuclear ribosomal protein S7 gene intron 1. We analyze population samples from: two primary Great Lakes' invasion fronts (at the Illinois River outside of Chicago, IL in Lake Michigan and in the Wabash River, which leads into the Maumee River and western Lake Erie), the original establishment "core" in the Lower Mississippi River, and expansion areas in the Upper Mississippi and Missouri rivers. We analyze and compare our results with bighead and other invasive carps, and cyprinid relatives. Results reveal that the silver carp invasion possesses moderate levels of genetic diversity, with more mtDNA haplotypes and unique microsatellite alleles in the "core" Lower Mississippi River population, which also diverges the most. The two invasion fronts also significantly genetically differ. About 3% of individuals (including all populations except the Illinois River) contain a unique and very divergent mtDNA haplotype, which likely stems from historic introgression in Asia with female largescale silver carp H. harmandi. The nuclear microsatellites and S7 sequences of the introgressed individuals do not differ from silver carp and are very distant from bighead carp. These sequence variation data are employed to design and evaluate a targeted high-throughput metabarcoding sequence assay that identifies and distinguishes among species of invasive carps (i.e., silver, bighead, grass, black, and common carps, along with goldfish), as well as native cyprinids, using cytochrome b. Our assay further differentiates among selected silver carp haplotypes (including between H. molitrix and H. harmandi), for use in population genetics and future analyses of spread pathways. We test and evaluate this assay on environmental (e)DNA water samples from 48 bait shops in the Great Lakes' region (along the Lake Erie, Lake St. Clair, and Wabash River watersheds), using positive and negative controls and custom bioinformatic processing. Test results discern silver carp eDNA in four of the shops-three in Lake Erie and one in the Wabash River watershed-and bighead carp from one of the same Lake Erie venues, suggesting that retailers (who often source from established southerly populations) comprise another introduction vector. Our overall findings thus provide key population genetic and phylogenetic data for understanding and tracing introductions, vectors, and spread pathways for silver carp, their variants, and their relatives.
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Affiliation(s)
- Carol A. Stepien
- NOAA Pacific Marine Environmental Laboratory, Genetics and Genomics Group (G3), Seattle, WA, United States of America
| | - Matthew R. Snyder
- NOAA Pacific Marine Environmental Laboratory, Genetics and Genomics Group (G3), Seattle, WA, United States of America
| | - Anna E. Elz
- NOAA Pacific Marine Environmental Laboratory, Genetics and Genomics Group (G3), Seattle, WA, United States of America
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King TL, Eackles M, Aunins A, McGreevy TJ, Husband TP, Tur A, Kovach AI. Microsatellite marker development from next-generation sequencing in the New England cottontail (Sylvilagus transitionalis) and cross-amplification in the eastern cottontail (S. floridanus). BMC Res Notes 2017; 10:741. [PMID: 29246260 PMCID: PMC5732487 DOI: 10.1186/s13104-017-3062-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/02/2017] [Indexed: 11/10/2022] Open
Abstract
Objective The New England cottontail (Sylvilagus transitionalis) is a species of high conservation priority in the Northeastern United States, and was a candidate for federal listing under the Endangered Species Act until a recent decision determined that conservation actions were sufficient to preclude listing. The aim of this study was to develop a suite of microsatellite loci to guide future research efforts such as the analysis of population genetic structure, genetic variation, dispersal, and genetic mark-recapture population estimation. Results Thirty-five microsatellite markers containing tri- and tetranucleotide sequences were developed from shotgun genomic sequencing of tissue from S. transitionalis, S. obscurus, and S. floridanus. These loci were screened in n = 33 wild S. transitionalis sampled from a population in eastern Massachusetts, USA. Thirty-two of the 35 loci were polymorphic with 2–6 alleles, and observed heterozygosities of 0.06–0.82. All loci conformed to Hardy–Weinberg Equilibrium proportions and there was no evidence of linkage disequilibrium or null alleles. Primers for 33 of the 35 loci amplified DNA extracted from n = 6 eastern cottontail (S. floridanus) samples, of which nine revealed putative species-diagnostic alleles. These loci will provide a useful tool for conservation genetics investigations of S. transitionalis and a potential diagnostic species assay for differentiating sympatric eastern and New England cottontails.
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Affiliation(s)
- Timothy L King
- U.S. Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV, 25430, USA
| | - Michael Eackles
- U.S. Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV, 25430, USA
| | - Aaron Aunins
- Natural Systems Analysts, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV, 25430, USA.
| | - Thomas J McGreevy
- Department of Natural Resources Science, University of Rhode Island, 1 Greenhouse Road, Kingston, RI, 02881, USA
| | - Thomas P Husband
- Department of Natural Resources Science, University of Rhode Island, 1 Greenhouse Road, Kingston, RI, 02881, USA
| | - Anthony Tur
- United States Fish and Wildlife Service, 300 Westgate Center Drive, Hadley, MA, 01035, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, 56 College Road, Durham, NH, 03824, USA
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Kang TH, Han SH, Lee HS. Genetic structure and demographic history of Lymantria dispar (Linnaeus, 1758) (Lepidoptera: Erebidae) in its area of origin and adjacent areas. Ecol Evol 2017; 7:9162-9178. [PMID: 29152205 PMCID: PMC5677484 DOI: 10.1002/ece3.3467] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 08/04/2017] [Accepted: 09/01/2017] [Indexed: 12/02/2022] Open
Abstract
We analyzed the population genetic structure and demographic history of 20 Lymantria dispar populations from Far East Asia using microsatellite loci and mitochondrial genes. In the microsatellite analysis, the genetic distances based on pairwise FST values ranged from 0.0087 to 0.1171. A NeighborNet network based on pairwise FST genetic distances showed that the 20 regional populations were divided into five groups. Bayesian clustering analysis (K = 3) demonstrated the same groupings. The populations in the Korean Peninsula and adjacent regions, in particular, showed a mixed genetic pattern. In the mitochondrial genetic analysis based on 98 haplotypes, the median‐joining network exhibited a star shape that was focused on three high‐frequency haplotypes (Haplotype 1: central Korea and adjacent regions, Group 1; Haplotype 37: southern Korea, Group 2; and Haplotype 90: Hokkaido area, Group 3) connected by low‐frequency haplotypes. The mismatch distribution dividing the three groups was unimodal. In the neutral test, Tajima's D and Fu's FS tests were negative. We can thus infer that the Far East Asian populations of L. dispar underwent a sudden population expansion. Based on the age expansion parameter, the expansion time was inferred to be approximately 53,652 years before present (ybp) for Group 1, approximately 65,043 ybp for Group 2, and approximately 76,086 ybp for Group 3. We propose that the mixed genetic pattern of the inland populations of Far East Asia is due to these expansions and that the inland populations of the region should be treated as valid subspecies that are distinguishable from other subspecies by genetic traits.
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Affiliation(s)
- Tae Hwa Kang
- Bio Control Research Center Jeonnam Bioindustry Foundation Gokseong-gun Korea
| | - Sang Hoon Han
- Department of Life Science College of Natural Science Kyonggi University Suwon Korea
| | - Heung Sik Lee
- Plant Quarantine Technology Center Animal and Plant Quarantine Agency Gimcheon-si Korea
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Phylogeography and population genetics of introduced Silver Carp (Hypophthalmichthys molitrix) and Bighead Carp (H. nobilis) in North America. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1484-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Wang J, Lamer JT, Gaughan S, Wachholtz M, Wang C, Lu G. Transcriptomic comparison of invasive bigheaded carps ( Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) and their hybrids. Ecol Evol 2016; 6:8452-8459. [PMID: 28031797 PMCID: PMC5167015 DOI: 10.1002/ece3.2574] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 09/30/2016] [Accepted: 10/05/2016] [Indexed: 11/15/2022] Open
Abstract
Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), collectively called bigheaded carps, are invasive species in the Mississippi River Basin (MRB). Interspecific hybridization between bigheaded carps has been considered rare within their native rivers in China; however, it is prevalent in the MRB. We conducted de novo transcriptome analysis of pure and hybrid bigheaded carps and obtained 40,759 to 51,706 transcripts for pure, F1 hybrid, and backcross bigheaded carps. The search against protein databases resulted in 20,336–28,133 annotated transcripts (over 50% of the transcriptome) with over 13,000 transcripts mapped to 23 Gene Ontology biological processes and 127 KEGG metabolic pathways. More transcripts were detected in silver carp than in bighead carp; however, comparable numbers of transcripts were annotated. Transcriptomic variation detected between two F1 hybrids may indicate a potential loss of fitness in hybrids. The neighbor‐joining distance tree constructed using over 2,500 one‐to‐one orthologous sequences suggests transcriptomes could be used to infer the history of introgression and hybridization. Moreover, we detected 24,792 candidate SNPs that can be used to identify different species. The transcriptomes, orthologous sequences, and candidate SNPs obtained in this study should provide further knowledge of interspecific hybridization and introgression.
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Affiliation(s)
- Jun Wang
- Department of Biology University of Nebraska at Omaha Omaha NE 68182 USA; Key Laboratory of Freshwater Fisheries Germplasm Resources Ministry of Agriculture Shanghai Ocean University Shanghai 201306 China
| | - James T Lamer
- Department of Biological Sciences Western Illinois University Macomb IL 61455 USA
| | - Sarah Gaughan
- Department of Biology University of Nebraska at Omaha Omaha NE 68182 USA
| | - Michael Wachholtz
- Department of Biology University of Nebraska at Omaha Omaha NE 68182 USA
| | - Chenghui Wang
- Key Laboratory of Freshwater Fisheries Germplasm Resources Ministry of Agriculture Shanghai Ocean University Shanghai 201306 China
| | - Guoqing Lu
- Department of Biology University of Nebraska at Omaha Omaha NE 68182 USA; School of Interdisciplinary Informatics University of Nebraska at Omaha Omaha NE 68182 USA
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Wedchaparn O, Zhao L, Fan Y, He D, Zhang H, Ivan LN, Liu Q, Ayisi CL. Comparison of the trophic niches between two planktivorous fishes in two large lakes using stable isotope analysis. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kang TH, Han SH, Park SJ. Development of Seven Microsatellite Markers Using Next Generation Sequencing for the Conservation on the Korean Population of Dorcus hopei (E. Saunders, 1854) (Coleoptera, Lucanidae). Int J Mol Sci 2015; 16:21330-41. [PMID: 26370965 PMCID: PMC4613255 DOI: 10.3390/ijms160921330] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 11/17/2022] Open
Abstract
We developed microsatellite markers for genetic structural analyses of Dorcus hopei, a stag beetle species, using next generation sequencing and polymerase chain reaction (PCR)-based genotyping for regional populations. A total of 407,070,351 base pairs of genomic DNA containing >4000 microsatellite loci except AT repeats were sequenced. From 76 loci selected for primer design, 27 were polymorphic. Of these 27 markers, 10 were tested on three regional populations: two Chinese (Shichuan and Guangxi) and one Korean (Wanju). Three markers were excluded due to inconsistent amplification, genotyping errors, and Hardy-Weinberg equilibrium (HWE). By multi-locus genotyping, the allele number, observed heterozygosity and polymorphism information content of seven microsatellite loci were ranged 2‒10, 0.1333‒1.0000, and 0.1228‒0.8509, respectively. In an analysis on the genetic differentiation among regional populations including one Japanese population and one cross-breeding population, the individual colored bar-plots showed that both Chinese populations were closer to each other than to the Far East Asian populations. In Far East Asian populations, Wanju and Nirasaki populations could not be distinguished from each other because the frequency of genetic contents was very similar in some individuals of two populations. Moreover, the cross-breeding population contained all patterns of genetic contents shown in Chinese, Korean, and Japanese populations, compared with the genetic content frequency of each regional population. As a result, we examined whether the cross-breeding population might be a hybrid population, and might contain a possibility of interbreeding with Chinese populations in parental generations. Therefore, these markers will be useful for analyses of genetic diversity in populations, genetic relationships between regional populations, genetic structure analyses, and origin tests.
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Affiliation(s)
- Tae Hwa Kang
- Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, 234-3, Mangpo-dong, Yeongtong-gu, Suwon, Gyeonggi-do 443-400, Korea.
| | - Sang Hoon Han
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42, Gwanggyeongsan-ro, Yeongtong-gu, Suwon, Gyeonggi-do 443-780, Korea.
| | - Sun Jae Park
- Biological Resources Research Department, National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 404-170, Korea.
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Lamer JT, Ruebush BC, Arbieva ZH, McClelland MA, Epifanio JM, Sass GG. Diagnostic SNPs reveal widespread introgressive hybridization between introduced bighead and silver carp in the Mississippi River Basin. Mol Ecol 2015; 24:3931-43. [DOI: 10.1111/mec.13285] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 05/31/2015] [Accepted: 06/18/2015] [Indexed: 01/07/2023]
Affiliation(s)
- James T. Lamer
- Department of Natural Resources and Environmental Sciences; University of Illinois; 1102 South Goodwin Ave. Urbana IL 61801 USA
- Department of Biological Sciences; Western Illinois University; 1 University Circle Macomb IL 61455 USA
| | - Blake C. Ruebush
- Illinois Department of Natural Resources; One Natural Resources Way Springfield IL 62702 USA
| | - Zarema H. Arbieva
- Core Genomics Facility; University of Illinois at Chicago; 835 S. Wolcott Avenue Chicago IL 60612 USA
| | | | - John M. Epifanio
- Illinois Natural History Survey; 1816 S. Oak Street Champaign IL 61820 USA
| | - Greg G. Sass
- Escanaba Lake Research Station; Wisconsin Department of Natural Resources; 10810 County Hwy N Boulder Junction WI 54512 USA
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Rapid isolation of microsatellite DNAs and identification of polymorphic mitochondrial DNA regions in the fish rotan (Perccottus glenii) invading European Russia. CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-015-0430-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Next-generation genomic shotgun sequencing indicates greater genetic variability in the mitochondria of Hypophthalmichthys molitrix relative to H. nobilis from the Mississippi River, USA and provides tools for research and detection. CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-014-0296-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Hunter ME, Nico LG. Genetic analysis of invasive Asian Black Carp (Mylopharyngodon piceus) in the Mississippi River Basin: evidence for multiple introductions. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0708-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Lamer JT, Sass GG, Boone JQ, Arbieva ZH, Green SJ, Epifanio JM. Restriction site-associated DNA sequencing generates high-quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the United States and China. Mol Ecol Resour 2013; 14:79-86. [PMID: 23957862 DOI: 10.1111/1755-0998.12152] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/25/2013] [Accepted: 06/30/2013] [Indexed: 11/26/2022]
Abstract
Bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are invasive species and listed as US federally injurious species under the Lacy Act. They have established populations in much of the Mississippi River Basin (MRB; Mississippi, Illinois, and Missouri rivers) and are capable of producing fertile hybrids and complex introgression. Characterizing the composition of this admixture requires a large set of high-quality, evolutionarily conserved, diagnostic genetic markers to aid in the identification and management of these species in the midst of morphological ambiguity. Restriction site-associated DNA (RAD) sequencing of 45 barcoded bighead and silver carp from the United States and China produced reads that were aligned to the silver carp transcriptome yielded 261 candidate single nucleotide polymorphisms (SNPs) with fixed allelic differences between the two species. We selected the highest quality 112 SNP loci for validation using 194 putative pure-species and F1 hybrids from the MRB and putative bighead carp and silver carp pure species from China (Amur, Pearl and Yangtze rivers). Fifty SNPs were omitted due to design/amplification failure or lack of diagnostic utility. A total of 57 species-diagnostic SNPs conserved between carp species in US and Chinese rivers were identified; 32 were annotated to functional gene loci. Twenty-seven of the 181 (15%) putative pure species were identified as hybrid backcrosses after validation, including three backcrosses from the Amur River, where hybridization has not been documented previously. The 57 SNPs identified through RAD sequencing provide a diagnostic tool to detect population admixture and to identify hybrid and pure-species Asian carps in the United States and China.
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Affiliation(s)
- James T Lamer
- Department of Biological Sciences, Western Illinois University, 1 University Circle, Macomb, IL, 61455, USA; Illinois Natural History Survey, 1816 S. Oak Street, Champaign, IL, 61820, USA
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Hunter ME, Hart KM. Rapid Microsatellite Marker Development Using Next Generation Pyrosequencing to Inform Invasive Burmese Python-Python molurus bivittatus-Management. Int J Mol Sci 2013; 14:4793-804. [PMID: 23449030 PMCID: PMC3634432 DOI: 10.3390/ijms14034793] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 02/06/2013] [Accepted: 02/13/2013] [Indexed: 01/29/2023] Open
Abstract
Invasive species represent an increasing threat to native ecosystems, harming indigenous taxa through predation, habitat modification, cross-species hybridization and alteration of ecosystem processes. Additionally, high economic costs are associated with environmental damage, restoration and control measures. The Burmese python, Python molurus bivittatus, is one of the most notable invasive species in the US, due to the threat it poses to imperiled species and the Greater Everglades ecosystem. To address population structure and relatedness, next generation sequencing was used to rapidly produce species-specific microsatellite loci. The Roche 454 GS-FLX Titanium platform provided 6616 di-, tri- and tetra-nucleotide repeats in 117,516 sequences. Using stringent criteria, 24 of 26 selected tri- and tetra-nucleotide loci were polymerase chain reaction (PCR) amplified and 18 were polymorphic. An additional six cross-species loci were amplified, and the resulting 24 loci were incorporated into eight PCR multiplexes. Multi-locus genotypes yielded an average of 61% (39%–77%) heterozygosity and 3.7 (2–6) alleles per locus. Population-level studies using the developed microsatellites will track the invasion front and monitor population-suppression dynamics. Additionally, cross-species amplification was detected in the invasive Ball, P. regius, and Northern African python, P. sebae. These markers can be used to address the hybridization potential of Burmese pythons and the larger, more aggressive P. sebae.
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Affiliation(s)
- Margaret E. Hunter
- U.S. Geological Survey, Southeast Ecological Science Center, 7920 NW 71st Street, Gainesville, FL 32653, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-352-264-3484; Fax: +1-352-374-8080
| | - Kristen M. Hart
- U.S. Geological Survey, Southeast Ecological Science Center, 3205 College Avenue, Davie, FL 33314, USA; E-Mail:
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