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Alanzor Puente JM, Pons Barro ÁL, González Ariza A, Martínez Martínez MDA, Delgado Bermejo JV, Navas González FJ. Integrated Discriminant Evaluation of Molecular Genetic Markers and Genetic Diversity Parameters of Endangered Balearic Dog Breeds. Int J Mol Sci 2024; 25:2706. [PMID: 38473952 DOI: 10.3390/ijms25052706] [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: 01/27/2024] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
The genetic diversity analysis of six dog breeds, including Ca de Bestiar (CB), Ca de Bou (CBOU), Podenco Ibicenco (PI), Ca Rater (CR), Ca Mè (CM), and Ca de Conills (CC), reveals insightful findings. CB showcases the highest mean number of alleles (6.17) and heterozygosity values, with significant deviations from Hardy-Weinberg equilibrium (HWE) observed in five markers, indicating high intra-racial genetic diversity (average observed heterozygosity (Ho) = 0.754, expected heterozygosity (He) = 0.761). In contrast, CBOU presents the lowest mean number of alleles (5.05) and heterozygosity values, coupled with moderate polymorphic information content (PIC) values and a moderate level of intra-racial genetic diversity (average Ho = 0.313, He = 0.394). PI demonstrates moderate genetic diversity with an average of 5.75 alleles and highly informative PIC values, while CR displays robust genetic diversity with an average of 6.61 alleles and deviations from equilibrium, indicating potential risks of inbreeding (average Ho = 0.563, He = 0.658). CM exhibits moderate genetic diversity and deviations from equilibrium, similar to CBOU, with an average of 6.5 alleles and moderate PIC values (average Ho = 0.598, He = 0.676). Conversely, CC shows a wider range of allelic diversity and deviations from equilibrium (average Ho = 0.611, He = 0.706), suggesting a more diverse genetic background. Inter-racial analysis underscores distinct genetic differentiation between breeds, emphasizing the importance of informed breeding decisions and proactive genetic management strategies to preserve diversity, promote breed health, and ensure long-term sustainability across all breeds studied.
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Affiliation(s)
- José Manuel Alanzor Puente
- Institut de Reserca i Formaciò Agroalimentaria de les Illes Balears IRFAP, Conselleria d'Agricultura, Pesca i Alimentació, Govern Illes Balears, 07009 Palma, Spain
| | - Águeda Laura Pons Barro
- Institut de Reserca i Formaciò Agroalimentaria de les Illes Balears IRFAP, Conselleria d'Agricultura, Pesca i Alimentació, Govern Illes Balears, 07009 Palma, Spain
| | - Antonio González Ariza
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14014 Córdoba, Spain
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Zhao C, Wang D, Teng J, Yang C, Zhang X, Wei X, Zhang Q. Breed identification using breed-informative SNPs and machine learning based on whole genome sequence data and SNP chip data. J Anim Sci Biotechnol 2023; 14:85. [PMID: 37259083 DOI: 10.1186/s40104-023-00880-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/05/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND Breed identification is useful in a variety of biological contexts. Breed identification usually involves two stages, i.e., detection of breed-informative SNPs and breed assignment. For both stages, there are several methods proposed. However, what is the optimal combination of these methods remain unclear. In this study, using the whole genome sequence data available for 13 cattle breeds from Run 8 of the 1,000 Bull Genomes Project, we compared the combinations of three methods (Delta, FST, and In) for breed-informative SNP detection and five machine learning methods (KNN, SVM, RF, NB, and ANN) for breed assignment with respect to different reference population sizes and difference numbers of most breed-informative SNPs. In addition, we evaluated the accuracy of breed identification using SNP chip data of different densities. RESULTS We found that all combinations performed quite well with identification accuracies over 95% in all scenarios. However, there was no combination which performed the best and robust across all scenarios. We proposed to integrate the three breed-informative detection methods, named DFI, and integrate the three machine learning methods, KNN, SVM, and RF, named KSR. We found that the combination of these two integrated methods outperformed the other combinations with accuracies over 99% in most cases and was very robust in all scenarios. The accuracies from using SNP chip data were only slightly lower than that from using sequence data in most cases. CONCLUSIONS The current study showed that the combination of DFI and KSR was the optimal strategy. Using sequence data resulted in higher accuracies than using chip data in most cases. However, the differences were generally small. In view of the cost of genotyping, using chip data is also a good option for breed identification.
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Affiliation(s)
- Changheng Zhao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Dan Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Jun Teng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Cheng Yang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Xinyi Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Xianming Wei
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China.
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Gebeyehu A, Hammenhag C, Tesfaye K, Vetukuri RR, Ortiz R, Geleta M. RNA-Seq Provides Novel Genomic Resources for Noug ( Guizotia abyssinica) and Reveals Microsatellite Frequency and Distribution in Its Transcriptome. FRONTIERS IN PLANT SCIENCE 2022; 13:882136. [PMID: 35646044 PMCID: PMC9132581 DOI: 10.3389/fpls.2022.882136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/23/2022] [Indexed: 06/02/2023]
Abstract
Genomic resources and tools are essential for improving crops and conserving their genetic resources. Guizotia abyssinica (noug), an outcrossing edible oilseed crop, has highly limited genomic resources. Hence, RNA-Seq based transcriptome sequencing of 30 noug genotypes was performed to generate novel genomic resources and assess their usefulness. The genotypes include self-compatible and self-incompatible types, which differ in maturity time, photoperiod sensitivity, or oil content and quality. RNA-Seq was performed on Illumina HiSeq 2500 platform, and the transcript was reconstructed de novo, resulting in 409,309 unigenes. The unigenes were characterized for simple sequence repeats (SSRs), and served as a reference for single nucleotide polymorphism (SNP) calling. In total, 40,776 SSRs were identified in 35,639 of the 409,309 unigenes. Of these, mono, di, tri, tetra, penta and hexanucleotide repeats accounted for 55.4, 20.8, 21.1, 2.3, 0.2, and 0.2%, respectively. The average G+C content of the unigenes and their SSRs were 40 and 22.1%, respectively. The vast majority of mononucleotide repeat SSRs (97%) were of the A/T type. AG/CT and CCA/TGG were the most frequent di and trinucleotide repeat SSRs. A different number of single nucleotide polymorphism (SNP) loci were discovered in each genotype, of which 1,687 were common to all 30 genotypes and 5,531 to 28 of them. The mean observed heterozygosity of the 5,531 SNPs was 0.22; 19.4% of them had polymorphism information content above 0.30 while 17.2% deviated significantly from Hardy-Weinberg equilibrium (P < 0.05). In both cluster and principal coordinate analyses, the genotypes were grouped into four major clusters. In terms of population structure, the genotypes are best represented by three genetic populations, with significant admixture within each. Genetic similarity between self-compatible genotypes was higher, due to the narrow genetic basis, than that between self-incompatible genotypes. The genotypes that shared desirable characteristics, such as early maturity, and high oil content were found to be genetically diverse, and hence superior cultivars with multiple desirable traits can be developed through crossbreeding. The genomic resources developed in this study are vital for advancing research in noug, such as genetic linkage mapping and genome-wide association studies, which could lead to genomic-led breeding.
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Affiliation(s)
- Adane Gebeyehu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Kassahun Tesfaye
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Ramesh R. Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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Rius M, Turon X. Phylogeography and the Description of Geographic Patterns in Invasion Genomics. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.595711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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New Transcriptome-Based SNP Markers for Noug ( Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses. Genes (Basel) 2020; 11:genes11111373. [PMID: 33233626 PMCID: PMC7709008 DOI: 10.3390/genes11111373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 11/17/2022] Open
Abstract
The development and use of genomic resources are essential for understanding the population genetics of crops for their efficient conservation and enhancement. Noug (Guizotia abyssinica) is an economically important oilseed crop in Ethiopia and India. The present study sought to develop new DNA markers for this crop. Transcriptome sequencing was conducted on two genotypes and 628 transcript sequences containing 959 single nucleotide polymorphisms (SNPs) were developed. A competitive allele-specific PCR (KASP) assay was developed for the SNPs and used for genotyping of 24 accessions. A total of 554 loci were successfully genotyped across the accessions, and 202 polymorphic loci were used for population genetics analyses. Polymorphism information content (PIC) of the loci varied from 0.01 to 0.37 with a mean of 0.24, and about 49% of the loci showed significant deviation from the Hardy-Weinberg equilibrium. The mean expected heterozygosity was 0.27 suggesting moderately high genetic variation within accessions. Low but significant differentiation existed among accessions (FST = 0.045, p < 0.0001). Landrace populations from isolated areas may have useful mutations and should be conserved and used in breeding this crop. The genomic resources developed in this study were shown to be useful for population genetics research and can also be used in, e.g., association genetics.
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Mining whole genome sequence data to efficiently attribute individuals to source populations. Sci Rep 2020; 10:12124. [PMID: 32699222 PMCID: PMC7376179 DOI: 10.1038/s41598-020-68740-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/15/2020] [Indexed: 11/27/2022] Open
Abstract
Whole genome sequence (WGS) data could transform our ability to attribute individuals to source populations. However, methods that efficiently mine these data are yet to be developed. We present a minimal multilocus distance (MMD) method which rapidly deals with these large data sets as well as methods for optimally selecting loci. This was applied on WGS data to determine the source of human campylobacteriosis, the geographical origin of diverse biological species including humans and proteomic data to classify breast cancer tumours. The MMD method provides a highly accurate attribution which is computationally efficient for extended genotypes. These methods are generic, easy to implement for WGS and proteomic data and have wide application.
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Billerman SM, Jesmer BR, Watts AG, Schlichting PE, Fortin MJ, Funk WC, Hapeman P, Muths E, Murphy MA. Testing theoretical metapopulation conditions with genotypic data from Boreal Chorus Frogs (Pseudacris maculata). CAN J ZOOL 2019. [DOI: 10.1139/cjz-2018-0275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The metapopulation concept has far-reaching implications in ecology and conservation biology. Hanski’s criteria operationally define metapopulations, yet testing them is hindered by logistical and financial constraints inherent to the collection of long-term demographic data. Hence, ecologists and conservationists often assume metapopulation existence for dispersal-limited species that occupy patchy habitats. To advance understanding of metapopulation theory and improve conservation of metapopulations, we used population and landscape genetic tools to develop a methodological framework for evaluating Hanski’s criteria. We used genotypic data (11 microsatellite loci) from a purported metapopulation of Boreal Chorus Frogs (Pseudacris maculata (Agassiz, 1850)) in Colorado, U.S.A., to test Hanski’s four criteria. We found support for each criterion: (1) significant genetic differentiation between wetlands, suggesting distinct breeding populations; (2) wetlands had small effective population sizes and recent bottlenecks, suggesting populations do not experience long-term persistence; (3) population graphs provided evidence of gene flow between patches, indicating potential for recolonization; and (4) multiscale bottleneck analyses suggest asynchrony, indicating that simultaneous extinction of all populations was unlikely. Our methodological framework provides a logistically and financially feasible alternative to long-term demographic data for identifying amphibian metapopulations.
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Affiliation(s)
- Shawn M. Billerman
- Program in Ecology, Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, U.S.A
- University of Wyoming, Laramie, WY 82071, U.S.A
| | - Brett R. Jesmer
- Program in Ecology, Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, U.S.A
- University of Wyoming, Laramie, WY 82071, U.S.A
| | - Alexander G. Watts
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada
| | - Peter E. Schlichting
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX 79409, U.S.A
- Arizona State University – Polytechnic Campus, Mesa, AZ 85212, U.S.A
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - W. Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Paul Hapeman
- Department of Biology, Central Connecticut State University, New Britain, CT 06053, U.S.A
| | - Erin Muths
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO 80526, U.S.A
| | - Melanie A. Murphy
- University of Wyoming, Laramie, WY 82071, U.S.A
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, WY 82071, U.S.A
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Millon A, Lambin X, Devillard S, Schaub M. Quantifying the contribution of immigration to population dynamics: a review of methods, evidence and perspectives in birds and mammals. Biol Rev Camb Philos Soc 2019; 94:2049-2067. [DOI: 10.1111/brv.12549] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Alexandre Millon
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Technopôle Arbois‐Méditerranée, Bât. Villemin – BP 80 F‐13545 Aix‐en‐Provence cedex 04 France
| | - Xavier Lambin
- School of Biological SciencesUniversity of Aberdeen Tillydrone Avenue, Zoology Building, University of Aberdeen, AB24 2TZ Aberdeen U.K
| | - Sébastien Devillard
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive F‐69100 Villeurbanne France
| | - Michael Schaub
- Swiss Ornithological Institute Seerose 1, 6204 Sempach Switzerland
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Ojaveer H, Galil BS, Carlton JT, Alleway H, Goulletquer P, Lehtiniemi M, Marchini A, Miller W, Occhipinti-Ambrogi A, Peharda M, Ruiz GM, Williams SL, Zaiko A. Historical baselines in marine bioinvasions: Implications for policy and management. PLoS One 2018; 13:e0202383. [PMID: 30114232 PMCID: PMC6095587 DOI: 10.1371/journal.pone.0202383] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The human-mediated introduction of marine non-indigenous species is a centuries- if not millennia-old phenomenon, but was only recently acknowledged as a potent driver of change in the sea. We provide a synopsis of key historical milestones for marine bioinvasions, including timelines of (a) discovery and understanding of the invasion process, focusing on transfer mechanisms and outcomes, (b) methodologies used for detection and monitoring, (c) approaches to ecological impacts research, and (d) management and policy responses. Early (until the mid-1900s) marine bioinvasions were given little attention, and in a number of cases actively and routinely facilitated. Beginning in the second half of the 20th century, several conspicuous non-indigenous species outbreaks with strong environmental, economic, and public health impacts raised widespread concerns and initiated shifts in public and scientific perceptions. These high-profile invasions led to policy documents and strategies to reduce the introduction and spread of non-indigenous species, although with significant time lags and limited success and focused on only a subset of transfer mechanisms. Integrated, multi-vector management within an ecosystem-based marine management context is urgently needed to address the complex interactions of natural and human pressures that drive invasions in marine ecosystems.
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Affiliation(s)
- Henn Ojaveer
- Estonian Marine Institute, University of Tartu, Pärnu, Estonia
| | - Bella S. Galil
- The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - James T. Carlton
- Maritime Studies Program of Williams College and Mystic Seaport, Mystic, Connecticut, United States of America
| | - Heidi Alleway
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | | | - Maiju Lehtiniemi
- Marine Research Centre, Finnish Environment Institute, Helsinki, Finland
| | - Agnese Marchini
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Whitman Miller
- Marine Invasion Research Laboratory, Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | | | | | - Gregory M. Ruiz
- Marine Invasion Research Laboratory, Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - Susan L. Williams
- Bodega Marine Laboratory and Department of Evolution and Ecology, University of California at Davis, Bodega Bay, California, United States of America
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Marine Research Institute, Klaipeda University, Klaipeda, Lithuania
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Pélissié B, Crossley MS, Cohen ZP, Schoville SD. Rapid evolution in insect pests: the importance of space and time in population genomics studies. CURRENT OPINION IN INSECT SCIENCE 2018; 26:8-16. [PMID: 29764665 DOI: 10.1016/j.cois.2017.12.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/28/2017] [Accepted: 12/31/2017] [Indexed: 06/08/2023]
Abstract
Pest species in agroecosystems often exhibit patterns of rapid evolution to environmental and human-imposed selection pressures. Although the role of adaptive processes is well accepted, few insect pests have been studied in detail and most research has focused on selection at insecticide resistance candidate genes. Emerging genomic datasets provide opportunities to detect and quantify selection in insect pest populations, and address long-standing questions about mechanisms underlying rapid evolutionary change. We examine the strengths of recent studies that stratify population samples both in space (along environmental gradients and comparing ancestral vs. derived populations) and in time (using chronological sampling, museum specimens and comparative phylogenomics), resulting in critical insights on evolutionary processes, and providing new directions for studying pests in agroecosystems.
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Affiliation(s)
- Benjamin Pélissié
- University of Wisconsin-Madison, Department of Entomology, 1630 Linden Drive, 637-643 Russell Labs, Madison, WI 53706, USA.
| | - Michael S Crossley
- University of Wisconsin-Madison, Department of Entomology, 1630 Linden Drive, 637-643 Russell Labs, Madison, WI 53706, USA
| | - Zachary Paul Cohen
- University of Wisconsin-Madison, Department of Entomology, 1630 Linden Drive, 637-643 Russell Labs, Madison, WI 53706, USA
| | - Sean D Schoville
- University of Wisconsin-Madison, Department of Entomology, 1630 Linden Drive, 637-643 Russell Labs, Madison, WI 53706, USA
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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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Wu Y, Li F, Li Z, Stejskal V, Kučerová Z, Opit G, Aulicky R, Zhang T, He P, Cao Y. Microsatellite markers for Cryptolestes ferrugineus (Coleoptera: Laemophloeidae) and other Cryptolestes species. BULLETIN OF ENTOMOLOGICAL RESEARCH 2016; 106:154-160. [PMID: 26584625 DOI: 10.1017/s0007485315000899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cryptolestes ferrugineus (Stephens, 1831) is an important insect pest of stored products. Due to its broad host range, short life cycle, and high reproductive capacity, this species has rapidly colonized temperate and tropical regions around the world. In this study, we isolated 18 novel polymorphic microsatellite loci from an enriched genomic library based on a biotin/streptavidin capture protocol. These loci will be useful tool to better understand the genetic structure and migration patterns of C. ferrugineus throughout the world. The genetic parameters were estimated based on 80 individual C. ferrugineus from two natural populations. The results revealed that 18 loci were different polymorphic levels. The numbers of alleles ranged from 3 to 12, and eleven loci demonstrated polymorphic information contents greater than 0.5. The observed (H O) and expected (H E) heterozygosities ranged from 0.051 to 0.883 and 0.173 to 0.815, respectively. Five locus/population combinations significantly deviated from Hardy-Weinberg equilibrium. We also demonstrated the potential utility of the C. ferrugineus microsatellites as population and species markers for four additional Cryptolestes species.
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Affiliation(s)
- Y Wu
- Academy of State Administration of Grain,No. 11 Baiwanzhuang Street,Beijing,China
| | - F Li
- Academy of State Administration of Grain,No. 11 Baiwanzhuang Street,Beijing,China
| | - Z Li
- Department of Entomology,China Agricultural University,No. 2 Yuanmingyuan West Road,Beijing,China
| | - V Stejskal
- Department of Pest Control of Stored Products and Food Safety,Crop Research Institute,Drnovská 507,Prague,Czech Republic
| | - Z Kučerová
- Department of Pest Control of Stored Products and Food Safety,Crop Research Institute,Drnovská 507,Prague,Czech Republic
| | - G Opit
- Department of Entomology and Plant Pathology,Oklahoma State University,127 Noble Research Center,Stillwater,Oklahoma,USA
| | - R Aulicky
- Department of Pest Control of Stored Products and Food Safety,Crop Research Institute,Drnovská 507,Prague,Czech Republic
| | - T Zhang
- Academy of State Administration of Grain,No. 11 Baiwanzhuang Street,Beijing,China
| | - P He
- Academy of State Administration of Grain,No. 11 Baiwanzhuang Street,Beijing,China
| | - Y Cao
- Academy of State Administration of Grain,No. 11 Baiwanzhuang Street,Beijing,China
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14
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Wilton CM, Belant JL, Van Stappen JF, Paetkau D. American black bear population abundance and genetic structure on an island archipelago. URSUS 2015. [DOI: 10.2192/ursus-d-15-00008.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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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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Padhukasahasram B. Inferring ancestry from population genomic data and its applications. Front Genet 2014; 5:204. [PMID: 25071832 PMCID: PMC4080679 DOI: 10.3389/fgene.2014.00204] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/17/2014] [Indexed: 12/26/2022] Open
Abstract
Ancestry inference is a frequently encountered problem and has many applications such as forensic analyses, genetic association studies, and personal genomics. The main goal of ancestry inference is to identify an individual’s population of origin based on our knowledge of natural populations. Because both self-reported ancestry in humans or the sampling location of an organism can be inaccurate for this purpose, the use of genetic markers can facilitate accurate and reliable inference of an individual’s ancestral origins. At a higher level, there are two different paradigms in ancestry inference: global ancestry inference which tries to compute the genome-wide average of the population contributions and local ancestry inference which tries to identify the regional ancestry of a genomic segment. In this mini review, I describe the numerous approaches that are currently available for both kinds of ancestry inference from population genomic datasets. I first describe the general ideas underlying such inference methods and their relationship to one another. Then, I describe practical applications in which inference of ancestry has proven useful. Lastly, I discuss challenges and directions for future research work in this area.
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Affiliation(s)
- Badri Padhukasahasram
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI USA
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Invasion history of Caprella scaura Templeton, 1836 (Amphipoda: Caprellidae) in the Iberian Peninsula: multiple introductions revealed by mitochondrial sequence data. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0660-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Veale AJ, Edge KA, McMurtrie P, Fewster RM, Clout MN, Gleeson DM. Using genetic techniques to quantify reinvasion, survival andin situbreeding rates during control operations. Mol Ecol 2013; 22:5071-83. [DOI: 10.1111/mec.12453] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 07/08/2013] [Accepted: 07/09/2013] [Indexed: 11/30/2022]
Affiliation(s)
- A. J. Veale
- School of Biological Sciences; Tamaki Campus; University of Auckland; Private Bag 92019 Auckland New Zealand
| | - K.-A. Edge
- Department of Conservation Te Anau; PO Box 29 Te Anau 9640 New Zealand
| | - P. McMurtrie
- Department of Conservation Te Anau; PO Box 29 Te Anau 9640 New Zealand
| | - R. M. Fewster
- Department of Statistics; University of Auckland; Private Bag 92019 Auckland New Zealand
| | - M. N. Clout
- School of Biological Sciences; Tamaki Campus; University of Auckland; Private Bag 92019 Auckland New Zealand
| | - D. M. Gleeson
- Institute for Applied Ecology; University of Canberra; Bruce ACT 2601 Australia
- Ecological Genetics Laboratory; Landcare Research; Private Bag 92170 Auckland 1142 New Zealand
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Brazeau DA, Lesser MP, Slattery M. Genetic structure in the coral, Montastraea cavernosa: assessing genetic differentiation among and within Mesophotic reefs. PLoS One 2013; 8:e65845. [PMID: 23734263 PMCID: PMC3666989 DOI: 10.1371/journal.pone.0065845] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 05/03/2013] [Indexed: 11/18/2022] Open
Abstract
Mesophotic coral reefs (30–150 m) have recently received increased attention as a potential source of larvae (e.g., the refugia hypothesis) to repopulate a select subset of the shallow water (<30 m) coral fauna. To test the refugia hypothesis we used highly polymorphic Amplified Fragment Length Polymorphism (AFLP) markers as a means to assess small-scale genetic heterogeneity between geographic locations and across depth clines in the Caribbean coral, Montastraea cavernosa. Zooxanthellae-free DNA extracts of coral samples (N = 105) were analyzed from four depths, shallow (3–10 m), medium (15–25 m), deep (30–50 m) and very deep (60–90 m) from Little Cayman Island (LCI), Lee Stocking Island (LSI), Bahamas and San Salvador (SS), Bahamas which range in distance from 170 to 1,600 km apart. Using AMOVA analysis there were significant differences in ΦST values in pair wise comparisons between LCI and LSI. Among depths at LCI, there was significant genetic differentiation between shallow and medium versus deep and very deep depths in contrast there were no significant differences in ΦST values among depths at LSI. The assignment program AFLPOP, however, correctly assigned 95.7% of the LCI and LSI samples to the depths from which they were collected, differentiating among populations as little as 10 to 20 m in depth from one another. Discriminant function analysis of the data showed significant differentiation among samples when categorized by collection site as well as collection depth. FST outlier analyses identified 2 loci under positive selection and 3 under balancing selection at LCI. At LSI 2 loci were identified, both showing balancing selection. This data shows that adult populations of M. cavernosa separated by depths of tens of meters exhibits significant genetic structure, indicative of low population connectivity among and within sites and are not supplying successful recruits to adjacent coral reefs less than 30 m in depth.
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Affiliation(s)
- Daniel A Brazeau
- Department of Pharmaceutical Sciences, University of New England, Portland, Maine, USA.
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Apodaca JJ, Trexler JC, Jue NK, Schrader M, Travis J. Large-Scale Natural Disturbance Alters Genetic Population Structure of the Sailfin Molly, Poecilia latipinna. Am Nat 2013; 181:254-63. [DOI: 10.1086/668831] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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21
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Keever CC, Nieman C, Ramsay L, Ritland CE, Bauer LS, Lyons DB, Cory JS. Microsatellite population genetics of the emerald ash borer (Agrilus planipennis Fairmaire): comparisons between Asian and North American populations. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0389-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Sonsthagen SA, McClaren EL, Doyle FI, Titus K, Sage GK, Wilson RE, Gust JR, Talbot SL. Identification of metapopulation dynamics among Northern Goshawks of the Alexander Archipelago, Alaska, and Coastal British Columbia. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0352-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Tools for the management and conservation of genetic diversity in brook trout (Salvelinus fontinalis): tri- and tetranucleotide microsatellite markers for the assessment of genetic diversity, phylogeography, and historical demographics. CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-012-9603-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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24
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Assessing genetic diversity, fine-scale population structure, and demographics in the narrow endemic chittenango ovate amber snail (Novisuccinea chittenangoensis). CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-011-9568-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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25
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Veale AJ, Clout MN, Gleeson DM. Genetic population assignment reveals a long-distance incursion to an island by a stoat (Mustela erminea). Biol Invasions 2011. [DOI: 10.1007/s10530-011-0113-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Tri- and tetra-nucleotide microsatellite DNA markers for assessing genetic diversity, population structure, and demographics in the Holmgren milk-vetch (Astragalus holmgreniorum). CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-011-9468-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tooman LK, Rose CJ, Carraher C, Suckling DM, Paquette SR, Ledezma LA, Gilligan TM, Epstein M, Barr NB, Newcomb RD. Patterns of mitochondrial haplotype diversity in the invasive pest Epiphyas postvittana (Lepidoptera: Tortricidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2011; 104:920-932. [PMID: 21735912 DOI: 10.1603/ec10342] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The light brown apple moth, Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae), is a horticultural pest of Australia and New Zealand that has more recently invaded Hawaii, Europe, and California. A 2,216-bp region of the mitochondrial genome containing the cytochrome oxidase I and II genes was sequenced from 752 individuals. Haplotype network analyses revealed a major split between a predominantly Western Australian clade and all other samples, suggestive of either a deep genetic divergence or a cryptic species. Nucleotide and haplotype diversity were highest in the country of origin, Australia, and in New Zealand populations, with evidence of haplotype sharing between New Zealand and Tasmania. Nucleotide and haplotype diversity were higher in California than within the British Isles or Hawaii. From the total of 96 haplotypes, seven were found in California, of which four were private. Within California, there have been at least two introductions; based on genetic diversity we were unable to assign a likely source for a single moth found and eradicated in Los Angeles in 2007; however, our data suggest it is unlikely that Hawaii and the British Isles are sources of the major E. postvittana population found throughout the rest of the state since 2006.
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Affiliation(s)
- Leah K Tooman
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
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Wilkinson S, Wiener P, Archibald AL, Law A, Schnabel RD, McKay SD, Taylor JF, Ogden R. Evaluation of approaches for identifying population informative markers from high density SNP chips. BMC Genet 2011; 12:45. [PMID: 21569514 PMCID: PMC3118130 DOI: 10.1186/1471-2156-12-45] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 05/13/2011] [Indexed: 12/31/2022] Open
Abstract
Background Genetic markers can be used to identify and verify the origin of individuals. Motivation for the inference of ancestry ranges from conservation genetics to forensic analysis. High density assays featuring Single Nucleotide Polymorphism (SNP) markers can be exploited to create a reduced panel containing the most informative markers for these purposes. The objectives of this study were to evaluate methods of marker selection and determine the minimum number of markers from the BovineSNP50 BeadChip required to verify the origin of individuals in European cattle breeds. Delta, Wright's FST, Weir & Cockerham's FST and PCA methods for population differentiation were compared. The level of informativeness of each SNP was estimated from the breed specific allele frequencies. Individual assignment analysis was performed using the ranked informative markers. Stringency levels were applied by log-likelihood ratio to assess the confidence of the assignment test. Results A 95% assignment success rate for the 384 individually genotyped animals was achieved with < 80, < 100, < 140 and < 200 SNP markers (with increasing stringency threshold levels) across all the examined methods for marker selection. No further gain in power of assignment was achieved by sampling in excess of 200 SNP markers. The marker selection method that required the lowest number of SNP markers to verify the animal's breed origin was Wright's FST (60 to 140 SNPs depending on the chosen degree of confidence). Certain breeds required fewer markers (< 100) to achieve 100% assignment success. In contrast, closely related breeds require more markers (~200) to achieve > 95% assignment success. The power of assignment success, and therefore the number of SNP markers required, is dependent on the levels of genetic heterogeneity and pool of samples considered. Conclusions While all SNP selection methods produced marker panels capable of breed identification, the power of assignment varied markedly among analysis methods. Thus, with effective exploration of available high density genetic markers, a diagnostic panel of highly informative markers can be produced.
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Affiliation(s)
- Samantha Wilkinson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK.
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King TL, Eackles MS, Chapman DC. Tools for assessing kinship, population structure, phylogeography, and interspecific hybridization in Asian carps invasive to the Mississippi River, USA: isolation and characterization of novel tetranucleotide microsatellite DNA loci in silver carp Hypophthalmichthys molitrix. CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-010-9285-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ramakrishnan AP, Musial T, Cruzan MB. Shifting dispersal modes at an expanding species' range margin. Mol Ecol 2010; 19:1134-46. [PMID: 20456225 DOI: 10.1111/j.1365-294x.2010.04543.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While it is generally recognized that noncontiguous (long-distance) dispersal of small numbers of individuals is important for range expansion over large geographic areas, it is often assumed that colonization on more local scales proceeds by population expansion and diffusion dispersal (larger numbers of individuals colonizing adjacent sites). There are few empirical studies of dispersal modes at the front of expanding ranges, and very little information is available on dispersal dynamics at smaller geographic scales where we expect contiguous (diffusion) dispersal to be prevalent. We used highly polymorphic genetic markers to characterize dispersal modes at a local geographic scale for populations at the edge of the range of a newly invasive grass species (Brachypodium sylvaticum) that is undergoing rapid range expansion in the Pacific Northwest of North America. Comparisons of Bayesian clustering of populations, patterns of genetic diversity, and gametic disequilibrium indicate that new populations are colonized ahead of the invasion front by noncontiguous dispersal from source populations, with admixture occurring as populations age. This pattern of noncontiguous colonization was maintained even at a local scale. Absence of evidence for dispersal among adjacent pioneer sites at the edge of the expanding range of this species suggests that pioneer populations undergo an establishment phase during which they do not contribute emigrants for colonization of neighbouring sites. Our data indicate that dispersal modes change as the invasion matures: initial colonization processes appear to be dominated by noncontiguous dispersal from only a few sources, while contiguous dispersal may play a greater role once populations become established.
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Affiliation(s)
- Alisa P Ramakrishnan
- Department of Biology, Portland State University, PO Box 751, Portland, OR 97207-0751, USA.
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King TL, Johnson RL. Novel tetra-nucleotide microsatellite DNA markers for assessing the evolutionary genetics and demographics of Northern Snakehead (Channa argus) invading North America. CONSERV GENET RESOUR 2010. [DOI: 10.1007/s12686-010-9256-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Palsbøll PJ, Zachariah Peery M, Bérubé M. Detecting populations in the 'ambiguous' zone: kinship-based estimation of population structure at low genetic divergence. Mol Ecol Resour 2010; 10:797-805. [PMID: 21565091 DOI: 10.1111/j.1755-0998.2010.02887.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Identifying population structure is one of the most common and important objectives of spatial analyses using population genetic data. Population structure is detected either by rejecting the null hypothesis of a homogenous distribution of genetic variation, or by estimating low migration rates. Issues arise with most current population genetic inference methods when the genetic divergence is low among putative populations. Low levels of genetic divergence may be as a result of either high ongoing migration or historic high migration but no current, ongoing migration. We direct attention to recent developments in the use of the tempo-spatial distribution of closely related individuals to detect population structure or estimate current migration rates. These 'kinship-based' approaches complement more traditional population-based genetic inference methods by providing a means to detect population structure and estimate current migration rates when genetic divergence is low. However, for kinship-based methods to become widely adopted, formal estimation procedures applicable to a range of species life histories are needed.
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Affiliation(s)
- Per J Palsbøll
- Department of Genetics, Microbiology and Toxicology, Stockholm University, SE-106 91 Stockholm, Sweden Department of Forest and Wildlife Ecology, University of Wisconsin Madison, 1630 Linden Drive, Madison, WI 53706, USA
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Foster JT, Allan GJ, Chan AP, Rabinowicz PD, Ravel J, Jackson PJ, Keim P. Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis). BMC PLANT BIOLOGY 2010; 10:13. [PMID: 20082707 PMCID: PMC2832895 DOI: 10.1186/1471-2229-10-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 01/18/2010] [Indexed: 05/21/2023]
Abstract
BACKGROUND Castor bean (Ricinus communis) is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale). We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs) at 48 loci. RESULTS Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74%) followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population phiPT values, p < 0.01). CONCLUSION Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity.
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Affiliation(s)
- Jeffrey T Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073 USA
| | - Gerard J Allan
- Department of Biological Sciences, Environmental Genetics and Genomics Laboratory, Northern Arizona University, Flagstaff, AZ 86011-5640 USA
| | - Agnes P Chan
- J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850 USA
| | - Pablo D Rabinowicz
- J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850 USA
- Institute for Genome Sciences, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201 USA
- Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201 USA
| | - Jacques Ravel
- J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850 USA
- Institute for Genome Sciences, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201 USA
- Department of Microbiology & Immunology, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201 USA
| | - Paul J Jackson
- Defense Biology Division, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073 USA
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Geller JB, Darling JA, Carlton JT. Genetic perspectives on marine biological invasions. ANNUAL REVIEW OF MARINE SCIENCE 2010; 2:367-93. [PMID: 21141669 DOI: 10.1146/annurev.marine.010908.163745] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The extent to which the geographic distributions of marine organisms have been reshaped by human activities remains underappreciated, and so does, consequently, the impact of invasive species on marine ecosystems. The application of molecular genetic data in fields such as population genetics, phylogeography, and evolutionary biology have improved our ability to make inferences regarding invasion histories. Genetic methods have helped to resolve longstanding questions regarding the cryptogenic status of marine species, facilitated recognition of cryptic marine biodiversity, and provided means to determine the sources of introduced marine populations and to begin to recover the patterns of anthropogenic reshuffling of the ocean's biota. These approaches stand to aid materially in the development of effective management strategies and sustainable science-based policies. Continued advancements in the statistical analysis of genetic data promise to overcome some existing limitations of current approaches. Still other limitations will be best addressed by concerted collaborative and multidisciplinary efforts that recognize the important synergy between understanding the extent of biological invasions and coming to a more complete picture of both modern-day and historical marine biogeography.
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Affiliation(s)
- Jonathan B Geller
- Moss Landing Marine Laboratories, Moss Landing, California 95039, USA.
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Survivors or reinvaders? Using genetic assignment to identify invasive pests following eradication. Biol Invasions 2009. [DOI: 10.1007/s10530-009-9586-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mukesh M, Sodhi M, Kataria R, Mishra B. Use of microsatellite multilocus genotypic data for individual assignment assay in six native cattle breeds from north-western region of India. Livest Sci 2009. [DOI: 10.1016/j.livsci.2008.05.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Keller SR, Taylor DR. History, chance and adaptation during biological invasion: separating stochastic phenotypic evolution from response to selection. Ecol Lett 2008; 11:852-66. [PMID: 18422638 DOI: 10.1111/j.1461-0248.2008.01188.x] [Citation(s) in RCA: 236] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Stephen R Keller
- Department of Biology, University of Virginia, Charlottesville, VA 22904-4328, USA.
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Dudaniec RY, Gardner MG, Donnellan S, Kleindorfer S. Genetic variation in the invasive avian parasite, Philornis downsi (Diptera, Muscidae) on the Galápagos archipelago. BMC Ecol 2008; 8:13. [PMID: 18671861 PMCID: PMC2527555 DOI: 10.1186/1472-6785-8-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Accepted: 07/31/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the dispersal and genetic structure of invasive insects across islands is important for designing management plans that are appropriate at spatial and temporal scales. For invasive parasites, population dynamics are largely determined by the distribution and density of their host species. The introduced parasitic fly, Philornis downsi, parasitises nestlings of endemic birds on all major islands of the Galápagos archipelago. The fly's high mortality and fitness impacts are of conservation concern for vulnerable and declining species of Darwin's finches. Using microsatellite data in Bayesian clustering and landscape genetic analyses, we examine gene flow and dispersal in P. downsi between three islands and across habitats (highlands, lowlands) and examine for the presence of population bottlenecks. We also examine variation at the mitochondrial gene CO1 across islands to establish if cryptic species were present. RESULTS Both the mitochondrial and microsatellite data were consistent with there being a single species across islands. We found low genetic differentiation between islands and strong evidence for inter-island gene flow, or shared recent ancestry among individuals. Landscape genetic analysis identified two genetic clusters: one encompassing Santa Cruz and Isabela, and one on Floreana Island. There was no evidence of genetic differentiation between habitats and molecular variance was mainly attributable to within individuals. The combined P. downsi population was found to have undergone a population bottleneck. CONCLUSION Philornis downsi populations have high connectivity within and between islands, with low levels of genetic differentiation between Floreana and the other two islands examined. The genetic bottleneck found across islands suggests there was a small founding population or few introduction events of P. downsi. The high dispersal capacity and wide habitat use of P. downsi highlights the significant threat that this parasite poses to the Galápagos avifauna. Our findings are relevant for assessing the viability of methods to control P. downsi on Galápagos, such as the sterile insect technique.
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Affiliation(s)
- Rachael Y Dudaniec
- School of Biological Sciences, Flinders University GPO Box 2100, Adelaide, South Australia 5001, Australia.
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Lozier JD, Roderick GK, Mills NJ. Tracing the invasion history of mealy plum aphid, Hyalopterus pruni (Hemiptera: Aphididae), in North America: a population genetics approach. Biol Invasions 2008. [DOI: 10.1007/s10530-008-9248-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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ORSINI L, CORANDER J, ALASENTIE A, HANSKI I. Genetic spatial structure in a butterfly metapopulation correlates better with past than present demographic structure. Mol Ecol 2008; 17:2629-42. [DOI: 10.1111/j.1365-294x.2008.03782.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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MUIRHEAD JIMR, GRAY DEREKK, KELLY DAVIDW, ELLIS SANDRAM, HEATH DANIELD, MACISAAC HUGHJ. Identifying the source of species invasions: sampling intensity vs. genetic diversity. Mol Ecol 2008; 17:1020-35. [DOI: 10.1111/j.1365-294x.2008.03669.x] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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OKADA MIKI, AHMAD RIAZ, JASIENIUK MARIE. Microsatellite variation points to local landscape plantings as sources of invasive pampas grass (Cortaderia selloana) in California. Mol Ecol 2007; 16:4956-71. [DOI: 10.1111/j.1365-294x.2007.03568.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Pope LC, Butlin RK, Wilson GJ, Woodroffe R, Erven K, Conyers CM, Franklin T, Delahay RJ, Cheeseman CL, Burke T. Genetic evidence that culling increases badger movement: implications for the spread of bovine tuberculosis. Mol Ecol 2007; 16:4919-29. [PMID: 17944854 DOI: 10.1111/j.1365-294x.2007.03553.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Eurasian badger (Meles meles) has been implicated in the transmission of bovine tuberculosis (TB, caused by Mycobacterium bovis) to cattle. However, evidence suggests that attempts to reduce the spread of TB among cattle in Britain by culling badgers have mixed effects. A large-scale field experiment (the randomized badger culling trial, RBCT) showed that widespread proactive badger culling reduced the incidence of TB in cattle within culled areas but that TB incidence increased in adjoining areas. Additionally, localized reactive badger culling increased the incidence of TB in cattle. It has been suggested that culling-induced perturbation of badger social structure may increase individual movements and elevate the risk of disease transmission between badgers and cattle. Field studies support this hypothesis, by demonstrating increases in badger group ranges and the prevalence of TB infection in badgers following culling. However, more evidence on the effect of culling on badger movements is needed in order to predict the epidemiological consequences of this control strategy. Here, analysis of the genetic signatures of badger populations in the RBCT revealed increased dispersal following culling. While standard tests provided evidence for greater dispersal after culling, a novel method indicated that this was due to medium- and long-distance dispersal, in addition to previously reported increases in home-range size. Our results also indicated that, on average, badgers infected with M. bovis moved significantly farther than did uninfected badgers. A disease control strategy that included culling would need to take account of the potentially negative epidemiological consequences of increased badger dispersal.
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Affiliation(s)
- Lisa C Pope
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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45
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Pascual M, Chapuis MP, Mestres F, Balanyà J, Huey RB, Gilchrist GW, Serra L, Estoup A. Introduction history of Drosophila subobscura in the New World: a microsatellite-based survey using ABC methods. Mol Ecol 2007; 16:3069-83. [PMID: 17651188 DOI: 10.1111/j.1365-294x.2007.03336.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Drosophila subobscura is a Palearctic species that was first observed in South and North America in the early 1980s, and that rapidly invaded broad latitudinal ranges on both continents. To trace the source and history of this invasion, we obtained genotypic data on nine microsatellite loci from two South American, two North American and five European populations of D. subobscura. We analysed these data with traditional statistics as well as with an approximate Bayesian computation (ABC) framework. ABC methods yielded the strongest support for the scenario involving a serial introduction with founder events from Europe into South America, and then from South America into North America. Stable effective population size of the source population was very large (around one million individuals), and the propagule size was notably smaller for the introduction into South America (i.e. high bottleneck severity index with only a few effective founders) but considerably larger for the subsequent introduction into North America (i.e. low bottleneck severity index with around 100-150 effective founders). Finally, the Mediterranean region of Europe (and most likely Barcelona from the localities so far analysed) is proposed as the source of the New World flies, based on mean individual assignment statistics.
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Affiliation(s)
- M Pascual
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain.
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46
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Song BH, Mitchell-Olds T. High genetic diversity and population differentiation in Boechera fecunda, a rare relative of Arabidopsis. Mol Ecol 2007; 16:4079-88. [PMID: 17784916 DOI: 10.1111/j.1365-294x.2007.03500.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Conservation of endangered species becomes a critical issue with the increasing rates of extinction. In this study, we use 13 microsatellite loci and 27 single-copy nuclear loci to investigate the population genetics of Boechera fecunda, a rare relative of Arabidopsis thaliana, known from only 21 populations in Montana. We investigated levels of genetic diversity and population structure in comparison to its widespread congener, Boechera stricta, which shares similar life history and mating system. Despite its rarity, B. fecunda had levels of genetic diversity similar to B. stricta for both microsatellites and nucleotide polymorphism. Populations of B. fecunda are highly differentiated, with a majority of genetic diversity existing among populations (F(ST) = 0.57). Differences in molecular diversity and allele frequencies between western and eastern population groups suggest they experienced very different evolutionary histories.
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Affiliation(s)
- Bao-Hua Song
- Department of Biology, Duke University, PO Box 90338, Durham, NC 27708, USA
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47
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Kruse I, Hare MP. GENETIC DIVERSITY AND EXPANDING NONINDIGENOUS RANGE OF THE RHIZOCEPHALAN LOXOTHYLACUS PANOPAEI PARASITIZING MUD CRABS IN THE WESTERN NORTH ATLANTIC. J Parasitol 2007; 93:575-82. [PMID: 17626349 DOI: 10.1645/ge-888r.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Nonindigenous parasite introductions and range expansions have become a major concern because of their potential to restructure communities and impact fisheries. Molecular markers provide an important tool for reconstructing the pattern of introduction. The parasitic castrator Loxothylacus panopaei, a rhizocephalan barnacle, infects estuarine mud crabs in the Gulf of Mexico and southeastern Florida. A similar parasite introduced into Chesapeake Bay before 1964, presumably via infected crabs associated with oysters from the Gulf of Mexico, was identified as L. panopaei. Our samples of this species during 2004 and 2005 show that the introduced range has expanded as far south as Edgewater, Florida, just north of the northern endemic range limit. The nonindigenous range expanded southward at a rate of up to 165 km/yr with relatively high prevalence, ranging from 30 to 93%. Mitochondrial DNA sequences from the cytochrome oxidase I gene showed that these nonindigenous L. panopaei are genetically distinct from the endemic parasites in southeastern Florida and the eastern Gulf of Mexico. The genetic difference was also associated with distinct host spectra. These results are incompatible with an eastern Gulf source population, but suggest that unrecognized genetic and phenotypic population structure may occur among Gulf of Mexico populations of Loxothvlacus.
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Affiliation(s)
- Inken Kruse
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA.
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48
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Taylor DR, Keller SR. Historical range expansion determines the phylogenetic diversity introduced during contemporary species invasion. Evolution 2007; 61:334-45. [PMID: 17348944 DOI: 10.1111/j.1558-5646.2007.00037.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For a species rapidly expanding its geographic range, such as during biological invasion, most alleles in the introduced range will have their evolutionary origins in the native range. Yet, the way in which historical processes occurring over evolutionary time in the native range contribute to the diversity sampled during contemporary invasion is largely unknown. We used chloroplast DNA (cpDNA) gene genealogies and coalescent methods to study two congeneric plants, Silene latifolia and S. vulgaris. We examined how phylogenetic diversity was shaped by demographic growth and historical range expansions in the native European range, and how this history affected the diversity sampled during their recent invasion of North America. Genealogies from both species depart from neutrality, likely as a result of demographic expansion in the ancestral range, the timing of which corresponds to shortly after each species originated. However, the species differ in the spatial distribution of cpDNA lineages across the native range. Silene latifolia shows a highly significant phylogeographic structure that most likely reflects different avenues of the post-glacial expansion into northern Europe from Mediterranean refugia. By contrast, cpDNA lineages in S. vulgaris have been widely scattered across Europe during, or since, the most recent post-glacial expansion. These different evolutionary histories resulted in dramatic differences in how phylogenetic diversity was sampled during invasion of North America. In S. latifolia, relatively few, discrete invasion events from a structured native range resulted in a rather severe genetic bottleneck, but also opportunities for admixture among previously isolated lineages. In S. vulgaris, lack of genetic structure was accompanied by more representative sampling of phylogenetic diversity during invasion, and reduced potential for admixture. Our results provide clear insights into how historical processes may feed forward to influence the phylogenetic diversity of species invading new geographic ranges.
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Affiliation(s)
- Douglas R Taylor
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904-4328, USA.
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49
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Lee PLM, Luschi P, Hays GC. Detecting female precise natal philopatry in green turtles using assignment methods. Mol Ecol 2007; 16:61-74. [PMID: 17181721 DOI: 10.1111/j.1365-294x.2006.03115.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
It is well established that sea turtles return to natal rookeries to mate and lay their eggs, and that individual females are faithful to particular nesting sites within the rookery. Less certain is whether females are precisely returning to their natal beach. Attempts to demonstrate such precise natal philopatry with genetic data have had mixed success. Here we focused on the green turtles of three nesting sites in the Ascension Island rookery, separated by 5-15 km. Our approach differed from previous work in two key areas. First, we used male microsatellite data (five loci) reconstructed from samples collected from their offspring (N = 17) in addition to data for samples taken directly from females (N = 139). Second, we employed assignment methods in addition to the more traditional F-statistics. No significant genetic structure could be demonstrated with F(ST). However, when average assignment probabilities of females were examined, those for nesting populations in which they were sampled were indeed significantly higher than their probabilities for other populations (Mann-Whitney U-test: P < 0.001). Further evidence was provided by a significant result for the mAI(C) test (P < 0.001), supporting greater natal philopatry for females compared with males. The results suggest that female natal site fidelity was not sufficient for significant genetic differentiation among the nesting populations within the rookery, but detectable with assignment tests.
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Affiliation(s)
- Patricia L M Lee
- Institute of Environmental Sustainability, Department of Biological Sciences, University of Wales Swansea, Swansea SA2 8PP, UK.
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50
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Mao Y, Chang H, Yang Z, Zhang L, Xu M, Sun W, Chang G, Song G. Genetic Structure and Differentiation of Three Chinese Indigenous Cattle Populations. Biochem Genet 2007; 45:195-209. [PMID: 17265139 DOI: 10.1007/s10528-006-9061-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Levels of genetic differentiation, gene flow, and genetic structure of three indigenous cattle populations (Luxi, Bohai, and Minnan) and two reference cattle populations (Chinese Holstein and Qinhai yak) in China were estimated using the information from 12 microsatellites, and 141 microsatellite alleles were identified. The mean number of alleles per locus ranged from 2.9005 in yak to 4.9722 in Holstein. The observed heterozygosity ranged from 0.5325 (yak) to 0.7719 (Holstein); 29 private alleles were detected. The global heterozygote deficit across all populations amounted to 58.5% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds amounted to 43.2%. The five cattle populations were highly differentiated (F (st) = 26.9%, p < 0.001) at all loci. The heterozygote deficit within the population was highest in Luxi cattle and lowest in yak. The average number of effective migrants exchanged per generation was highest (1.149) between Luxi and Holstein, and lowest (0.509) between Luxi and yak. With the application of prior population information, cluster analysis achieved posterior probabilities from 91% to 98% of correctly assigning individuals to populations. Combining the information of cluster analysis, gene flow, and Structure analysis, the five cattle populations belong to three genetic clusters, a taurine (Luxi and Chinese Holstein), a zebu (Bohai and Minnan), and a yak cluster. This indicates that Bohai black is closer to Bos indicus than Luxi cattle. The evolution and development of three indigenous cattle populations are discussed.
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Affiliation(s)
- Yongjiang Mao
- Animal Science and Technology College, Yangzhou University, Yangzhou, Jiangsu 225009, P.R. China
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