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Purificacion M, Shah RBM, De Meeûs T, Bakar SB, Savantil AB, Yusof MM, Amalin D, Nguyen H, Sulistyowati E, Budiman A, Ekayanti A, Niogret J, Ravel S, Vreysen MJB, Abd-Alla AMM. Development and characterization of microsatellite markers for population genetics of the cocoa pod borer Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae). PLoS One 2024; 19:e0297662. [PMID: 38603675 PMCID: PMC11008836 DOI: 10.1371/journal.pone.0297662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 01/09/2024] [Indexed: 04/13/2024] Open
Abstract
The cocoa pod borer (CPB) Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae) is one of the major constraints for cocoa production in South East Asia. In addition to cultural and chemical control methods, autocidal control tactics such as the Sterile Insect Technique (SIT) could be an efficient addition to the currently control strategy, however SIT implementation will depend on the population genetics of the targeted pest. The aim of the present work was to search for suitable microsatellite loci in the genome of CPB that is partially sequenced. Twelve microsatellites were initially selected and used to analyze moths collected from Indonesia, Malaysia, and the Philippines. A quality control verification process was carried out and seven microsatellites found to be suitable and efficient to distinguish differences between CPB populations from different locations. The selected microsatellites were also tested against a closely related species, i.e. the lychee fruit borer Conopomorpha sinensis (LFB) from Vietnam and eight loci were found to be suitable. The availability of these novel microsatellite loci will provide useful tools for the analysis of the population genetics and gene flow of these pests, to select suitable CPB strains to implement the SIT.
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Affiliation(s)
- Marynold Purificacion
- Biological Control Research Unit, Center for Natural Science and Environmental Research, De La Salle University, Manila, Philippines
| | - Roslina Binti Mohd Shah
- Centre for Cocoa Biotechnology Research, Malaysian Cocoa Board, Kota Kinabalu, Sabah, Malaysia
| | - Thierry De Meeûs
- Intertryp, Univ Montpellier, Cirad, IRD, Montpellier, France
- IRD, UMR Intertryp, Cirad, Campus International de Baillarguet, Montpellier, France
| | | | - Anisah Bintil Savantil
- Centre for Cocoa Biotechnology Research, Malaysian Cocoa Board, Kota Kinabalu, Sabah, Malaysia
| | - Meriam Mohd Yusof
- Centre for Cocoa Biotechnology Research, Malaysian Cocoa Board, Kota Kinabalu, Sabah, Malaysia
| | - Divina Amalin
- Biological Control Research Unit, Center for Natural Science and Environmental Research, De La Salle University, Manila, Philippines
| | - Hien Nguyen
- Plant Protection Research Institute, Duc Thang, Hanoi, Vietnam
| | | | - Aris Budiman
- Indonesian Coffee and Cocoa Research Institute, Jember, Indonesia
| | - Arni Ekayanti
- Mars Cocoa Research Centre, Mars Wrigley, Sulawesi Selatan, Indonesia
| | - Jerome Niogret
- Mars Wrigley, Centre for Tropical Environmental & Sustainability Science, James Cook University Nguma-bada Campus, Smithfield, Australia
| | - Sophie Ravel
- Intertryp, Univ Montpellier, Cirad, IRD, Montpellier, France
| | - Marc J. B. Vreysen
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | - Adly M. M. Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna, Austria
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Ojeda-Marín C, Cervantes I, Formoso-Rafferty N, Gutiérrez JP. Genomic inbreeding measures applied to a population of mice divergently selected for birth weight environmental variance. Front Genet 2023; 14:1303748. [PMID: 38155710 PMCID: PMC10752941 DOI: 10.3389/fgene.2023.1303748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023] Open
Abstract
This study aimed to compare different inbreeding measures estimated from pedigree and molecular data from two divergent mouse lines selected for environmental birth weight during 26 generations. Furthermore, the performance of different approaches and both molecular and pedigree data sources for estimating Ne were tested in this population. A total of 1,699 individuals were genotyped using a high-density genotyping array. Genomic relationship matrices were used to calculate molecular inbreeding: Nejati-Javaremi (F NEJ), Li and Horvitz (F L&H), Van Raden method 1 (F VR1) and method 2 (F VR2), and Yang (F YAN). Inbreeding based on runs of homozygosity (F ROH) and pedigree inbreeding (F PED) were also computed. F ROH, F NEJ, and F L&H were also adjusted for their average values in the first generation of selection and named F ROH0, F NEJ0, and F L&H0. ∆F was calculated from pedigrees as the individual inbreeding rate between the individual and his parents (∆F PEDt) and individual increases in inbreeding (∆F PEDi). Moreover, individual ∆F was calculated from the different molecular inbreeding coefficients (∆F NEJ0, ∆F L&H, ∆F L&H0, ∆F VR1, ∆F VR2, ∆F YAN, and ∆F ROH0). The Ne was obtained from different ∆F, such as Ne PEDt, Ne PEDi, Ne NEJ0, Ne L&H, Ne L&H0, Ne VR1, Ne VR2, Ne YAN, and Ne ROH0. Comparing with F PED , F ROH , F NEJ and F VR2 overestimated inbreeding while F NEJ0 , F L&H , F L&H0 , F VR1 and F YAN underestimated inbreeding. Correlations between inbreeding coefficients and ∆F were calculated. F ROH had the highest correlation with F PED (0.89); F YAN had correlations >0.95 with all the other molecular inbreeding coefficients. Ne PEDi was more reliable than Ne PEDt and presented similar behaviour to Ne L&H0 and Ne NEJ0. Stable trends in Ne were not observed until the 10th generation. In the 10th generation Ne PEDi was 42.20, Ne L&H0 was 45.04 and Ne NEJ0 was 45.05 and in the last generation these Ne were 35.65, 35.94 and 35.93, respectively F ROH presented the highest correlation with F PED, which addresses the identity by descent probability (IBD). The evolution of Ne L&H0 and Ne NEJ0 was the most similar to that of Ne PEDi. Data from several generations was necessary to reach a stable trend for Ne, both with pedigree and molecular data. This population was useful to test different approaches to computing inbreeding coefficients and Ne using molecular and pedigree data.
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Affiliation(s)
- Candela Ojeda-Marín
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Isabel Cervantes
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Nora Formoso-Rafferty
- Departamento de Producción Agraria, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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Diaz-Martin Z, Cisternas-Fuentes A, Kay KM, Raguso RA, Skogen K, Fant J. Reproductive strategies and their consequences for divergence, gene flow, and genetic diversity in three taxa of Clarkia. Heredity (Edinb) 2023; 131:338-349. [PMID: 37700028 PMCID: PMC10673949 DOI: 10.1038/s41437-023-00649-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/14/2023] Open
Abstract
Differences in reproductive strategies can have important implications for macro- and micro-evolutionary processes. We used a comparative approach through a population genetics lens to evaluate how three distinct reproductive strategies shape patterns of divergence among as well as gene flow and genetic diversity within three closely related taxa in the genus Clarkia. One taxon is a predominantly autonomous self-fertilizer and the other two taxa are predominantly outcrossing but vary in the primary pollinator they attract. In genotyping populations using genotyping-by-sequencing and comparing loci shared across taxa, our results suggest that differences in reproductive strategies in part promote evolutionary divergence among these closely related taxa. Contrary to expectations, we found that the selfing taxon had the highest levels of heterozygosity but a low rate of polymorphism. The high levels of fixed heterozygosity for a subset of loci suggests this pattern is driven by the presence of structural rearrangements in chromosomes common in other Clarkia taxa. In evaluating patterns within taxa, we found a complex interplay between reproductive strategy and geographic distribution. Differences in the mobility of primary pollinators did not translate to a difference in rates of genetic diversity and gene flow within taxa - a pattern likely due to one taxon having a patchier distribution and a less temporally and spatially reliable pollinator. Taken together, this work advances our understanding of the factors that shape gene flow and the distribution of genetic diversity within and among closely related taxa.
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Affiliation(s)
- Zoe Diaz-Martin
- Department of Biology, Spelman College, Atlanta, GA, 30314, USA.
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60035, USA.
| | - Anita Cisternas-Fuentes
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60035, USA
- Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, IL, 60208, USA
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, 130 McAllister Way, Santa Cruz, CA, 95060, USA
| | - Robert A Raguso
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Krissa Skogen
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60035, USA
- Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, IL, 60208, USA
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29631, USA
| | - Jeremie Fant
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60035, USA
- Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, IL, 60208, USA
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Arias KD, Gutiérrez JP, Fernández I, Álvarez I, Goyache F. Approaching autozygosity in a small pedigree of Gochu Asturcelta pigs. Genet Sel Evol 2023; 55:74. [PMID: 37880572 PMCID: PMC10601182 DOI: 10.1186/s12711-023-00846-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 10/03/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND In spite of the availability of single nucleotide polymorphism (SNP) array data, differentiation between observed homozygosity and that caused by mating between relatives (autozygosity) introduces major difficulties. Homozygosity estimators show large variation due to different causes, namely, Mendelian sampling, population structure, and differences among chromosomes. Therefore, the ascertainment of how inbreeding is reflected in the genome is still an issue. The aim of this research was to study the usefulness of genomic information for the assessment of genetic diversity in the highly endangered Gochu Asturcelta pig breed. Pedigree depth varied from 0 (founders) to 4 equivalent discrete generations (t). Four homozygosity parameters (runs of homozygosity, FROH; heterozygosity-rich regions, FHRR; Li and Horvitz's, FLH; and Yang and colleague's FYAN) were computed for each individual, adjusted for the variability in the base population (BP; six individuals) and further jackknifed over autosomes. Individual increases in homozygosity (depending on t) and increases in pairwise homozygosity (i.e., increase in the parents' mean) were computed for each individual in the pedigree, and effective population size (Ne) was computed for five subpopulations (cohorts). Genealogical parameters (individual inbreeding, individual increase in inbreeding, and Ne) were used for comparisons. RESULTS The mean F was 0.120 ± 0.074 and the mean BP-adjusted homozygosity ranged from 0.099 ± 0.081 (FLH) to 0.152 ± 0.075 (FYAN). After jackknifing, the mean values were slightly lower. The increase in pairwise homozygosity tended to be twofold higher than the corresponding individual increase in homozygosity values. When compared with genealogical estimates, estimates of Ne obtained using FYAN tended to have low root-mean-squared errors. However, Ne estimates based on increases in pairwise homozygosity using both FROH and FHRR estimates of genomic inbreeding had lower root-mean-squared errors. CONCLUSIONS Parameters characterizing homozygosity may not accurately depict losses of variability in small populations in which breeding policy prohibits matings between close relatives. After BP adjustment, the performance of FROH and FHRR was highly consistent. Assuming that an increase in homozygosity depends only on pedigree depth can lead to underestimating it in populations with shallow pedigrees. An increase in pairwise homozygosity computed from either FROH or FHRR is a promising approach for characterizing autozygosity.
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Affiliation(s)
- Katherine D Arias
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Universidad Complutense de Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
| | - Iván Fernández
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Spain
| | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Spain
| | - Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Spain.
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Feigs JT, Holzhauer SIJ, Huang S, Brunet J, Diekmann M, Hedwall PO, Kramp K, Naaf T. Pollinator movement activity influences genetic diversity and differentiation of spatially isolated populations of clonal forest herbs. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.908258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In agricultural landscapes, forest herbs live in small, spatially isolated forest patches. For their long-term survival, their populations depend on animals as genetic linkers that provide pollen- or seed-mediated gene flow among different forest patches. However, whether insect pollinators serve as genetic linkers among spatially isolated forest herb populations in agricultural landscapes remains to be shown. Here, we used population genetic methods to analyze: (A) the genetic diversity and genetic differentiation of populations of two common, slow-colonizing temperate forest herb species [Polygonatum multiflorum (L.) All. and Anemone nemorosa L.] in spatially isolated populations within three agricultural landscapes in Germany and Sweden and (B) the movement activity of their most relevant associated pollinator species, i.e., the bumblebee Bombus pascuorum (Scopoli, 1,763) and the hoverfly Melanostoma scalare (Fabricus, 1,794), respectively, which differ in their mobility. We tested whether the indicated pollinator movement activity affected the genetic diversity and genetic differentiation of the forest herb populations. Bumblebee movement indicators that solely indicated movement activity between the forest patches affected both genetic diversity and genetic differentiation of the associated forest herb P. multiflorum in a way that can be explained by pollen-mediated gene flow among the forest herb populations. In contrast, movement indicators reflecting the total movement activity at a forest patch (including within-forest patch movement activity) showed unexpected effects for both plant-pollinator pairs that might be explained by accelerated genetic drift due to enhanced sexual reproduction. Our integrated approach revealed that bumblebees serve as genetic linkers of associated forest herb populations, even if they are more than 2 km apart from each other. No such evidence was found for the forest associated hoverfly species which showed significant genetic differentiation among forest patches itself. Our approach also indicated that a higher within-forest patch movement activity of both pollinator species might enhance sexual recruitment and thus diminishes the temporal buffer that clonal growth provides against habitat fragmentation effects.
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6
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Waples RS.
TheWeight
: A simple and flexible algorithm for simulating non‐ideal, age‐structured populations. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robin S. Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration Seattle, WA, 98112 USA
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Guo Y, Liang J, Lv C, Wang Y, Wu G, Ding X, Quan G. Sequencing Reveals Population Structure and Selection Signatures for Reproductive Traits in Yunnan Semi-Fine Wool Sheep ( Ovis aries). Front Genet 2022; 13:812753. [PMID: 35345667 PMCID: PMC8957090 DOI: 10.3389/fgene.2022.812753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/18/2022] [Indexed: 12/30/2022] Open
Abstract
Yunnan semi-fine wool sheep are among the most important cultivated sheep breeds in China. However, their population structure, genetic characteristics and traits of interest are poorly studied. In this study, we systematically studied the population characteristics and selection signatures of 40 Yunnan semi-fine wool sheep using SNPs obtained from whole-genome resequencing data. A total of 1393 Gb of clean data were acquired. The mapping rate against the reference genome was 91.23% on average (86.01%–92.26%), and the average sequence depth was 9.51X. After filtering, 28,593,198 SNPs and 4,725,259 indels with high quality were obtained. The heterozygosity rate, inbreeding coefficient and effective population size of the sheep were calculated to preliminarily explore their genetic characteristics. The average heterozygosity rate was 0.264, the average inbreeding coefficient was 0.0099, and the effective population size estimated from the heterozygote excess (HE) was 242.9. Based on the Tajima’s D and integrated haplotype score (iHS) approaches, 562 windows and 11,356 core SNPs showed selection signatures in the Yunnan semi-fine wool sheep population. After genome annotation and gene enrichment analysis, we found traces of early domestication in sensory organs, behavioural activity and the nervous system as well as adaptive changes in reproductive and wool traits under selection in this population. Some selected genes related to litter size, including FSHR, BMPR1B and OXT, were identified as being under selection. Specific missense mutations of the FSHR gene that differed from the reference genome were also identified in the population, and we found some SNP variations that may affect litter size. Our findings provide a theoretical basis for the conservation and utilization of Yunnan semi-fine wool sheep. Furthermore, our results reveal some changes common to sheep after domestication and provide a new opportunity to investigate the genetic variation influencing fecundity within a population evolving under artificial selection.
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Affiliation(s)
- Yi Guo
- Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiachong Liang
- Yunnan Provincial Genebank of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Chunrong Lv
- Yunnan Provincial Genebank of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Yi Wang
- Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Guoquan Wu
- Yunnan Provincial Genebank of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Xiangdong Ding
- Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Guobo Quan
- Yunnan Provincial Genebank of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
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Nadachowska‐Brzyska K, Konczal M, Babik W. Navigating the temporal continuum of effective population size. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13740] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | - Wieslaw Babik
- Jagiellonian University in Kraków Faculty of Biology Institute of Environmental Sciences Kraków Poland
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9
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Kidner J, Theodorou P, Engler JO, Taubert M, Husemann M. A brief history and popularity of methods and tools used to estimate micro-evolutionary forces. Ecol Evol 2021; 11:13723-13743. [PMID: 34707813 PMCID: PMC8525119 DOI: 10.1002/ece3.8076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/12/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022] Open
Abstract
Population genetics is a field of research that predates the current generations of sequencing technology. Those approaches, that were established before massively parallel sequencing methods, have been adapted to these new marker systems (in some cases involving the development of new methods) that allow genome-wide estimates of the four major micro-evolutionary forces-mutation, gene flow, genetic drift, and selection. Nevertheless, classic population genetic markers are still commonly used and a plethora of analysis methods and programs is available for these and high-throughput sequencing (HTS) data. These methods employ various and diverse theoretical and statistical frameworks, to varying degrees of success, to estimate similar evolutionary parameters making it difficult to get a concise overview across the available approaches. Presently, reviews on this topic generally focus on a particular class of methods to estimate one or two evolutionary parameters. Here, we provide a brief history of methods and a comprehensive list of available programs for estimating micro-evolutionary forces. We furthermore analyzed their usage within the research community based on popularity (citation bias) and discuss the implications of this bias for the software community. We found that a few programs received the majority of citations, with program success being independent of both the parameters estimated and the computing platform. The only deviation from a model of exponential growth in the number of citations was found for the presence of a graphical user interface (GUI). Interestingly, no relationship was found for the impact factor of the journals, when the tools were published, suggesting accessibility might be more important than visibility.
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Affiliation(s)
- Jonathan Kidner
- General Zoology Institute for Biology Martin Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Panagiotis Theodorou
- General Zoology Institute for Biology Martin Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Jan O Engler
- Terrestrial Ecology Unit Department of Biology Ghent University Ghent Belgium
| | - Martin Taubert
- Aquatic Geomicrobiology Institute for Biodiversity Friedrich Schiller University Jena Jena Germany
| | - Martin Husemann
- General Zoology Institute for Biology Martin Luther University Halle-Wittenberg Halle (Saale) Germany
- Centrum für Naturkunde University of Hamburg Hamburg Germany
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10
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Disentangling the genetic origin of Heracleum persicum (Apiaceae) in Europe: multiple introductions from multiple source populations. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02618-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Moska M, Mucha A, Wierzbicki H, Nowak B. Edible dormouse (
Glis glis
) population study in south‐western Poland provides evidence of multiple paternity and communal nesting. J Zool (1987) 2021. [DOI: 10.1111/jzo.12881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Moska
- Department of Genetics Wroclaw University of Environmental and Life Sciences Wroclaw Poland
| | - A. Mucha
- Department of Genetics Wroclaw University of Environmental and Life Sciences Wroclaw Poland
| | - H. Wierzbicki
- Department of Genetics Wroclaw University of Environmental and Life Sciences Wroclaw Poland
| | - B. Nowak
- Department of Genetics Wroclaw University of Environmental and Life Sciences Wroclaw Poland
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12
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Wright PGR, Schofield H, Mathews F. Can effective population size estimates be used to monitor population trends of woodland bats? A case study of Myotis bechsteinii. Ecol Evol 2021; 11:2015-2023. [PMID: 33717438 PMCID: PMC7920762 DOI: 10.1002/ece3.7143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 12/01/2022] Open
Abstract
Molecular approaches to calculate effective population size estimates (Ne) are increasingly used as an alternative to long-term demographic monitoring of wildlife populations. However, the complex ecology of most long-lived species and the consequent uncertainties in model assumptions means that effective population size estimates are often imprecise. Although methods exist to incorporate age structure into Ne estimations for long-lived species with overlapping generations, they are rarely used owing to the lack of relevant information for most wild populations. Here, we performed a case study on an elusive woodland bat, Myotis bechsteinii, to compare the use of the parentage assignment Ne estimator (EPA) with the more commonly used linkage disequilibrium (LD) Ne estimator in detecting long-term population trends, and assessed the impacts of deploying different overall sample sizes. We used genotypic data from a previously published study, and simulated 48 contrasting demographic scenarios over 150 years using the life history characteristics of this species The LD method strongly outperformed the EPA method. As expected, smaller sample sizes resulted in a reduced ability to detect population trends. Nevertheless, even the smallest sample size tested (n = 30) could detect important changes (60%-80% decline) with the LD method. These results demonstrate that genetic approaches can be an effective way to monitor long-lived species, such as bats, provided that they are undertaken over multiple decades.
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Affiliation(s)
- Patrick G. R. Wright
- Department of Life SciencesUniversity of SussexFalmerUK
- Vincent Wildlife TrustLedburyUK
| | | | - Fiona Mathews
- Department of Life SciencesUniversity of SussexFalmerUK
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García-Castro KL, Rangel-Medrano JD, Landínez-García RM, Márquez EJ. Population genetics of the endangered catfish Pseudoplatystoma magdaleniatum (Siluriformes: Pimelodidae) based on species-specific microsatellite loci. NEOTROPICAL ICHTHYOLOGY 2021. [DOI: 10.1590/1982-0224-2020-0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT The Neotropical catfish genus Pseudoplatystoma comprises eight species of large size, widely distributed in South American basins. The endangered species P. magdaleniatum is endemic to Magdalena basin (Colombia), experiences high fishing pressure and its population genetics is relatively unknown. To study the genetic status and structure of P. magdaleniatum, 25 species-specific polymorphic microsatellite loci were developed using next-generation sequencing and then tested in samples collected in the Magdalena-Cauca basin. Based on 15 of these loci, P. magdaleniatum showed a high number of alleles per locus (9-10), high values of observed (0.762-0.798) and expected (0.770-0.791) heterozygosities, recent reduction of population size and gene flow. These findings constitute a baseline to measure potential changes in genetic diversity and structure of this commercially important species in a basin undergoing high anthropogenic activities.
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14
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He C, DU J, Zhu D, Zhang L. Population viability analysis of small population: a case study for Asian elephant in China. Integr Zool 2020; 15:350-362. [PMID: 32246885 DOI: 10.1111/1749-4877.12432] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small populations are at risk of extinction from deterministic and stochastic factors. Less than 250 Asian elephants (Elephas maximus) remain in China, and are distributed in a few isolated areas; yet, population viability analyses of this endangered population have not been conducted. Here, the current genetic status of the Pu'Er-Mengyang Asian elephant populations in China was analyzed, and the risk of extinction was predicted over the next 500 years. Factors affecting the viability of this population were determined through simulations. The genetic diversity of the population was very low (mean allele number: 3.1; expected heterozygosity: 0.463), even though a recent population bottleneck was not detected. The effective population size was approximately 24.1 adult elephants. Enough adult breeding individuals exist to maintain population viability. VORTEX simulation model showed that this population would not go extinct in the next 500 years. However, illegal poaching and harvesting could negatively affect population size. A sensitivity analysis showed that the mean stochastic growth rate of the study population is sensitive to sex ratio, number of breeding females, mortality of females of different age classes, carrying capacity, and lethal equivalents. Based on our results, we suggest that action should be taken to alleviate inbreeding and any further loss of genetic diversity, by connecting fragmented elephant habitat or by translocating individual elephants. In addition, human-elephant conflict should be mitigated using various modern approaches, including crop guarding techniques, and by encouraging farmers to switch to crops and income sources not vulnerable to elephant raids.
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Affiliation(s)
- Changhuan He
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jiaojiao DU
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Di Zhu
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Li Zhang
- College of Life Sciences, Beijing Normal University, Beijing, China
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15
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Francisco SM, Robalo JI. Time matters: genetic composition and evaluation of effective population size in temperate coastal fish species. PeerJ 2020; 8:e9098. [PMID: 32391212 PMCID: PMC7197400 DOI: 10.7717/peerj.9098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/09/2020] [Indexed: 12/16/2022] Open
Abstract
Background Extensive knowledge on the genetic characterization of marine organisms has been assembled, mainly concerning the spatial distribution and structuring of populations. Temporal monitoring assesses not only the stability in genetic composition but also its trajectory over time, providing critical information for the accurate forecast of changes in genetic diversity of marine populations, particularly important for both fisheries and endangered species management. We assessed fluctuations in genetic composition among different sampling periods in the western Portuguese shore in three fish species. Methods White seabream Diplodus sargus, sand smelt Atherina presbyter and shanny Lipophrys pholis were chosen, because of their genetic patterns in distinct ecological environments, insight into historical and contemporary factors influencing population effective size (Ne), and degree of commercial exploitation. Samples were obtained near Lisbon between 2003 and 2014 and screened for genetic variation with mitochondrial and nuclear markers. Analyses included genealogies, genetic diversities, temporal structures and contemporary Ne. Results For mtDNA no temporal structure was detected, while for nDNA significant differences were recorded between some sampling periods for the shanny and the sand smelt. Haplotype networks revealed deep genealogies, with various levels of diversification. The shanny revealed a smaller Ne/generation when compared to the other species, which, in turn, revealed no evidence of genetic drift for most study periods. These results highlight the fact that temporal variations in genetic pool composition should be considered when evaluating the population structure of fish species with long distance dispersal, which are more vulnerable to recruitment fluctuations.
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Affiliation(s)
- Sara M Francisco
- MARE-Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Lisbon, Portugal
| | - Joana I Robalo
- MARE-Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Lisbon, Portugal
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16
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Ma L, Cao L, Hoffmann AA, Gong Y, Chen J, Chen H, Wang X, Zeng A, Wei S, Zhou Z. Rapid and strong population genetic differentiation and genomic signatures of climatic adaptation in an invasive mealybug. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Ling Ma
- State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant Protection Chinese Academy of Agricultural Sciences Beijing China
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing China
- Institute of Insect Science Hunan Agriculture University Changsha China
| | - Li‐Jun Cao
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing China
| | - Ary A. Hoffmann
- School of BioSciences Bio21 Institute The University of Melbourne Melbourne Victoria Australia
| | - Ya‐Jun Gong
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing China
| | - Jin‐Cui Chen
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing China
| | - Hong‐Song Chen
- Guangxi Key Laboratory for Biology of Crop Diseases and Insect Pests Institute of Plant Protection Guangxi Academy of Agricultural Sciences Nanning China
| | - Xu‐Bo Wang
- Yunnan Academy of Biodiversity, Southwest Forestry University Kunming China
| | - Ai‐Ping Zeng
- Institute of Insect Science Hunan Agriculture University Changsha China
| | - Shu‐Jun Wei
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing China
| | - Zhong‐Shi Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant Protection Chinese Academy of Agricultural Sciences Beijing China
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17
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Moss JB, Gerber GP, Welch ME. Heterozygosity-Fitness Correlations Reveal Inbreeding Depression in Neonatal Body Size in a Critically Endangered Rock Iguana. J Hered 2019; 110:818-829. [PMID: 31617903 DOI: 10.1093/jhered/esz060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/09/2019] [Indexed: 01/16/2023] Open
Abstract
Inbreeding depression, though challenging to identify in nature, may play an important role in regulating the dynamics of small and isolated populations. Conversely, greater expression of genetic load can enhance opportunities for natural selection. Conditional expression concentrates these opportunities for selection and may lead to failure of detection. This study investigates the possibility for age-dependent expression of inbreeding depression in a critically endangered population of rock iguanas, Cyclura nubila caymanensis. We employ heterozygote-fitness correlations to examine the contributions of individual genetic factors to body size, a fitness-related trait. Nonsignificant reductions in homozygosity (up to 7%) were detected between neonates and individuals surviving past their first year, which may reflect natural absorption of inbreeding effects by this small, fecund population. The majority of variation in neonate body size was attributed to maternal or environmental effects (i.e., clutch identity and incubation length); however, heterozygosity across 22 microsatellite loci also contributed significantly and positively to model predictions. Conversely, effects of heterozygosity on fitness were not detectable when adults were examined, suggesting that inbreeding depression in body size may be age dependent in this taxon. Overall, these findings emphasize the importance of taking holistic, cross-generational approaches to genetic monitoring of endangered populations.
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Affiliation(s)
- Jeanette B Moss
- Biological Sciences Department, Mississippi State University, Mississippi State, MS
| | - Glenn P Gerber
- Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Mark E Welch
- Biological Sciences Department, Mississippi State University, Mississippi State, MS
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18
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Hössjer O, Tyvand PA. Local fluctuations of genetic processes defined on two time scales, with applications to effective size estimation. Theor Popul Biol 2019; 131:79-99. [PMID: 31778709 DOI: 10.1016/j.tpb.2019.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 11/29/2022]
Abstract
In this paper we develop a general framework for how the genetic composition of a structured population with strong migration between its subunits, evolves over time. The dynamics is described in terms of a vector-valued Markov process of allele, genotype or haplotype frequencies that varies on two time scales. The more rapid changes are random fluctuations in terms of a multivariate autoregressive process, around a quasi equilibrium fix point, whereas the fix point itself varies more slowly according to a diffusion process, along a lower-dimensional subspace. Under mild regularity conditions, the fluctuations have a magnitude inversely proportional to the square root of the population size N, and hence can be used to estimate a broad class of genetically effective population sizes Ne, with genetic data from one time point only. In this way we are able to unify a number of existing notions of effective size, as well as proposing new ones, for instance one that quantifies the extent to which genotype frequencies fluctuate around Hardy-Weinberg equilibrium.
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Affiliation(s)
- Ola Hössjer
- Department of Mathematics, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Peder A Tyvand
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, N-1432 Ås, Norway.
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19
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Nearly unbiased estimator of contemporary effective mother size using within-cohort maternal sibling pairs incorporating parental and nonparental reproductive variations. Heredity (Edinb) 2019; 124:299-312. [PMID: 31578462 PMCID: PMC6972959 DOI: 10.1038/s41437-019-0271-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/30/2019] [Accepted: 09/05/2019] [Indexed: 11/25/2022] Open
Abstract
In this study, we developed a nearly unbiased estimator of contemporary effective mother size in a population, which is based on a known maternal half-sibling relationship found within the same cohort. Our method allows for variance of the average number of offspring per mother (i.e., parental variation, such as age-specific fecundity) and variance of the number of offspring among mothers with identical reproductive potential (i.e., nonparental variation, such as family-correlated survivorship). We also developed estimators of the variance and coefficient of variation of contemporary effective mother size and qualitatively evaluated the performance of the estimators by running an individual-based model. Our results provide guidance for (i) a sample size to ensure the required accuracy and precision when the order of effective mother size is available and (ii) a degree of uncertainty regarding the estimated effective mother size when information about the size is unavailable. To the best of our knowledge, this is the first report to demonstrate the derivation of a nearly unbiased estimator of effective population size; however, its current application is limited to effective mother size and situations, in which the sample size is not particularly small and maternal half-sibling relationships can be detected without error. The results of this study demonstrate the usefulness of a sibship assignment method for estimating effective population size; in addition, they have the potential to greatly widen the scope of genetic monitoring, especially in the situation of small sample size.
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20
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Burrell AM, Goddard JHR, Greer PJ, Williams RJ, Pepper AE. Sporadic Genetic Connectivity among Small Insular Populations of the Rare Geoendemic Plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower). J Hered 2019; 110:587-600. [PMID: 31062855 DOI: 10.1093/jhered/esz029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/06/2019] [Indexed: 11/13/2022] Open
Abstract
Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of C. ampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne < 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g., >1 km), possibly via zoochory.
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Affiliation(s)
- A Millie Burrell
- Department of Biology, Texas A&M University, College Station, TX
| | | | | | - Ryan J Williams
- Department of Biology, Texas A&M University, College Station, TX
| | - Alan E Pepper
- Department of Biology, Texas A&M University, College Station, TX
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21
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Jones AT, Lavery SD, Le Port A, Wang YG, Blower D, Ovenden J. Sweepstakes reproductive success is absent in a New Zealand snapper (Chrysophrus auratus) population protected from fishing despite "tiny" N e /N ratios elsewhere. Mol Ecol 2019; 28:2986-2995. [PMID: 31087739 DOI: 10.1111/mec.15130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 01/07/2023]
Abstract
A landmark study published in 2002 estimated a very small Ne /N ratio (around 10-5 ) in a population of pink snapper (Chrysophrys auratus, Forster, 1801) in the Hauraki Gulf in New Zealand. It epitomized the tiny Ne /N ratios (<10-3 ) reported in marine species due to the hypothesized operation of sweepstakes reproductive success (SRS). Here we re-evaluate the occurrence of SRS in marine species and the potential effect of fishing on the Ne /N ratio by studying the same species in the same region, but in a population that has been protected from fishing since 1975. We combine empirical, simulation and model-based approaches to estimate Ne (and Nb ) from genotypes of 1,044 adult fish and estimate N using recapture-probabilities. The estimated Ne /N ratio was much larger (0.33, SE: 0.14) than expected. The magnitude of estimates of population-wide variance in individual lifetime reproductive success (10-18) suggested that the sweepstakes effect was negligible in the study population. After evaluating factors that could explain the contrast between studies - experimental design, life history differences, environmental effects and the influence of exploitation on the Ne /N ratio - we conclude that the low Ne of the Hauraki Gulf population is associated with demographic instability in the harvested compared to the protected population despite circumstantial evidence that the 2002 study may have underestimated Ne . This study has broad implications for the prevailing view that reproductive success in the sea is largely driven by chance, and for genetic monitoring of populations using the Ne /N ratio and Nb .
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Affiliation(s)
- Andrew T Jones
- School of Mathematics and Physics, University of Queensland, Brisbane, Queensland, Australia
| | - Shane D Lavery
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Agnès Le Port
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
| | - You-Gan Wang
- Science and Engineering Faculty, School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Dean Blower
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia.,Molecular Fisheries Laboratory and School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Jennifer Ovenden
- Molecular Fisheries Laboratory and School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
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22
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Waples RS. Making sense of genetic estimates of effective population size. Mol Ecol 2019; 25:4689-91. [PMID: 27671356 DOI: 10.1111/mec.13814] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/12/2016] [Accepted: 08/16/2016] [Indexed: 01/20/2023]
Abstract
The last decade has seen an explosion of interest in use of genetic markers to estimate effective population size, Ne . Effective population size is important both theoretically (Ne is a key parameter in almost every aspect of evolutionary biology) and for practical application (Ne determines rates of genetic drift and loss of genetic variability and modulates the effectiveness of selection, so it is crucial to consider in conservation). As documented by Palstra & Fraser (), most of the recent growth in Ne estimation can be attributed to development or refinement of methods that can use a single sample of individuals (the older temporal method requires at least two samples separated in time). As with other population genetic methods, performance of new Ne estimators is typically evaluated with simulated data for a few scenarios selected by the author(s). Inevitably, these initial evaluations fail to fully consider the consequences of violating simplifying assumptions, such as discrete generations, closed populations of constant size and selective neutrality. Subsequently, many researchers studying natural or captive populations have reported estimates of Ne for multiple methods; often these estimates are congruent, but that is not always the case. Because true Ne is rarely known in these empirical studies, it is difficult to make sense of the results when estimates differ substantially among methods. What is needed is a rigorous, comparative analysis under realistic scenarios for which true Ne is known. Recently, Gilbert & Whitlock () did just that for both single-sample and temporal methods under a wide range of migration schemes. In the current issue of Molecular Ecology, Wang () uses simulations to evaluate performance of four single-sample Ne estimators. In addition to assessing effects of true Ne , sample size, and number of loci, Wang also evaluated performance under changing abundance, physical linkage and genotyping errors, as well as for some alternative life histories (high rates of selfing; haplodiploids). Wang showed that the sibship frequency (SF) and linkage disequilibrium (LD) methods perform dramatically better than the heterozygote excess and molecular coancestry methods under most scenarios (see Fig. 1, modified from figure 2 in Wang ), and he also concluded that SF is generally more versatile than LD. This article represents a truly Herculean effort, and results should be of considerable value to researchers interested in applying these methods to real-world situations.
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Affiliation(s)
- Robin S Waples
- NOAA Fisheries, Northwest Fisheries Science Center, 2725 Montlake Blvd. East, Seattle, WA, 98112, USA.
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23
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Montarry J, Bardou-Valette S, Mabon R, Jan PL, Fournet S, Grenier E, Petit EJ. Exploring the causes of small effective population sizes in cyst nematodes using artificial Globodera pallida populations. Proc Biol Sci 2019; 286:20182359. [PMID: 30963865 PMCID: PMC6367184 DOI: 10.1098/rspb.2018.2359] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/12/2018] [Indexed: 02/02/2023] Open
Abstract
The effective size of a population is the size of an ideal population which would undergo genetic drift at the same rate as the real population. The balance between selection and genetic drift depends on the effective population size ( Ne), rather than the real numbers of individuals in the population ( N). The objectives of the present study were to estimate Ne in the potato cyst nematode Globodera pallida and to explore the causes of a low Ne/ N ratio in cyst nematodes using artificial populations. Using a temporal analysis of 24 independent populations, the median Ne was 58 individuals (min Ne = 25 and max Ne = 228). Ne is commonly lower than N but in the case of cyst nematodes, the Ne/ N ratio was extremely low. Using artificial populations showed that this low ratio did not result from migration, selection and overlapping generations, but could be explain by the fact that G. pallida populations deviate in structure from the assumptions of the ideal population by having unequal sex ratios, high levels of inbreeding and a high variance in family sizes. The consequences of a low Ne, resulting in a strong intensity of genetic drift, could be important for their control because G. pallida populations will have a low capacity to adapt to changing environments.
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Affiliation(s)
- Josselin Montarry
- INRA, UMR1349 IGEPP, Institute of Genetic Environment and Plant Protection, 35653 Le Rheu, France
| | - Sylvie Bardou-Valette
- INRA, UMR1349 IGEPP, Institute of Genetic Environment and Plant Protection, 35653 Le Rheu, France
| | - Romain Mabon
- INRA, UMR1349 IGEPP, Institute of Genetic Environment and Plant Protection, 35653 Le Rheu, France
| | - Pierre-Loup Jan
- INRA, Agrocampus-Ouest, UMR985 ESE, Ecology and Ecosystem Health, 35042 Rennes, France
| | - Sylvain Fournet
- INRA, UMR1349 IGEPP, Institute of Genetic Environment and Plant Protection, 35653 Le Rheu, France
| | - Eric Grenier
- INRA, UMR1349 IGEPP, Institute of Genetic Environment and Plant Protection, 35653 Le Rheu, France
| | - Eric J. Petit
- INRA, Agrocampus-Ouest, UMR985 ESE, Ecology and Ecosystem Health, 35042 Rennes, France
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24
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Pierson JC, Graves TA, Banks SC, Kendall KC, Lindenmayer DB. Relationship between effective and demographic population size in continuously distributed populations. Evol Appl 2018; 11:1162-1175. [PMID: 30026804 PMCID: PMC6050178 DOI: 10.1111/eva.12636] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 03/24/2018] [Indexed: 01/18/2023] Open
Abstract
Genetic monitoring of wild populations can offer insights into demographic and genetic information simultaneously. However, widespread application of genetic monitoring is hindered by large uncertainty in the estimation and interpretation of target metrics such as contemporary effective population size, Ne . We used four long-term genetic and demographic studies (≥9 years) to evaluate the temporal stability of the relationship between Ne and demographic population size (Nc ). These case studies focused on mammals that are continuously distributed, yet dispersal-limited within the spatial scale of the study. We estimated local, contemporary Ne with single-sample methods (LDNE, Heterozygosity Excess, and Molecular Ancestry) and demographic abundance with either mark-recapture estimates or catch-per-unit effort indices. Estimates of Ne varied widely within each case study suggesting interpretation of estimates is challenging. We found inconsistent correlations and trends both among estimates of Ne and between Ne and Nc suggesting the value of Ne as an indicator of Nc is limited in some cases. In the two case studies with consistent trends between Ne and Nc , FIS was more stable over time and lower, suggesting FIS may be a good indicator that the population was sampled at a spatial scale at which genetic structure is not biasing estimates of Ne . These results suggest that more empirical work on the estimation of Ne in continuous populations is needed to understand the appropriate context to use LDNe as a useful metric in a monitoring programme to detect temporal trends in either Ne or Nc .
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Affiliation(s)
- Jennifer C. Pierson
- Fenner School of Environment and SocietyThe Australian National UniversityCanberraACTAustralia
- ACT Parks and Conservation ServiceEnvironment and Planning and Sustainable Development DirectorateTharwaACTAustralia
| | - Tabitha A. Graves
- Northern Rocky Mountain Science CenterUnited States Geological SurveyWest GlacierMontana
| | - Sam C. Banks
- Fenner School of Environment and SocietyThe Australian National UniversityCanberraACTAustralia
| | - Katherine C. Kendall
- Northern Rocky Mountain Science CenterUnited States Geological SurveyWest GlacierMontana
| | - David B. Lindenmayer
- Fenner School of Environment and SocietyThe Australian National UniversityCanberraACTAustralia
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25
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da Silva FM, Miño CI, Izbicki R, Del Lama SN. Considerations for monitoring population trends of colonial waterbirds using the effective number of breeders and census estimates. Ecol Evol 2018; 8:8088-8101. [PMID: 30250686 PMCID: PMC6144984 DOI: 10.1002/ece3.4347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/04/2018] [Accepted: 06/15/2018] [Indexed: 11/24/2022] Open
Abstract
Detecting trends in population size fluctuations is a major focus in ecology, evolution, and conservation biology. Populations of colonial waterbirds have been monitored using demographic approaches to determine annual census size (Na). We propose the addition of genetic estimates of the effective number of breeders (Nb) as indirect measures of the risk of loss of genetic diversity to improve the evaluation of demographics and increase the accuracy of trend estimates in breeding colonies. Here, we investigated which methods of the estimation of Nb are more precise under conditions of moderate genetic diversity, limited sample sizes and few microsatellite loci, as often occurs with natural populations. We used the wood stork as a model species and we offered a workflow that researchers can follow for monitoring bird breeding colonies. Our approach started with simulations using five estimators of Nb and the theoretical results were validated with empirical data collected from breeding colonies settled in the Brazilian Pantanal wetland. In parallel, we estimated census size using a corrected method based on counting active nests. Both in simulations and in natural populations, the approximate Bayesian computation (ABC) and sibship assignment (SA) methods yielded more precise estimates than the linkage disequilibrium, heterozygosity excess, and molecular coancestry methods. In particular, the ABC method performed best with few loci and small sample sizes, while the other estimators required larger sample sizes and at least 13 loci to not underestimate Nb. Moreover, according to our Nb/Na estimates (values were often ≤0.1), the wood stork colonies evaluated could be facing the loss of genetic diversity. We demonstrate that the combination of genetic and census estimates is a useful approach for monitoring natural breeding bird populations. This methodology has been recommended for populations of rare species or with a known history of population decline to support conservation efforts.
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Affiliation(s)
- Fagner M. da Silva
- Departamento de Genética e EvoluçãoUniversidade Federal de São CarlosSão CarlosSão PauloBrazil
| | - Carolina I. Miño
- Instituto de Biología Subtropical (IBS)Universidad Nacional de MisionesCONICETPosadasMisionesArgentina
| | - Rafael Izbicki
- Departamento de EstatísticaUniversidade Federal de São CarlosSão CarlosSão PauloBrazil
| | - Silvia N. Del Lama
- Departamento de Genética e EvoluçãoUniversidade Federal de São CarlosSão CarlosSão PauloBrazil
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26
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Mora M, Medina-Vogel G, Sepúlveda MA, Noll D, Álvarez-Varas R, Vianna JA. Genetic structure of introduced American mink (Neovison vison) in Patagonia: colonisation insights and implications for control and management strategies. WILDLIFE RESEARCH 2018. [DOI: 10.1071/wr18026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Biological invasions have caused dramatic changes in native biodiversity and ecosystem function. Studies of genetic variation and evolutionary changes are useful for understanding population dynamics during biological invasions, and shed light on management, prevention and restoration strategies.
Aims
This study aimed to investigate the structure and genetic variability of American mink (Neovison vison), an invasive species in southern South America, introduced for fur farming in the 1930s.
Methods
Samples from 153 mink were obtained from 12 locations in southern Chile to sequence the mitochondrial DNA (mtDNA) control region and to genotype 11 polymorphic microsatellite loci.
Key results
The highest mtDNA diversity was detected in Puerto Cisnes, suggesting multiple introductions and/or the most probable area where mink was first introduced. The latter is also supported by microsatellite data, because a high percentage of individuals from different locations were assigned to this location. All other locations showed low or no mtDNA diversity, possibly due to founder effect. The results also indicate marked population structure, with three genetic clusters coincident with the main historical introduction points, with low dispersal among them.
Conclusions
The results suggest that control strategies for American mink in southern Chile should be concentrated on these three genetically differentiated management units, and particularly on source populations and locations with low effective population size and restricted connectivity.
Implications
Genetic approaches have been used for the management of numerous alien species worldwide. Recommendations delivered here for American mink control could also be implemented in other regions and for other invasive species with similar genetic diversity distribution and connectivity.
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27
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Stanisic LJ, Aleksic JM, Dimitrijevic V, Simeunovic P, Glavinic U, Stevanovic J, Stanimirovic Z. New insights into the origin and the genetic status of the Balkan donkey from Serbia. Anim Genet 2017; 48:580-590. [PMID: 28815638 DOI: 10.1111/age.12589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2017] [Indexed: 11/30/2022]
Abstract
The Balkan donkey (Equus asinus L.) is commonly regarded as a large-sized, unselected, unstructured and traditionally managed donkey breed. We assessed the current genetic status of the three largest E. asinus populations in the central Balkans (Serbia) by analysing the variability of nuclear microsatellites and the mitochondrial (mtDNA) control region of 77 and 49 individuals respectively. We further analysed our mtDNA dataset along with 209 published mtDNA sequences of ancient and modern individuals from 19 European and African populations to provide new insights into the origin and the history of the Balkan donkey. Serbian donkey populations are highly genetically diverse at both the nuclear and mtDNA levels despite severe population decline. Traditional Balkan donkeys in Serbia are rather heterogeneous; we found two groups of individuals with similar phenotypic features, somewhat distinct nuclear backgrounds and different proportions of mtDNA haplotypes belonging to matrilineal Clades 1 and 2. Another group, characterized by larger body size, different coat colour, distinct nuclear gene pool and predominantly Clade 2 haplotypes, was delineated as the Banat donkey breed. The maternal landscape of the large Balkan donkey population is highly heterogeneous and more complex than previously thought. Given the two independent domestication events in donkeys, multiple waves of introductions into the Balkans from Greece are hypothesized. Clade 2 donkeys probably appeared in Greece prior to those belonging to Clade 1, whereas expansion and diversification of Clade 1 donkeys within the Balkans predated that of Clade 2 donkeys.
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Affiliation(s)
- L J Stanisic
- Department of Reproduction, Fertility and Artificial Insemination, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, PO Box 310, 11000, Belgrade, Serbia
| | - J M Aleksic
- Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Vojvode Stepe 444a, PO Box 23, 11010, Belgrade, Serbia
| | - V Dimitrijevic
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, PO Box 310, 11000, Belgrade, Serbia
| | - P Simeunovic
- Department of Farm Animal Diseases, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, PO Box 310, 11000, Belgrade, Serbia
| | - U Glavinic
- Department of Reproduction, Fertility and Artificial Insemination, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, PO Box 310, 11000, Belgrade, Serbia
| | - J Stevanovic
- Department of Reproduction, Fertility and Artificial Insemination, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, PO Box 310, 11000, Belgrade, Serbia
| | - Z Stanimirovic
- Department of Reproduction, Fertility and Artificial Insemination, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, PO Box 310, 11000, Belgrade, Serbia
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Svengren H, Prettejohn M, Bunge D, Fundi P, Björklund M. Relatedness and genetic variation in wild and captive populations of Mountain Bongo in Kenya obtained from genome-wide single-nucleotide polymorphism (SNP) data. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.07.001] [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] Open
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Waples RS, Elz A, Arnsberg BD, Faulkner JR, Hard JJ, Timmins-Schiffman E, Park LK. Human-mediated evolution in a threatened species? Juvenile life-history changes in Snake River salmon. Evol Appl 2017; 10:667-681. [PMID: 28717387 PMCID: PMC5511361 DOI: 10.1111/eva.12468] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 02/10/2017] [Indexed: 01/21/2023] Open
Abstract
Evaluations of human impacts on Earth's ecosystems often ignore evolutionary changes in response to altered selective regimes. Freshwater habitats for Snake River fall Chinook salmon (SRFCS), a threatened species in the US, have been dramatically changed by hydropower development and other watershed modifications. Associated biological changes include a shift in juvenile life history: Historically essentially 100% of juveniles migrated to sea as subyearlings, but a substantial fraction have migrated as yearlings in recent years. In contemplating future management actions for this species should major Snake River dams ever be removed (as many have proposed), it will be important to understand whether evolution is at least partially responsible for this life-history change. We hypothesized that if this trait is genetically based, parents who migrated to sea as subyearlings should produce faster-growing offspring that would be more likely to reach a size threshold to migrate to sea in their first year. We tested this with phenotypic data for over 2,600 juvenile SRFCS that were genetically matched to parents of hatchery and natural origin. Three lines of evidence supported our hypothesis: (i) the animal model estimated substantial heritability for juvenile growth rate for three consecutive cohorts; (ii) linear modeling showed an association between juvenile life history of parents and offspring growth rate; and (iii) faster-growing juveniles migrated at greater speeds, as expected if they were more likely to be heading to sea. Surprisingly, we also found that parents reared a full year in a hatchery produced the fastest growing offspring of all-apparently an example of cross-generational plasticity associated with artificial propagation. We suggest that SRFCS is an example of a potentially large class of species that can be considered to be "anthro-evolutionary"-signifying those whose evolutionary trajectories have been profoundly shaped by altered selective regimes in human-dominated landscapes.
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle WA USA
| | - Anna Elz
- Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle WA USA
| | - Billy D Arnsberg
- Department of Fisheries Resources Management Nez Perce Tribe Lapwai ID USA
| | - James R Faulkner
- Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle WA USA
| | - Jeffrey J Hard
- Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle WA USA
| | - Emma Timmins-Schiffman
- Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle WA USA.,Department of Genome Sciences University of Washington Seattle WA USA
| | - Linda K Park
- Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle WA USA
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Carlson MO, Gazave E, Gore MA, Smart CD. Temporal Genetic Dynamics of an Experimental, Biparental Field Population of Phytophthora capsici. Front Genet 2017; 8:26. [PMID: 28348576 PMCID: PMC5347166 DOI: 10.3389/fgene.2017.00026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/20/2017] [Indexed: 01/01/2023] Open
Abstract
Defining the contributions of dispersal, reproductive mode, and mating system to the population structure of a pathogenic organism is essential to estimating its evolutionary potential. After introduction of the devastating plant pathogen, Phytophthora capsici, into a grower's field, a lack of aerial spore dispersal restricts migration. Once established, coexistence of both mating types results in formation of overwintering recombinant oospores, engendering persistent pathogen populations. To mimic these conditions, in 2008, we inoculated a field with two P. capsici isolates of opposite mating type. We analyzed pathogenic isolates collected in 2009-2013 from this experimental population, using genome-wide single-nucleotide polymorphism markers. By tracking heterozygosity across years, we show that the population underwent a generational shift; transitioning from exclusively F1 in 2009-2010, to multi-generational in 2011, and ultimately all inbred in 2012-2013. Survival of F1 oospores, characterized by heterozygosity excess, coupled with a low rate of selfing, delayed declines in heterozygosity due to inbreeding and attainment of equilibrium genotypic frequencies. Large allele and haplotype frequency changes in specific genomic regions accompanied the generational shift, representing putative signatures of selection. Finally, we identified an approximately 1.6 Mb region associated with mating type determination, constituting the first detailed genomic analysis of a mating type region (MTR) in Phytophthora. Segregation patterns in the MTR exhibited tropes of sex-linkage, where maintenance of allele frequency differences between isolates of opposite mating type was associated with elevated heterozygosity despite inbreeding. Characterizing the trajectory of this experimental system provides key insights into the processes driving persistent, sexual pathogen populations.
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Affiliation(s)
- Maryn O. Carlson
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityGeneva, NY, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Elodie Gazave
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Michael A. Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Christine D. Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityGeneva, NY, USA
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Whiteley AR, Coombs JA, O'Donnell MJ, Nislow KH, Letcher BH. Keeping things local: Subpopulation Nb and Ne in a stream network with partial barriers to fish migration. Evol Appl 2017; 10:348-365. [PMID: 28352295 PMCID: PMC5367083 DOI: 10.1111/eva.12454] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 12/11/2016] [Indexed: 01/17/2023] Open
Abstract
For organisms with overlapping generations that occur in metapopulations, uncertainty remains regarding the spatiotemporal scale of inference of estimates of the effective number of breeders (N^b) and whether these estimates can be used to predict generational Ne. We conducted a series of tests of the spatiotemporal scale of inference of estimates of Nb in nine consecutive cohorts within a long‐term study of brook trout (Salvelinus fontinalis). We also tested a recently developed approach to estimate generational Ne from N^b and compared this to an alternative approach for estimating N^e that also accounts for age structure. Multiple lines of evidence were consistent with N^b corresponding to the local (subpopulation) spatial scale and the cohort‐specific temporal scale. We found that at least four consecutive cohort‐specific estimates of N^b were necessary to obtain reliable estimates of harmonic mean N^b for a subpopulation. Generational N^e derived from cohort‐specific N^b was within 7%–50% of an alternative approach to obtain N^e, suggesting some population specificity for concordance between approaches. Our results regarding the spatiotemporal scale of inference for Nb should apply broadly to many taxa that exhibit overlapping generations and metapopulation structure and point to promising avenues for using cohort‐specific N^b for local‐scale genetic monitoring.
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Affiliation(s)
- Andrew R Whiteley
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences College of Forestry and Conservation University of Montana Missoula MT USA
| | - Jason A Coombs
- Department of Environmental Conservation University of Massachusetts Amherst Amherst MA USA; U.S. Forest Service Northern Research Station University of Massachusetts Amherst MA USA
| | - Matthew J O'Donnell
- U.S. Geological Survey Leetown Science Center S.O. Conte Anadromous Fish Research Center Turners Falls MA USA
| | - Keith H Nislow
- U.S. Forest Service Northern Research Station University of Massachusetts Amherst MA USA
| | - Benjamin H Letcher
- U.S. Geological Survey Leetown Science Center S.O. Conte Anadromous Fish Research Center Turners Falls MA USA
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32
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Zhang J, Wang X, Yao J, Li Q, Liu F, Yotsukura N, Krupnova TN, Duan D. Effect of domestication on the genetic diversity and structure of Saccharina japonica populations in China. Sci Rep 2017; 7:42158. [PMID: 28176848 PMCID: PMC5296902 DOI: 10.1038/srep42158] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 01/09/2017] [Indexed: 11/08/2022] Open
Abstract
Saccharina japonica is a commercially and ecologically important seaweed and is an excellent system for understanding the effects of domestication on marine crops. In this study, we used 19 selected simple sequence repeat (SSR) markers to investigate the influence of domestication on the genetic diversity and structure of S. japonica populations. Wild kelp populations exhibited higher genetic diversity than cultivated populations based on total NA, HE, HO, NP and AR. Discriminant analysis of principal components (DAPC), a neighbour-joining (NJ) tree and STRUCTURE analyses indicated that S. japonica populations could be divided into two groups (a cultivated/introduced group and a wild indigenous group) with significant genetic differentiation (P < 0.0001). Divergent selection, continuous inbreeding and inter-specific hybridization have caused the divergence of these two genetically separate gene pools. The significant genetic differentiation between northern and southern cultivated populations appears to be due to inter-specific hybridization and wild germplasm introduction during the domestication process. In addition, the cultivation of S. japonica has not resulted in any serious genetic disturbance of wild introduced S. japonica populations. An understanding of the genetic diversity and genetic structure of domesticated S. japonica will be necessary for further genetic improvement and effective use of germplasm.
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Affiliation(s)
- Jie Zhang
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuliang Wang
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jianting Yao
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Qiuying Li
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fuli Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Norishige Yotsukura
- Field Science Centre for Northern Biosphere, Hokkaido University, Sapporo, 060-0809, Japan
| | - Tatiana N. Krupnova
- Pacific Research Fisheries Centre (TINRO-Centre), Vladivostok, 690600, Russia
| | - Delin Duan
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
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Wang J, Santiago E, Caballero A. Prediction and estimation of effective population size. Heredity (Edinb) 2016; 117:193-206. [PMID: 27353047 PMCID: PMC5026755 DOI: 10.1038/hdy.2016.43] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 05/03/2016] [Accepted: 05/16/2016] [Indexed: 12/19/2022] Open
Abstract
Effective population size (Ne) is a key parameter in population genetics. It has important applications in evolutionary biology, conservation genetics and plant and animal breeding, because it measures the rates of genetic drift and inbreeding and affects the efficacy of systematic evolutionary forces, such as mutation, selection and migration. We review the developments in predictive equations and estimation methodologies of effective size. In the prediction part, we focus on the equations for populations with different modes of reproduction, for populations under selection for unlinked or linked loci and for the specific applications to conservation genetics. In the estimation part, we focus on methods developed for estimating the current or recent effective size from molecular marker or sequence data. We discuss some underdeveloped areas in predicting and estimating Ne for future research.
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Affiliation(s)
- J Wang
- Institute of Zoology, Zoological Society of London, London, UK
| | - E Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain
| | - A Caballero
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain
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34
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Multini LC, Wilke ABB, Suesdek L, Marrelli MT. Population Genetic Structure of Aedes fluviatilis (Diptera: Culicidae). PLoS One 2016; 11:e0162328. [PMID: 27598889 PMCID: PMC5012556 DOI: 10.1371/journal.pone.0162328] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 08/19/2016] [Indexed: 12/23/2022] Open
Abstract
Although Aedes fluviatilis is an anthropophilic mosquito found abundantly in urban environments, its biology, epidemiological potential and genetic characteristics are poorly understood. Climate change and urbanization processes that result in environmental modifications benefit certain anthropophilic mosquito species such as Ae. fluviatilis, greatly increasing their abundance in urban areas. To gain a better understanding of whether urbanization processes modulate the genetic structure of this species in the city of São Paulo, we used eight microsatellite loci to genetically characterize Ae. fluviatilis populations collected in nine urban parks in the city of São Paulo. Our results show that there is high gene flow among the populations of this species, heterozygosity deficiency and low genetic structure and that the species may have undergone a recent population expansion. There are two main hypotheses to explain these findings: (i) Ae. fluviatilis populations have undergone a population expansion as a result of urbanization; and (ii) as urbanization of the city of São Paulo occurred recently and was quite intense, the structuring of these populations cannot be observed yet, apart from in the populations of Ibirapuera and Piqueri parks, where the first signs of structuring have appeared. We believe that the expansion found in Ae. fluviatilis populations is probably correlated with the unplanned urbanization of the city of São Paulo, which transformed green areas into urbanized areas, as well as the increasing population density in the city.
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Affiliation(s)
- Laura Cristina Multini
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brasil
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, SP, Brasil
| | - André Barretto Bruno Wilke
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brasil
- * E-mail:
| | - Lincoln Suesdek
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, SP, Brasil
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, Brasil
| | - Mauro Toledo Marrelli
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brasil
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, SP, Brasil
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Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution. Genetics 2016; 204:723-735. [PMID: 27542959 PMCID: PMC5068858 DOI: 10.1534/genetics.116.191197] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/30/2016] [Indexed: 01/22/2023] Open
Abstract
The effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-term Ne. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related to Ne. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-seq). Pool-seq is cost-effective and often outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: Additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling, which increases the variance of allele frequency estimates. We propose a new estimator of Ne, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurate Ne estimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wide Ne estimates, we extend our method using a recursive partitioning approach to estimate Ne locally along the chromosome. Since the type I error is controlled, our method permits the identification of genomic regions that differ significantly in their Ne estimates. We present an application to Pool-seq data from experimental evolution with Drosophila and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R package at https://github.com/ThomasTaus/Nest.
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36
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Wang J. A comparison of single-sample estimators of effective population sizes from genetic marker data. Mol Ecol 2016; 25:4692-711. [DOI: 10.1111/mec.13725] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/18/2016] [Accepted: 06/02/2016] [Indexed: 01/20/2023]
Affiliation(s)
- Jinliang Wang
- Institute of Zoology; Zoological Society of London; Regent's Park London NW1 4RY UK
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37
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Benestan LM, Ferchaud A, Hohenlohe PA, Garner BA, Naylor GJP, Baums IB, Schwartz MK, Kelley JL, Luikart G. Conservation genomics of natural and managed populations: building a conceptual and practical framework. Mol Ecol 2016; 25:2967-77. [DOI: 10.1111/mec.13647] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/12/2016] [Accepted: 04/06/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Laura Marilyn Benestan
- Departement de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec G1V 0A6 Canada
| | - Anne‐Laure Ferchaud
- Departement de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec G1V 0A6 Canada
| | - Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow ID 83844 USA
| | - Brittany A. Garner
- Flathead Lake Biological Station Fish and Wildlife Genomic Group Division of Biological Science University of Montana Missoula MT 59812 USA
- Wildlife Program Fish and Wildlife Genomic Group College of Forestry and Conservation University of Montana Missoula MT 59812 USA
| | - Gavin J. P. Naylor
- Hollings Marine Lab College of Charleston and Medical University of South Carolina 331 Fort Johnson Rd. Charleston SC 29412 USA
| | - Iliana Brigitta Baums
- Department of Biology Pennsylvania State University 208 Mueller Lab University Park PA 1680 USA
| | - Michael K. Schwartz
- USDA Forest Service National Genomics Center for Wildlife and Fish Conservation 800 E. Beckwith Ave. Missoula MT 59801 USA
| | - Joanna L. Kelley
- School of Biological Sciences Washington State University Pullman WA 99164 USA
| | - Gordon Luikart
- Flathead Lake Biological Station Fish and Wildlife Genomic Group Division of Biological Science University of Montana Missoula MT 59812 USA
- Wildlife Program Fish and Wildlife Genomic Group College of Forestry and Conservation University of Montana Missoula MT 59812 USA
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38
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Muzhinji N, Woodhall JW, Truter M, van der Waals JE. Population genetic structure of Rhizoctonia solani AG 3-PT from potatoes in South Africa. Fungal Biol 2016; 120:701-10. [PMID: 27109367 DOI: 10.1016/j.funbio.2016.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 02/25/2016] [Accepted: 02/29/2016] [Indexed: 10/22/2022]
Abstract
Rhizoctonia solani AG 3-PT is an important potato pathogen causing significant yield and quality losses in potato production. However, little is known about the levels of genetic diversity and structure of this pathogen in South Africa. A total of 114 R. solani AG 3-PT isolates collected from four geographic regions were analysed for genetic diversity and structure using eight microsatellite loci. Microsatellite analysis found high intra-population genetic diversity, population differentiation and evidence of recombination. A total of 78 multilocus genotypes were identified with few shared among populations. Low levels of clonality (13-39 %) and high levels of population differentiation were observed among populations. Most of the loci were in Hardy-Weinberg equilibrium and all four populations showed evidence of a mixed reproductive mode of both clonality and recombination. The PCoA clustering method revealed genetically distinct geographic populations of R. solani AG 3-PT in South Africa. This study showed that populations of R. solani AG 3-PT in South Africa are genetically differentiated and disease management strategies should be applied accordingly. This is the first study of the population genetics of R. solani AG 3-PT in South Africa and results may help to develop knowledge-based disease management strategies.
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Affiliation(s)
- Norman Muzhinji
- Department of Plant Science, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa; Tobacco Research Board, Zimbabwe
| | - James W Woodhall
- Department of Plant, Soil and Entomological Sciences, Parma Research and Extension Center, University of Idaho, Parma, ID 83660, USA
| | - Mariette Truter
- Agricultural Research Council, Private Bag X134, Queenswood 0121, South Africa
| | - Jacquie E van der Waals
- Department of Plant Science, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa.
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Aplasca AC, Iverson JB, Welch ME, Colosimo G, Hekkala ER. Genetic diversity and structure in the Endangered Allen Cays Rock Iguana, Cyclura cychlura inornata. PeerJ 2016; 4:e1793. [PMID: 26989628 PMCID: PMC4793328 DOI: 10.7717/peerj.1793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/21/2016] [Indexed: 11/26/2022] Open
Abstract
The Endangered Allen Cays Rock Iguana (Cyclura cychlura inornata) is endemic to the Allen Cays, a tiny cluster of islands in the Bahamas. Naturally occurring populations exist on only two cays (<4 ha each). However, populations of unknown origin were recently discovered on four additional cays. To investigate patterns of genetic variation among these populations, we analyzed nuclear and mitochondrial markers for 268 individuals. Analysis of three mitochondrial gene regions (2,328 bp) and data for eight nuclear microsatellite loci indicated low genetic diversity overall. Estimates of effective population sizes based on multilocus genotypes were also extremely low. Despite low diversity, significant population structuring and variation in genetic diversity measures were detected among cays. Genetic data confirm the source population for an experimentally translocated population while raising concerns regarding other, unauthorized, translocations. Reduced heterozygosity is consistent with a documented historical population decline due to overharvest. This study provides the first range-wide genetic analysis of this subspecies. We suggest strategies to maximize genetic diversity during ongoing recovery including additional translocations to establish assurance populations and additional protective measures for the two remaining natural populations.
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Affiliation(s)
- Andrea C Aplasca
- Department of Biological Sciences, Fordham University, New York, NY, United States; Current affiliation: College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - John B Iverson
- Department of Biology, Earlham College , Richmond, IN , United States
| | - Mark E Welch
- Department of Biological Sciences, Mississippi State University , Mississippi, MS , United States
| | - Giuliano Colosimo
- Department of Biological Sciences, Mississippi State University , Mississippi, MS , United States
| | - Evon R Hekkala
- Department of Biological Sciences, Fordham University , New York, NY , United States
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40
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Fernández-Cruz J, Fernández-López J. Genetic structure of wild sweet chestnut (Castanea sativa Mill.) populations in northwest of Spain and their differences with other European stands. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0835-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ali S, Soubeyrand S, Gladieux P, Giraud T, Leconte M, Gautier A, Mboup M, Chen W, de Vallavieille-Pope C, Enjalbert J. cloncase: Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms. Mol Ecol Resour 2016; 16:845-61. [DOI: 10.1111/1755-0998.12511] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Sajid Ali
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
- Institute of Biotechnology and Genetic Engineering; the University of Agriculture, Peshawar; 25000 Peshawar Pakistan
| | - Samuel Soubeyrand
- UR546 Biostatistics and Spatial Processes; INRA; 84914 Avignon France
| | - Pierre Gladieux
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
- UMR385 Biologie et Génétique des Interactions Plante-Parasite; CIRAD; INRA; F-34398 Montpellier France
| | - Tatiana Giraud
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - Marc Leconte
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
| | - Angélique Gautier
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
| | - Mamadou Mboup
- DuPont de Nemours (France) SAS Crop Protection - European Research & Development Center; 24, rue du Moulin 68740 Nambsheim France
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests; Institute of Plant Protection; Chinese Academy of Agricultural Sciences; No. 2 Yuanmingyuan West Road Beijing 100193 China
| | | | - Jérôme Enjalbert
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
- GQE - Le Moulon; INRA; Univ. Paris-Sud; CNRS; AgroParisTech; Université Paris-Saclay; F-91190 Gif-sur-Yvette France
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42
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Jan P, Gracianne C, Fournet S, Olivier E, Arnaud J, Porte C, Bardou‐Valette S, Denis M, Petit EJ. Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 1. Insights from the estimation of effective population sizes. Evol Appl 2016; 9:489-501. [PMID: 26989440 PMCID: PMC4778111 DOI: 10.1111/eva.12352] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 12/14/2015] [Indexed: 12/05/2022] Open
Abstract
The sustainability of modern agriculture relies on strategies that can control the ability of pathogens to overcome chemicals or genetic resistances through natural selection. This evolutionary potential, which depends partly on effective population size (N e ), is greatly influenced by human activities. In this context, wild pathogen populations can provide valuable information for assessing the long-term risk associated with crop pests. In this study, we estimated the effective population size of the beet cyst nematode, Heterodera schachtii, by sampling 34 populations infecting the sea beet Beta vulgaris spp. maritima twice within a one-year period. Only 20 populations produced enough generations to analyze the variation in allele frequencies, with the remaining populations showing a high mortality rate of the host plant after only 1 year. The 20 analyzed populations showed surprisingly low effective population sizes, with most having N e close to 85 individuals. We attribute these low values to the variation in population size through time, systematic inbreeding, and unbalanced sex-ratios. Our results suggest that H. schachtii has low evolutionary potential in natural environments. Pest control strategies in which populations on crops mimic wild populations may help prevent parasite adaptation to host resistance.
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Affiliation(s)
- Pierre‐Loup Jan
- INRAUMR1349 IGEPPF‐35653Le Rheu CedexFrance
- INRAUMR985 ESEF‐35042Rennes CedexFrance
| | | | | | | | - Jean‐François Arnaud
- UMR CNRS 8198 Évolution, Écologie et PaléontologieUniversité Lille 1 – Sciences et Technologies59655Villeneuve d'Ascq CedexFrance
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43
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Grimm A, Gruber B, Hoehn M, Enders K, Henle K. A model-derived short-term estimation method of effective size for small populations with overlapping generations. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12530] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Annegret Grimm
- Department of Conservation Biology; UFZ - Helmholtz Centre for Environmental Research; Permoserstr. 15 04318 Leipzig Germany
- Faculty of Biosciences, Pharmacy and Psychology; Institute for Biology; University of Leipzig; Johannisallee 21 04103 Leipzig Germany
| | - Bernd Gruber
- Department of Conservation Biology; UFZ - Helmholtz Centre for Environmental Research; Permoserstr. 15 04318 Leipzig Germany
- Faculty of Applied Sciences; Institute for Applied Ecology; University of Canberra; Canberra ACT 2601 Australia
| | - Marion Hoehn
- Department of Conservation Biology; UFZ - Helmholtz Centre for Environmental Research; Permoserstr. 15 04318 Leipzig Germany
- Faculty of Applied Sciences; Institute for Applied Ecology; University of Canberra; Canberra ACT 2601 Australia
| | - Katrin Enders
- Department of Conservation Biology; UFZ - Helmholtz Centre for Environmental Research; Permoserstr. 15 04318 Leipzig Germany
| | - Klaus Henle
- Department of Conservation Biology; UFZ - Helmholtz Centre for Environmental Research; Permoserstr. 15 04318 Leipzig Germany
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44
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Diefenbach D, Hansen L, Bohling J, Miller‐Butterworth C. Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA. Ecol Evol 2015; 5:4885-95. [PMID: 26640668 PMCID: PMC4662311 DOI: 10.1002/ece3.1750] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 08/06/2015] [Accepted: 08/22/2015] [Indexed: 11/09/2022] Open
Abstract
In 1988-1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity and inbreeding. We amplified 12 nuclear microsatellite loci from DNA isolated from scats to establish genetic profiles to identify individuals. We used spatially explicit capture-recapture population estimation to estimate abundance. From nine unique genetic profiles, we estimate a population size of 14.4 (SE = 3.052) bobcats, with an effective population size (N e) of 5-8 breeding individuals. This is consistent with predictions of a population viability analysis conducted at the time of reintroduction, which estimated the population would average 12-13 bobcats after 10 years. We identified several pairs of related bobcats (parent-offspring and full siblings), but ~75% of the pairwise comparisons were typical of unrelated individuals, and only one individual appeared inbred. Despite the small population size and other indications that it has likely experienced a genetic bottleneck, levels of genetic diversity in the CUIS bobcat population remain high compared to other mammalian carnivores. The reintroduction of bobcats to CUIS provides an opportunity to study changes in genetic diversity in an insular population without risk to this common species. Opportunities for natural immigration to the island are limited; therefore, continued monitoring and supplemental bobcat reintroductions could be used to evaluate the effect of different management strategies to maintain genetic diversity and population viability. The successful reintroduction and maintenance of a bobcat population on CUIS illustrates the suitability of translocation as a management tool for re-establishing felid populations.
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Affiliation(s)
- Duane Diefenbach
- U.S. Geological SurveyPennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvania16802
| | - Leslie Hansen
- Los Alamos National LaboratoryMS M887P.O. Box 1663Los AlamosNew Mexico87545
| | - Justin Bohling
- Department of Ecosystem Science and ManagementThe Pennsylvania State UniversityUniversity ParkPennsylvania16802
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45
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Ozerov M, Jürgenstein T, Aykanat T, Vasemägi A. Use of sibling relationship reconstruction to complement traditional monitoring in fisheries management and conservation of brown trout. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:1164-1175. [PMID: 25773302 DOI: 10.1111/cobi.12480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/20/2014] [Indexed: 06/04/2023]
Abstract
Declining trends in the abundance of many fish urgently call for more efficient and informative monitoring methods that would provide necessary demographic data for the evaluation of existing conservation, restoration, and management actions. We investigated how genetic sibship reconstruction from young-of-the-year brown trout (Salmo trutta L.) juveniles provides valuable, complementary demographic information that allowed us to disentangle the effects of habitat quality and number of breeders on juvenile density. We studied restored (n = 15) and control (n = 15) spawning and nursery habitats in 16 brown trout rivers and streams over 2 consecutive years to evaluate the effectiveness of habitat restoration activities. Similar juvenile densities both in restored and control spawning and nursery grounds were observed. Similarly, no differences in the effective number of breeders, Nb(SA) , were detected between habitats, indicating that brown trout readily used recently restored spawning grounds. Only a weak relationship between the Nb(SA) and juvenile density was observed, suggesting that multiple factors affect juvenile abundance. In some areas, very low estimates of Nb(SA) were found at sites with high juvenile density, indicating that a small number of breeders can produce a high number of progeny in favorable conditions. In other sites, high Nb(SA) estimates were associated with low juvenile density, suggesting low habitat quality or lack of suitable spawning substrate in relation to available breeders. Based on these results, we recommend the incorporation of genetic sibship reconstruction to ongoing and future fish evaluation and monitoring programs to gain novel insights into local demographic and evolutionary processes relevant for fisheries management, habitat restoration, and conservation.
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Affiliation(s)
- Mikhail Ozerov
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014, Turku, Finland
| | - Tauno Jürgenstein
- Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, 51014, Tartu, Estonia
| | - Tutku Aykanat
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014, Turku, Finland
| | - Anti Vasemägi
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014, Turku, Finland
- Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, 51014, Tartu, Estonia
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46
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Gilbert KJ, Whitlock MC. Evaluating methods for estimating local effective population size with and without migration. Evolution 2015; 69:2154-66. [DOI: 10.1111/evo.12713] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 06/16/2015] [Accepted: 06/20/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Kimberly J. Gilbert
- Department of Zoology; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Michael C. Whitlock
- Department of Zoology; University of British Columbia; Vancouver BC V6T 1Z4 Canada
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Parreira BR, Chikhi L. On some genetic consequences of social structure, mating systems, dispersal, and sampling. Proc Natl Acad Sci U S A 2015; 112:E3318-26. [PMID: 26080393 PMCID: PMC4491764 DOI: 10.1073/pnas.1414463112] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Many species are spatially and socially organized, with complex social organizations and dispersal patterns that are increasingly documented. Social species typically consist of small age-structured units, where a limited number of individuals monopolize reproduction and exhibit complex mating strategies. Here, we model social groups as age-structured units and investigate the genetic consequences of social structure under distinct mating strategies commonly found in mammals. Our results show that sociality maximizes genotypic diversity, which contradicts the belief that social groups are necessarily subject to strong genetic drift and at high risk of inbreeding depression. Social structure generates an excess of genotypic diversity. This is commonly observed in ecological studies but rarely reported in population genetic studies that ignore social structure. This heterozygosity excess, when detected, is often interpreted as a consequence of inbreeding avoidance mechanisms, but we show that it can occur even in the absence of such mechanisms. Many seemly contradictory results from ecology and population genetics can be reconciled by genetic models that include the complexities of social species. We find that such discrepancies can be explained by the intrinsic properties of social groups and by the sampling strategies of real populations. In particular, the number of social groups and the nature of the individuals that compose samples (e.g., nonreproductive and reproductive individuals) are key factors in generating outbreeding signatures. Sociality is an important component of population structure that needs to be revisited by ecologists and population geneticists alike.
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Affiliation(s)
- Bárbara R Parreira
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal; Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal; CNRS, Université Paul Sabatier, Ecole Nationale de Formation Agronomique, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), F-31062 Toulouse, France
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48
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Marranca JM, Welsh AB, Roseman E. Genetic effects of habitat restoration in the Laurentian Great Lakes: an assessment of lake sturgeon origin and genetic diversity. Restor Ecol 2015. [DOI: 10.1111/rec.12200] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jamie M. Marranca
- Division of Forestry and Natural Resources; West Virginia University; P.O. Box 6125 Morgantown WV 26506 U.S.A
| | - Amy B. Welsh
- Division of Forestry and Natural Resources; West Virginia University; P.O. Box 6125 Morgantown WV 26506 U.S.A
| | - Edward Roseman
- Great Lakes Science Center; U.S. Geological Survey; 1451 Green Road Ann Arbor MI 48105-2807 U.S.A
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49
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Park L. Effective population size of korean populations. Genomics Inform 2015; 12:208-15. [PMID: 25705160 PMCID: PMC4330256 DOI: 10.5808/gi.2014.12.4.208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 09/29/2014] [Accepted: 10/07/2014] [Indexed: 11/20/2022] Open
Abstract
Recently, new methods have been developed for estimating the current and recent changes in effective population sizes. Based on the methods, the effective population sizes of Korean populations were estimated using data from the Korean Association Resource (KARE) project. The overall changes in the population sizes of the total populations were similar to CHB (Han Chinese in Beijing, China) and JPT (Japanese in Tokyo, Japan) of the HapMap project. There were no differences in past changes in population sizes with a comparison between an urban area and a rural area. Age-dependent current and recent effective population sizes represent the modern history of Korean populations, including the effects of World War II, the Korean War, and urbanization. The oldest age group showed that the population growth of Koreans had already been substantial at least since the end of the 19th century.
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Affiliation(s)
- Leeyoung Park
- Natural Science Research Institute, Yonsei University, Seoul 120-749, Korea
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50
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Kumar VP, Sharma LK, Shukla M, Sathyakumar S. Pragmatic perspective on conservation genetics and demographic history of the last surviving population of Kashmir red deer (Cervus elaphus hanglu) in India. PLoS One 2015; 10:e0117069. [PMID: 25671567 PMCID: PMC4324630 DOI: 10.1371/journal.pone.0117069] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/18/2014] [Indexed: 11/30/2022] Open
Abstract
The hangul (Cervus elaphus hanglu) is of great conservation concern because it represents the easternmost and only hope for an Asiatic survivor of the red deer species in the Indian subcontinent. Despite the rigorous conservation efforts of the Department of Wildlife Protection in Jammu & Kashmir, the hangul population has experienced a severe decline in numbers and range contraction in the past few decades. The hangul population once abundant in the past has largely become confined to the Dachigam landscape, with a recent population estimate of 218 individuals. We investigated the genetic variability and demographic history of the hangul population and found that it has shown a relatively low diversity estimates when compared to other red deer populations of the world. Neutrality tests, which are used to evaluate demographic effects, did not support population expansion, and the multimodal pattern of mismatch distribution indicated that the hangul population is under demographic equilibrium. Furthermore, the hangul population did not exhibit any signature of bottleneck footprints in the past, and Coalescent Bayesian Skyline plot analysis revealed that the population had not experienced any dramatic changes in the effective population size over the last several thousand years. We observed a strong evidence of sub-structuring in the population, wherein the majority of individuals were assigned to different clusters in Bayesian cluster analysis. Population viability analysis demonstrated insignificant changes in the mean population size, with a positive growth rate projected for the next hundred years. We discuss the phylogenetic status of hangul for the first time among the other red deer subspecies of the world and strongly recommend to upgrade hangul conservation status under IUCN that should be discrete from the other red deer subspecies of the world to draw more conservation attention from national and international bodies.
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Affiliation(s)
- Ved P Kumar
- Wildlife Institute of India, Chandrabani, Dehradun 248 001, Uttarakhand, India
| | - Lalit K Sharma
- Wildlife Institute of India, Chandrabani, Dehradun 248 001, Uttarakhand, India
| | - Malay Shukla
- Gujarat Forensic Sciences University, Gandhinagar 382007, Gujarat, India
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