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Goldberg ME, Noyes MD, Eichler EE, Quinlan AR, Harris K. Effects of parental age and polymer composition on short tandem repeat de novo mutation rates. Genetics 2024; 226:iyae013. [PMID: 38298127 PMCID: PMC10990422 DOI: 10.1093/genetics/iyae013] [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: 08/11/2023] [Revised: 08/11/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
Short tandem repeats (STRs) are hotspots of genomic variability in the human germline because of their high mutation rates, which have long been attributed largely to polymerase slippage during DNA replication. This model suggests that STR mutation rates should scale linearly with a father's age, as progenitor cells continually divide after puberty. In contrast, it suggests that STR mutation rates should not scale with a mother's age at her child's conception, since oocytes spend a mother's reproductive years arrested in meiosis II and undergo a fixed number of cell divisions that are independent of the age at ovulation. Yet, mirroring recent findings, we find that STR mutation rates covary with paternal and maternal age, implying that some STR mutations are caused by DNA damage in quiescent cells rather than polymerase slippage in replicating progenitor cells. These results echo the recent finding that DNA damage in oocytes is a significant source of de novo single nucleotide variants and corroborate evidence of STR expansion in postmitotic cells. However, we find that the maternal age effect is not confined to known hotspots of oocyte mutagenesis, nor are postzygotic mutations likely to contribute significantly. STR nucleotide composition demonstrates divergent effects on de novo mutation (DNM) rates between sexes. Unlike the paternal lineage, maternally derived DNMs at A/T STRs display a significantly greater association with maternal age than DNMs at G/C-containing STRs. These observations may suggest the mechanism and developmental timing of certain STR mutations and contradict prior attribution of replication slippage as the primary mechanism of STR mutagenesis.
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Affiliation(s)
- Michael E Goldberg
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA
| | - Michelle D Noyes
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Aaron R Quinlan
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Computational Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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2
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Rodrigues NT, Saranholi BH, Inforzato AR, Silveira L, Desbiez ALJ, Galetti PM. Reduced gene flow and bottleneck in the threatened giant armadillo (Priodontes maximus): implications for its conservation. Genet Mol Biol 2024; 47:e20230252. [PMID: 38446984 PMCID: PMC10917080 DOI: 10.1590/1678-4685-gmb-2023-0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/30/2023] [Indexed: 03/08/2024] Open
Abstract
The progressive fragmentation and loss of habitats represent the main threats for endangered species, causing genetic consequences that may have potential implications for a population's long-term persistence. Large mammals are the most affected species among vertebrates. The giant armadillo Priodontes maximus is a large South American mammal threatened species, showing nocturnal, solitary and fossorial behavior, occurring at low population densities, and its population dynamics are still poorly known. In this study, we carried out the first assessment of genetic variability and population genetic structure of the species, using a panel of 15 polymorphic microsatellites developed by high-throughput genome sequencing. The spatial Bayesian clustering, Fst and Dest results indicated the presence of two genetic clusters (K = 2) in the study area. These results suggest a reduction in gene flow between individuals inhabiting the Brazilian savanna (Cerrado) and the Pantanal wetlands, with the increased human-driven habitat modifications possibly contributing for this scenario. A bottleneck signal was detected in both populations, and a subpopulation structuring in the Cerrado may also be reflecting consequences of the extensive habitat modifications. Findings from this study provide important and useful information for the future maintenance of genetic diversity and long-term conservation of this flagship species.
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Affiliation(s)
- Nayra T. Rodrigues
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | - Bruno H. Saranholi
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
- Imperial College London, Department of Life Sciences, Ascot, United Kingdom
| | - Alexandre R. Inforzato
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | | | - Arnaud Leonard Jean Desbiez
- Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Mato Grosso do Sul, Brazil
- Royal Zoological Society of Scotland (RZSS), Murrayfield, Edinburgh, United Kingdom
- Instituto de Pesquisas Ecológicas (IPE), Nazaré Paulista, São Paulo, Brazil
| | - Pedro M. Galetti
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
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3
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Goldberg ME, Noyes MD, Eichler EE, Quinlan AR, Harris K. Effects of parental age and polymer composition on short tandem repeat de novo mutation rates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573131. [PMID: 38187618 PMCID: PMC10769404 DOI: 10.1101/2023.12.22.573131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Short tandem repeats (STRs) are hotspots of genomic variability in the human germline because of their high mutation rates, which have long been attributed largely to polymerase slippage during DNA replication. This model suggests that STR mutation rates should scale linearly with a father's age, as progenitor cells continually divide after puberty. In contrast, it suggests that STR mutation rates should not scale with a mother's age at her child's conception, since oocytes spend a mother's reproductive years arrested in meiosis II and undergo a fixed number of cell divisions that are independent of the age at ovulation. Yet, mirroring recent findings, we find that STR mutation rates covary with paternal and maternal age, implying that some STR mutations are caused by DNA damage in quiescent cells rather than the classical mechanism of polymerase slippage in replicating progenitor cells. These results also echo the recent finding that DNA damage in quiescent oocytes is a significant source of de novo SNVs and corroborate evidence of STR expansion in postmitotic cells. However, we find that the maternal age effect is not confined to previously discovered hotspots of oocyte mutagenesis, nor are post-zygotic mutations likely to contribute significantly. STR nucleotide composition demonstrates divergent effects on DNM rates between sexes. Unlike the paternal lineage, maternally derived DNMs at A/T STRs display a significantly greater association with maternal age than DNMs at GC-containing STRs. These observations may suggest the mechanism and developmental timing of certain STR mutations and are especially surprising considering the prior belief in replication slippage as the dominant mechanism of STR mutagenesis.
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Affiliation(s)
- Michael E. Goldberg
- Department of Genome Sciences, University of Washington, 3720 15 Ave NE, Seattle, WA, 98195
- Departments of Human Genetics and Biomedical Informatics, University of Utah, 15 S 2030 E, Salt Lake City, UT, 84112
| | - Michelle D. Noyes
- Department of Genome Sciences, University of Washington, 3720 15 Ave NE, Seattle, WA, 98195
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, 3720 15 Ave NE, Seattle, WA, 98195
- Howard Hughes Medical Institute, 3720 15 Ave NE, University of Washington, Seattle, WA, 98195
| | - Aaron R. Quinlan
- Departments of Human Genetics and Biomedical Informatics, University of Utah, 15 S 2030 E, Salt Lake City, UT, 84112
- These authors contributed equally to this work
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, 3720 15 Ave NE, Seattle, WA, 98195
- Computational Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109
- These authors contributed equally to this work
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4
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Sparks MM, Schraidt CE, Yin X, Seeb LW, Christie MR. Rapid genetic adaptation to a novel ecosystem despite a large founder event. Mol Ecol 2023. [PMID: 37668092 DOI: 10.1111/mec.17121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/17/2023] [Accepted: 08/09/2023] [Indexed: 09/06/2023]
Abstract
Introduced and invasive species make excellent natural experiments for investigating rapid evolution. Here, we describe the effects of genetic drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha) that were accidentally introduced to the Great Lakes via a single introduction event 31 generations ago. Using whole-genome resequencing for 134 fish spanning five sample groups across the native and introduced range, we estimate that the source population's effective population size was 146,886 at the time of introduction, whereas the founding population's effective population size was just 72-a 2040-fold decrease. As expected with a severe founder event, we show reductions in genome-wide measures of genetic diversity, specifically a 37.7% reduction in the number of SNPs and an 8.2% reduction in observed heterozygosity. Despite this decline in genetic diversity, we provide evidence for putative selection at 47 loci across multiple chromosomes in the introduced populations, including missense variants in genes associated with circadian rhythm, immunological response and maturation, which match expected or known phenotypic changes in the Great Lakes. For one of these genes, we use a species-specific agent-based model to rule out genetic drift and conclude our results support a strong response to selection occurring in a period gene (per2) that plays a predominant role in determining an organism's daily clock, matching large day length differences experienced by introduced salmon during important phenological periods. Together, these results inform how populations might evolve rapidly to new environments, even with a small pool of standing genetic variation.
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Affiliation(s)
- Morgan M Sparks
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Claire E Schraidt
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
| | - Xiaoshen Yin
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Mark R Christie
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
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5
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Zimmerman SJ, Aldridge CL, O'Donnell MS, Edmunds DR, Coates PS, Prochazka BG, Fike JA, Cross TB, Fedy BC, Oyler-McCance SJ. A genetic warning system for a hierarchically structured wildlife monitoring framework. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2787. [PMID: 36482030 DOI: 10.1002/eap.2787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 10/10/2022] [Accepted: 10/20/2022] [Indexed: 06/17/2023]
Abstract
Genetic variation is a well-known indicator of population fitness yet is not typically included in monitoring programs for sensitive species. Additionally, most programs monitor populations at one scale, which can lead to potential mismatches with ecological processes critical to species' conservation. Recently developed methods generating hierarchically nested population units (i.e., clusters of varying scales) for greater sage-grouse (Centrocercus urophasianus) have identified population trend declines across spatiotemporal scales to help managers target areas for conservation. The same clusters used as a proxy for spatial scale can alert managers to local units (i.e., neighborhood-scale) with low genetic diversity, further facilitating identification of management targets. We developed a genetic warning system utilizing previously developed hierarchical population units to identify management-relevant areas with low genetic diversity within the greater sage-grouse range. Within this warning system we characterized conservation concern thresholds based on values of genetic diversity and developed a statistical model for microsatellite data to robustly estimate these values for hierarchically nested populations. We found that 41 of 224 neighborhood-scale clusters had low genetic diversity, 23 of which were coupled with documented local population trend decline. We also found evidence of cross-scale low genetic diversity in the small and isolated Washington population, unlikely to be reversed through typical local management actions alone. The combination of low genetic diversity and a declining population suggests relatively high conservation concern. Our findings could further facilitate conservation action prioritization in combination with population trend assessments and (or) local information, and act as a base-line of genetic diversity for future comparison. Importantly, the approach we used is broadly applicable across taxa.
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Affiliation(s)
- Shawna J Zimmerman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Cameron L Aldridge
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Michael S O'Donnell
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - David R Edmunds
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Peter S Coates
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, California, USA
| | - Brian G Prochazka
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, California, USA
| | - Jennifer A Fike
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Todd B Cross
- School of Environment, Resources and Sustainability, University of Waterloo, Waterloo, Ontario, Canada
| | - Bradley C Fedy
- School of Environment, Resources and Sustainability, University of Waterloo, Waterloo, Ontario, Canada
| | - Sara J Oyler-McCance
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
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6
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Sequeira F, Aguilar FF, Madeira FM, Teixeira J, Crespo E, Ferrand N, Rebelo R. What can genetics tell us about the history of a human-mediated introduction of the golden-striped salamander south of its native range? EUR J WILDLIFE RES 2022. [DOI: 10.1007/s10344-022-01628-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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7
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Limeira DM, Santos MH, Mateus RP, Ruas CDF, Almeida MCD, Moreira Filho O, Artoni RF. Molecular data reveal a complex population genetic structure for Psalidodon scabripinnis (Teleostei: Characidae) in the Atlantic Rainforest, Brazil. Genet Mol Biol 2022; 45:e20210048. [PMID: 35238328 PMCID: PMC8892460 DOI: 10.1590/1678-4685-gmb-2021-0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 12/08/2021] [Indexed: 11/23/2022] Open
Abstract
Recently renamed, Psalidodon scabripinnis populations of Serra da Mantiqueira, previously known as Astyanax scabripinnis have been deeply studied in the last years. These populations are small and isolated and occur very close to the watershed between Paraíba do Sul River basin and Upper Paraná River basin, in Serra da Mantiqueira region in the Atlantic Rainforest. These conditions arouse the interest in knowing theor genetic conservation status and how they responded to the separation between the two rivers basins. Therefore, we accessed the genetic diversity of five P. scabripinnis populations of this region with microsatellites and mitochondrial data. The results showed a complex structure pattern that doesn’t match the simple basin separation and a reasonably conservation status when compared with other populations of the same family or with similar natural history.
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8
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Genetic Variability Trend of Lusitano Horse Breed Reared in Italy. Animals (Basel) 2022; 12:ani12010098. [PMID: 35011204 PMCID: PMC8749805 DOI: 10.3390/ani12010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 11/17/2022] Open
Abstract
The Lusitano Horse (LH) originates from Portugal, but is reared worldwide. Since 1994, the University of Milan has routinely tested the LHs bred in Italy for parentage control. This study aims to assess the genetic variability of the LH reared in Italy using 16 microsatellites markers. Moreover, the genetic variability changes over the years in the total population (n.384) and in unrelated horses (n.47) were evaluated. Horses were grouped according to their date of birth (1975–1990, 1991–2000, 2001–2010, 2010–2019). Standard genetic diversity parameters, including observed (Ho) and expected (He) heterozygosity, Hardy-Weinberg equilibrium (HWE; P-Val), allelic richness, and inbreeding coefficient (Fis) were estimated. In the whole period, the total population showed Ho as high as 0.69, low Fis (0.057), and imbalance for HWE. When considering the unrelated horses, Ho was seen to increase over time (from 0.594 in 1975–1990 to 0.68 in 2010–2019) and frequencies were in HWE, again having low and decreasing values of Fis (from 0.208 in 1975–1990 to 0.019 in 2010–2019). Bottleneck analysis excluded a recent population decline. Principal Coordinate Analysis at the individual level defined two clusters, the major cluster including all the most recent horses. An increasing number of dams (156% more from 2001–2010 to 2011–2019) supports the good variability recorded in the population so far. However, the high number of foals (77.2%) sired by only four stallions in recent years suggests caution in the choice of the sires for the future.
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9
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Reyne M, Dicks K, McFarlane C, Aubry A, Emmerson M, Marnell F, Reid N, Helyar S. Population genetic structure of the Natterjack toad (Epidalea calamita) in Ireland: implications for conservation management. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01421-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractMolecular methods can play a crucial role in species management and conservation. Despite the usefulness of genetic approaches, they are often not explicitly included as part of species recovery plans and conservation practises. The Natterjack toad (Epidalea calamita) is regionally Red-Listed as Endangered in Ireland. The species is declining and is now present at just seven sites within a highly restricted range. This study used 13 highly polymorphic microsatellite markers to analyse the population genetic diversity and structure. Genetic diversity was high with expected heterozygosity between 0.55 and 0.61 and allelic richness between 4.77 and 5.92. Effective population sizes were small (Ne < 100 individuals), but not abnormal for pond breeding amphibians. However, there was no evidence of historical or contemporary genetic bottlenecks or high levels of inbreeding. We identified a positive relationship between Ne and breeding pond surface area, suggesting that environmental factors are a key determinant of population size. Significant genetic structuring was detected throughout the species’ range, and we identified four genetic entities that should be considered in the species’ conservation strategies. Management should focus on preventing further population declines and future loss of genetic diversity overall and within genetic entities while maintaining adequate local effective population size through site-specific protection, human-mediated translocations and head-start programs. The apparent high levels of genetic variation give hope for the conservation of Ireland’s rarest amphibian if appropriately protected and managed.
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10
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Hauser SS, Athrey G, Leberg PL. Waste not, want not: Microsatellites remain an economical and informative technology for conservation genetics. Ecol Evol 2021; 11:15800-15814. [PMID: 34824791 PMCID: PMC8601879 DOI: 10.1002/ece3.8250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/07/2021] [Accepted: 09/16/2021] [Indexed: 11/07/2022] Open
Abstract
Comparisons of microsatellites and single-nucleotide polymorphisms (SNPs) have found that SNPs outperform microsatellites in population genetic analyses, questioning the continued utility of microsatellites in population and landscape genetics. Yet, highly polymorphic markers may be of value in species that have reduced genetic variation. This study repeated previous analyses that used microsatellites with SNPs developed from ddRAD sequencing in the black-capped vireo source-sink system. SNPs provided greater resolution of genetic diversity, population differentiation, and migrant detection but could not reconstruct parentage relationships due to insufficient heterozygosities. The biological inferences made by both sets of markers were similar: asymmetrical gene flow from source sites to the remaining sink sites. With the landscape genetic analyses, we found different results between the two molecular markers, but associations of the top environmental features (riparian, open habitat, agriculture, and human development) with dispersal estimates were shared between marker types. Despite the higher precision of SNPs, we find that microsatellites effectively uncover population processes and patterns and are superior for parentage analyses in this species with reduced genetic diversity. This study illustrates the continued applicability and relevance of microsatellites in population genetic research.
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Affiliation(s)
- Samantha S. Hauser
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisianaUSA
| | - Giridhar Athrey
- Faculty of Ecology and Evolutionary BiologyTexas A&M UniversityCollege StationTexasUSA
| | - Paul L. Leberg
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisianaUSA
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11
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Mairal M, Chown SL, Shaw J, Chala D, Chau JH, Hui C, Kalwij JM, Münzbergová Z, Jansen van Vuuren B, Le Roux JJ. Human activity strongly influences genetic dynamics of the most widespread invasive plant in the sub-Antarctic. Mol Ecol 2021; 31:1649-1665. [PMID: 34181792 DOI: 10.1111/mec.16045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/14/2021] [Accepted: 06/21/2021] [Indexed: 11/26/2022]
Abstract
The link between the successful establishment of alien species and propagule pressure is well-documented. Less known is how humans influence the post-introduction dynamics of invasive alien populations. The latter requires studying parallel invasions by the same species in habitats that are differently impacted by humans. We analysed microsatellite and genome size variation, and then compared the genetic diversity and structure of invasive Poa annua L. on two sub-Antarctic islands: human-occupied Marion Island and unoccupied Prince Edward Island. We also carried out niche modelling to map the potential distribution of the species on both islands. We found high levels of genetic diversity and evidence for extensive admixture between genetically distinct lineages of P. annua on Marion Island. By contrast, the Prince Edward Island populations showed low genetic diversity, no apparent admixture, and had smaller genomes. On both islands, high genetic diversity was apparent at human landing sites, and on Marion Island, also around human settlements, suggesting that these areas received multiple introductions and/or acted as initial introduction sites and secondary sources (bridgeheads) for invasive populations. More than 70 years of continuous human activity associated with a meteorological station on Marion Island led to a distribution of this species around human settlements and along footpaths, which facilitates ongoing gene flow among geographically separated populations. By contrast, this was not the case for Prince Edward Island, where P. annua populations showed high genetic structure. The high levels of genetic variation and admixture in P. annua facilitated by human activity, coupled with high habitat suitability on both islands, suggest that P. annua is likely to increase its distribution and abundance in the future.
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Affiliation(s)
- Mario Mairal
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa.,Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid, Spain
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Victoria, Australia
| | - Justine Shaw
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Desalegn Chala
- Natural History Museum, University of Oslo, Oslo, Norway
| | - John H Chau
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, South Africa
| | - Cang Hui
- Centre for Invasion Biology, Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa.,Biodiversity Informatics Unit, African Institute for Mathematical Sciences, Cape Town, South Africa
| | - Jesse M Kalwij
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, South Africa.,Institute of Geography and Geoecology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Zuzana Münzbergová
- Department of Botany, Charles University, Prague, Czech Republic.,Department of Population Ecology, Czech Academy of Science, Průhonice, Czech Republic
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, South Africa
| | - Johannes J Le Roux
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa.,Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
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12
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Habrich AK, Lawrence ER, Fraser DJ. Varying genetic imprints of road networks and human density in North American mammal populations. Evol Appl 2021; 14:1659-1672. [PMID: 34178111 PMCID: PMC8210797 DOI: 10.1111/eva.13232] [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: 05/23/2020] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 11/28/2022] Open
Abstract
Road networks and human density are major factors contributing to habitat fragmentation and loss, isolation of wildlife populations, and reduced genetic diversity. Terrestrial mammals are particularly sensitive to road networks and encroachment by human populations. However, there are limited assessments of the impacts of road networks and human density on population-specific nuclear genetic diversity, and it remains unclear how these impacts are modulated by life-history traits. Using generalized linear mixed models and microsatellite data from 1444 North American terrestrial mammal populations, we show that taxa with large home range sizes, dense populations, and large body sizes had reduced nuclear genetic diversity with increasing road impacts and human density, but the overall influence of life-history traits was generally weak. Instead, we observed a high degree of genus-specific variation in genetic responses to road impacts and human density. Human density negatively affected allelic diversity or heterozygosity more than road networks (13 vs. 5-7 of 25 assessed genera, respectively); increased road networks and human density also positively affected allelic diversity and heterozygosity in 15 and 6-9 genera, respectively. Large-bodied, human-averse species were generally more negatively impacted than small, urban-adapted species. Genus-specific responses to habitat fragmentation by ongoing road development and human encroachment likely depend on the specific capability to (i) navigate roads as either barriers or movement corridors, and (ii) exploit resource-rich urban environments. The nonuniform genetic response to roads and human density highlights the need to implement efforts to mitigate the risk of vehicular collisions, while also facilitating gene flow between populations of particularly vulnerable taxa.
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Affiliation(s)
- Andrew K. Habrich
- Department of BiologyConcordia UniversityMontrealQuebecCanada
- Department of BiologyCarleton UniversityOttawaOntarioCanada
| | | | - Dylan J. Fraser
- Department of BiologyConcordia UniversityMontrealQuebecCanada
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13
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Kinziger AP, White JL, Nakamoto RJ, Harvey BC. Recent, small beginnings: genetic analysis suggests Catostomus rimiculus (Klamath smallscale sucker) in the Smith River, California, are introduced. JOURNAL OF FISH BIOLOGY 2021; 98:1321-1328. [PMID: 33389757 DOI: 10.1111/jfb.14664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/07/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Identification of introduced species can be important to understanding ecological systems and meeting conservation and management goals, but the process can be surprisingly challenging. The Klamath smallscale sucker Catostomus rimiculus seems likely to be native to the Smith River because the drainage separates two basins believed to be within the fish's native range, the Rogue and Klamath rivers. Further, C. rimiculus is broadly distributed in the Smith River, and the indigenous Dee-ni' People of the Smith River have a unique word for sucker. Nonetheless, a historical survey of fishes that described C. rimiculus from the Rogue and Klamath rivers did not include C. rimiculus among the fishes of the Smith River. To determine whether the genetic structure of the Smith River C. rimiculus reflects expectations for a native sucker population, the authors of this study examined variation in microsatellite and mitochondrial genetic markers from the Smith River and surrounding drainages. The genetic analyses revealed a pattern consistent with extreme founder effects in Smith River C. rimiculus, as would be expected from a single introduction of six or fewer effective individuals. The sharing of a high-frequency haplotype between the Smith River and Klamath River that is not detected in the Rogue River suggests the Klamath River as the likely source for the introduction. The findings highlight that local-scale introductions can be easily overlooked because the newly established populations can appear to be parts of contiguous natural distributions.
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Affiliation(s)
- Andrew P Kinziger
- Department of Fisheries Biology, Humboldt State University, Arcata, California, USA
| | - Jason L White
- U.S. Forest Service, Pacific Southwest Research Station, Arcata, California, USA
| | - Rodney J Nakamoto
- U.S. Forest Service, Pacific Southwest Research Station, Arcata, California, USA
| | - Bret C Harvey
- U.S. Forest Service, Pacific Southwest Research Station, Arcata, California, USA
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Lewis DH, Jarvis DE, Maughan PJ. SSRgenotyper: A simple sequence repeat genotyping application for whole-genome resequencing and reduced representational sequencing projects. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11402. [PMID: 33344093 PMCID: PMC7742204 DOI: 10.1002/aps3.11402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/13/2020] [Indexed: 05/13/2023]
Abstract
PREMISE Many programs can identify simple sequence repeat (SSR) motifs in genomic data. SSRgenotyper extends SSR identification to en masse genotyping from resequencing data for diversity panels and linkage mapping populations. METHODS AND RESULTS SSRgenotyper will find and genotype SSRs from SAM files and an SSR reference FASTA. Several outputs are possible, including a simple table with the SSR marker name, position, and SSR alleles, defined by the repeat number of the repeat motif. Specific output files include a GENEPOP-formatted file for downstream genetic diversity analyses and a traditional A, H, B mapping file output that is phased to the parents of the population for biparental linkage map construction. Linkage maps produced using SSRgenotyper genotypes were highly collinear with physical maps and correctly inferred known phylogenies. CONCLUSIONS SSRgenotyper provides an easy-to-use, accurate, and scalable SSR genotyping platform for whole-genome resequencing data. SSRgenotyper is freely available at https://github.com/dlewis27/SSRgenotyper.
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Affiliation(s)
- Daniel H. Lewis
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUtah84058USA
| | - David E. Jarvis
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUtah84058USA
| | - Peter J. Maughan
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUtah84058USA
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15
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Wu Q, Zang F, Ma Y, Zheng Y, Zang D. Analysis of genetic diversity and population structure in endangered Populus wulianensis based on 18 newly developed EST-SSR markers. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01329] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Yuan N, Li M, Jia C. De novo transcriptome assembly and population genetic analyses of an important coastal shrub, Apocynum venetum L. BMC PLANT BIOLOGY 2020; 20:408. [PMID: 32883231 PMCID: PMC7470449 DOI: 10.1186/s12870-020-02626-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/27/2020] [Indexed: 05/07/2023]
Abstract
BACKGROUND Apocynum venetum L. is an important medicinal plant that is mainly distributed in the coastal areas and northwest of China. In addition to its high medical and economic value, its adaptation to saline-alkali and coastal saline lands makes A. venetum an ideal candidate for use in vegetation restoration. To date, the study of A. venetum has been limited in the northwest region of China, little attention has been paid to the genetic diversity and population structure of A. venetum populations in the coastal region. Here, we performed transcriptome sequencing of total RNA from A. venetum leaves and developed efficient expressed sequence tag-simple sequence repeat (EST-SSR) markers for analyzing the genetic diversity and population structure of A. venetum in the coastal region. RESULTS A total of 86,890 unigenes were generated after de novo assembly, and 68,751 of which were successfully annotated by searching against seven protein databases. Furthermore, 14,072 EST-SSR loci were detected and 10,243 primer pairs were successfully designed from these loci. One hundred primer pairs were randomly selected and synthesized, twelve primer pairs were identified as highly polymorphic and further used for population genetic analysis. Population genetic analyses showed that A. venetum exhibited low level of genetic diversity (mean alleles per locus, NA = 3.3; mean expected heterozygosity, HE = 0.342) and moderate level of genetic differentiation among the populations (genetic differentiation index, FST = 0.032-0.220) in the coastal region. Although the contemporary (mean mc = 0.056) and historical (mean mh = 0.106) migration rates among the six A. venetum populations were moderate, a decreasing trend over the last few generations was detected. Bayesian structure analysis clustered six populations into two major groups, and genetic bottlenecks were found to have occurred in two populations (QG, BH). CONCLUSIONS Using novel EST-SSR markers, we evaluated the genetic variation of A. venetum in the coastal region and determined conservation priorities based on these findings. The large dataset of unigenes and SSRs identified in our study, combining samples from a broader range, will support further research on the conservation and evolution of this important coastal plant and its related species.
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Affiliation(s)
- Na Yuan
- Institute of Crop Germplasm and Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
| | - Mimi Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Chunlin Jia
- Institute of Agricultural and Sustainable Development, Shandong Academy of Agricultural Sciences, Jinan, China
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17
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Population genetics of Liriomyza trifolii (Diptera: Agromyzidae) and comparison with four Liriomyza species in China based on COI, EF-1a and microsatellites loci. Sci Rep 2019; 9:17856. [PMID: 31780688 PMCID: PMC6882889 DOI: 10.1038/s41598-019-53886-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 11/04/2019] [Indexed: 11/08/2022] Open
Abstract
Liriomyza is a large genus that includes polyphagous and invasive species (L. trifolii, L. sativae, and L. huidobrensis), and oligophagous species such as L. Chinensis in China. Effective control of these invasive and oligophagous species is not easy due to the fast invasion rate, interspecific competition, and pesticide resistance. In this study, we investigated population genetics of five Liriomyza species L. trifolii, L. sativae, L. huidobrensis, L. bryoniae, and L. chinensis based on COI and EF-1a genes, and microsatellite DNA. These five Liriomyza species revealed highly conservative characteristics in the COI gene among populations collected from different geographical regions and host plants. By contrast, the mutation rate of the EF-1a gene was higher than COI, and phylogenetic tree based on EF-1a showed that haplotypes of L. trifolii and L. sativae were not distinguished well. Genetic differentiation in microsatellite loci was obvious among the five species. Our results also indicated that geographic isolation had a greater impact on genetic differentiation in L. trifolii than the host plant. Populations of L. trifolii in China showed a high to moderate level of genetic differentiation and they had divided into two groups representing the coastal areas of southern China and northern regions. The genetic diversity of the southern group was higher than the northern group. We speculated that the invasion of L. trifolii likely occurred in southern regions of China and then spread northward. Bottleneck analyses revealed that the L. trifolii population in China was in a steady growth period.
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18
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Abstract
Microsatellites are repetitive DNA sequences usually found in non-coding regions of the genome. Their quantification and analysis have applications in fields from population genetics to evolutionary biology. As genome assemblies become commonplace, the need for software that can facilitate analyses has never been greater. In particular, R packages that can analyze genomic data are particularly important since this is one of the most popular software environments for biologists. We created an R package, micRocounter, to quantify microsatellites. We have optimized our package for speed, accessibility, and portability, making the automated analysis of large genomic data sets feasible. Computationally intensive algorithms were built in C++ to increase speed. Tests using benchmark datasets show a 200-fold improvement in speed over existing software. A moderately sized genome of 500 Mb can be processed in under 50 sec. Results are output as an object in R increasing accessibility and flexibility for practitioners.
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Santos TL, Fernandes C, Henley MD, Dawson DA, Mumby HS. Conservation Genetic Assessment of Savannah Elephants ( Loxodonta africana) in the Greater Kruger Biosphere, South Africa. Genes (Basel) 2019; 10:E779. [PMID: 31590388 PMCID: PMC6826889 DOI: 10.3390/genes10100779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/12/2019] [Accepted: 09/29/2019] [Indexed: 11/24/2022] Open
Abstract
Savannah elephant populations have been severely reduced and fragmented throughout its remaining range. In general, however, there is limited information regarding their genetic status, which is essential knowledge for conservation. We investigated patterns of genetic variation in savannah elephants from the Greater Kruger Biosphere, with a focus on those in previously unstudied nature reserves adjacent to Kruger National Park, using dung samples from 294 individuals and 18 microsatellites. The results of genetic structure analyses using several different methods of ordination and Bayesian clustering strongly suggest that elephants throughout the Greater Kruger National Park (GKNP) constitute a single population. No evidence of a recent genetic bottleneck was detected using three moment-based approaches and two coalescent likelihood methods. The apparent absence of a recent genetic bottleneck associated with the known early 1900s demographic bottleneck may result from a combination of rapid post-bottleneck population growth, immigration and long generation time. Point estimates of contemporary effective population size (Ne) for the GKNP were ~ 500-700, that is, at the low end of the range of Ne values that have been proposed for maintaining evolutionary potential and the current ratio of Ne to census population size (Nc) may be quite low (<0.1). This study illustrates the difficulties in assessing the impacts on Ne in populations that have suffered demographic crashes but have recovered rapidly and received gene flow, particularly in species with long generation times in which genetic time lags are longer. This work provides a starting point and baseline information for genetic monitoring of the GKNP elephants.
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Affiliation(s)
- Teresa L Santos
- Bull Elephant Network Project, Conservation Science Group, David Attenborough Building, Pembroke St, Cambridge CB2 3QY, UK.
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire S10 2TN, UK.
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculty of Sciences, University of Lisbon, Lisbon 1749-016, Portugal.
| | - Carlos Fernandes
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculty of Sciences, University of Lisbon, Lisbon 1749-016, Portugal.
| | - Michelle D Henley
- Applied Behavioural Ecology and Ecosystem Research Unit, University of South Africa, Florida Campus, Private Bag X6, Florida 1710, Johannesburg, South Africa.
- Elephants Alive, P.O. Box 960. Hoedspruit 1380, South Africa.
| | - Deborah A Dawson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire S10 2TN, UK.
| | - Hannah S Mumby
- Bull Elephant Network Project, Conservation Science Group, David Attenborough Building, Pembroke St, Cambridge CB2 3QY, UK.
- Centre for African Ecology, School of Animal, Plant and Environmental Sciences, University of Witwatersrand, 1 Jan Smuts Avenue, Braamfontein, Johannesburg 2000, South Africa.
- Wissenschaftskolleg zu Berlin, Wallotstraße 19, Berlin 14193, Germany.
- School of Biological Sciences and Department of Politics and Public Administration, University of Hong Kong, Hong Kong, China.
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Zhang X, Su H, Yang J, Feng L, Li Z, Zhao G. Population genetic structure, migration, and polyploidy origin of a medicinal species Gynostemma pentaphyllum (Cucurbitaceae). Ecol Evol 2019; 9:11145-11170. [PMID: 31641462 PMCID: PMC6802062 DOI: 10.1002/ece3.5618] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 08/06/2019] [Accepted: 08/06/2019] [Indexed: 01/08/2023] Open
Abstract
Gynostemma pentaphyllum, a member of family Cucurbitaceae, is a perennial creeping herb used as a traditional medicinal plant in China. In this study, six polymorphic nSSR and four EST-SSR primers were used to genotype 1,020 individuals in 72 wild populations of G. pentaphyllum. The genetic diversity and population structure were investigated, and ecological niche modeling was performed to reveal the evolution and demographic history of its natural populations. The results show that G. pentaphyllum has a low level of genetic diversity and high level of variation among populations because of pervasive asexual propagation, genetic drift, and long-term habitat isolation. Results of the Mantel test demonstrate that the genetic distance and geographic distance are significantly correlated among G. pentaphyllum natural populations. The populations can be divided into two clusters on the basis of genetic structure. Asymmetrical patterns of historical gene flow were observed among the clusters. For the contemporary, almost all the bidirectional gene flow of the related pairs was symmetrical with slight differences. Recent bottlenecks were experienced by 34.72% of the studied populations. The geographic range of G. pentaphyllum continues to expand northward and eastward from Hengduan Mountains. The present distribution of G. pentaphyllum is a consequence of its complex evolution. Polyploidy in G. pentaphyllum is inferred to be polygenetic. Finally, G. pentaphyllum is a species in need of protection, so in situ and ex situ measures should be considered in the future.
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Affiliation(s)
- Xiao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education)College of Life SciencesNorthwest UniversityXi'anChina
| | - Hailun Su
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education)College of Life SciencesNorthwest UniversityXi'anChina
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education)College of Life SciencesNorthwest UniversityXi'anChina
| | - Li Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education)College of Life SciencesNorthwest UniversityXi'anChina
| | - Zhonghu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education)College of Life SciencesNorthwest UniversityXi'anChina
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education)College of Life SciencesNorthwest UniversityXi'anChina
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BORO PRASANTA, PATEL BHM, SAHOO NIHARRANJAN, GAUR GK, DUTT TRIVENI, SINGH MUKESH, NAHA BC. Genetic diversity analysis of Ghurrah pig based on microsatellite markers. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2019. [DOI: 10.56093/ijans.v89i8.93067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
For analysis of genetic variation within Ghurrah, the local pigs of Rohilkhand region was explored using 16 FAOISAG microsatellite markers with 40 genetically unrelated pigs from the native breeding tract. Genomic DNA was isolated and amplified with microsatellite primers labeled with fluorescent dyes and genotyped using genetic analyser. The estimates of various genetic diversity parameters revealed mean number of observed alleles (Na), effective number of alleles (Ne), observed (Ho) and expected (He) heterozygosity values, polymorphic information content (PIC) and F-values to be 8.5±0.99, 4.78±0.57, 0.47±0.04 and 0.74±0.05, 0.74±0.04 and 0.38±0.03, respectively. The high PIC value suggested that all the microsatellite markers were highly polymorphic and suitable for molecular characterization of this pig. There was substantial genetic variation and polymorphism across the studied loci. There was absence of genetic bottleneck in the studied population. The medium inbreeding coefficient indicates a need to formulate the appropriate breeding strategies to enhance heterozygosity in the population.
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22
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Genetic diversity and population structure of Garcinia paucinervis, an endangered species using microsatellite markers. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01176-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Pilczynska J, Cocito S, Boavida J, Serrão EA, Assis J, Fragkopoulou E, Queiroga H. Genetic diversity increases with depth in red gorgonian populations of the Mediterranean Sea and the Atlantic Ocean. PeerJ 2019; 7:e6794. [PMID: 31179167 PMCID: PMC6536111 DOI: 10.7717/peerj.6794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/16/2019] [Indexed: 11/20/2022] Open
Abstract
Background In the ocean, the variability of environmental conditions found along depth gradients exposes populations to contrasting levels of perturbation, which can be reflected in the overall patterns of species genetic diversity. At shallow sites, resource availability may structure large, persistent and well-connected populations with higher levels of diversity. In contrast, the more extreme conditions, such as thermal stress during heat waves, can lead to population bottlenecks and genetic erosion, inverting the natural expectation. Here we examine how genetic diversity varies along depth for a long-lived, important ecosystem-structuring species, the red gorgonian, Paramuricea clavata. Methods We used five polymorphic microsatellite markers to infer differences in genetic diversity and differentiation, and to detect bottleneck signs between shallow and deeper populations across the Atlantic Ocean and the Mediterranean Sea. We further explored the potential relationship between depth and environmental gradients (temperature, ocean currents, productivity and slope) on the observed patterns of diversity by means of generalized linear mixed models. Results An overall pattern of higher genetic diversity was found in the deeper sites of the Atlantic Ocean and the Mediterranean Sea. This pattern was largely explained by bottom temperatures, with a linear pattern of decreasing genetic diversity with increasing thermal stress. Genetic differentiation patterns showed higher gene flow within sites (i.e., shallow vs. deeper populations) than between sites. Recent genetic bottlenecks were found in two populations of shallow depths. Discussion Our results highlight the role of deep refugial populations safeguarding higher and unique genetic diversity for marine structuring species. Theoretical regression modelling demonstrated how thermal stress alone may reduce population sizes and diversity levels of shallow water populations. In fact, the examination of time series on a daily basis showed the upper water masses repeatedly reaching lethal temperatures for P. clavata. Differentiation patterns showed that the deep richer populations are isolated. Gene flow was also inferred across different depths; however, not in sufficient levels to offset the detrimental effects of surface environmental conditions on genetic diversity. The identification of deep isolated areas with high conservation value for the red gorgonian represents an important step in the face of ongoing and future climate changes.
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Affiliation(s)
- Joanna Pilczynska
- Departamento de Biologia and CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal.,Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Silvia Cocito
- Italian Agency for New Technologies, Energy and Sustainable Economic Development-ENEA, Marine Environment Research Centre, La Spezia, Italy
| | - Joana Boavida
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal.,Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
| | - Ester A Serrão
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Jorge Assis
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Eliza Fragkopoulou
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Henrique Queiroga
- Departamento de Biologia and CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
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24
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Demastes JW, Hafner DJ, Hafner MS, Light JE, Spradling TA. Loss of genetic diversity, recovery and allele surfing in a colonizing parasite, Geomydoecus aurei. Mol Ecol 2019; 28:703-720. [PMID: 30589151 DOI: 10.1111/mec.14997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 12/17/2018] [Indexed: 02/07/2023]
Abstract
Understanding the genetic consequences of changes in species distributions has wide-ranging implications for predicting future outcomes of climate change, for protecting threatened or endangered populations and for understanding the history that has led to current genetic patterns within species. Herein, we examine the genetic consequences of range expansion over a 25-year period in a parasite (Geomydoecus aurei) that is in the process of expanding its geographic range via invasion of a novel host. By sampling the genetics of 1,935 G. aurei lice taken from 64 host individuals collected over this time period using 12 microsatellite markers, we test hypotheses concerning linear spatial expansion, genetic recovery time and allele surfing. We find evidence of decreasing allelic richness (AR) with increasing distance from the source population, supporting a linear, stepping stone model of spatial expansion that emphasizes the effects of repeated bottleneck events during colonization. We provide evidence of post-bottleneck genetic recovery, with average AR of infrapopulations increasing about 30% over the 225-generation span of time observed directly in this study. Our estimates of recovery rate suggest, however, that recovery has plateaued and that this population may not reach genetic diversity levels of the source population without further immigration from the source population. Finally, we employ a grid-based sampling scheme in the region of ongoing population expansion and provide empirical evidence for the power of allele surfing to impart genetic structure on a population, even under conditions of selective neutrality and in a place that lacks strong barriers to gene flow.
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Affiliation(s)
- James W Demastes
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa
| | - David J Hafner
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico
| | - Mark S Hafner
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - Jessica E Light
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas
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Jensen EL, Edwards DL, Garrick RC, Miller JM, Gibbs JP, Cayot LJ, Tapia W, Caccone A, Russello MA. Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise. Evol Appl 2018; 11:1811-1821. [PMID: 30459831 PMCID: PMC6231475 DOI: 10.1111/eva.12682] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/09/2018] [Accepted: 07/16/2018] [Indexed: 12/26/2022] Open
Abstract
Population genetic theory related to the consequences of rapid population decline is well-developed, but there are very few empirical studies where sampling was conducted before and after a known bottleneck event. Such knowledge is of particular importance for species restoration, given links between genetic diversity and the probability of long-term persistence. To directly evaluate the relationship between current genetic diversity and past demographic events, we collected genome-wide single nucleotide polymorphism data from prebottleneck historical (c.1906) and postbottleneck contemporary (c.2014) samples of Pinzón giant tortoises (Chelonoidis duncanensis; n = 25 and 149 individuals, respectively) endemic to a single island in the Galapagos. Pinzón giant tortoises had a historically large population size that was reduced to just 150-200 individuals in the mid 20th century. Since then, Pinzón's tortoise population has recovered through an ex situ head-start programme in which eggs or pre-emergent individuals were collected from natural nests on the island, reared ex situ in captivity until they were 4-5 years old and subsequently repatriated. We found that the extent and distribution of genetic variation in the historical and contemporary samples were very similar, with the latter group not exhibiting the characteristic genetic patterns of recent population decline. No population structure was detected either spatially or temporally. We estimated an effective population size (N e) of 58 (95% CI = 50-69) for the postbottleneck population; no prebottleneck N e point estimate was attainable (95% CI = 39-infinity) likely due to the sample size being lower than the true N e. Overall, the historical sample provided a valuable benchmark for evaluating the head-start captive breeding programme, revealing high retention of genetic variation and no skew in representation despite the documented bottleneck event. Moreover, this work demonstrates the effectiveness of head-starting in rescuing the Pinzón giant tortoise from almost certain extinction.
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Affiliation(s)
- Evelyn L. Jensen
- Department of BiologyUniversity of British Columbia OkanaganKelownaBritish ColumbiaCanada
- Present address:
Department of BiologyQueen's UniversityKingstonOntarioCanada
| | | | - Ryan C. Garrick
- Department of BiologyUniversity of MississippiOxfordMississippi
| | - Joshua M. Miller
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - James P. Gibbs
- College of Environmental Science and ForestryState University of New YorkSyracuseNew York
| | | | - Washington Tapia
- Department of Applied ResearchGalapagos National Park ServicePuerto AyoraEcuador
- Galapagos ConservancySanta CruzEcuador
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - Michael A. Russello
- Department of BiologyUniversity of British Columbia OkanaganKelownaBritish ColumbiaCanada
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Díez-Del-Molino D, García-Berthou E, Araguas RM, Alcaraz C, Vidal O, Sanz N, García-Marín JL. Effects of water pollution and river fragmentation on population genetic structure of invasive mosquitofish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1372-1382. [PMID: 29801230 DOI: 10.1016/j.scitotenv.2018.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/13/2018] [Accepted: 05/01/2018] [Indexed: 06/08/2023]
Abstract
We analyzed variation at the GPI-2 locus and eleven microsatellite loci of eastern mosquitofish Gambusia holbrooki populations introduced to the Ebro River (Spain), sampling above and below a dam (Flix Reservoir) where severe chronic pollution has been well documented. Allele frequency changes at the GPI-2 locus in the sites nearest to the polluted sediments agree with previous results from studies in mercury-exposed populations of this highly invasive fish. Genetic distinction of the mosquitofish collected close to the polluted sediments was detected at the GPI locus but also at the presumptive neutral microsatellite loci. Recent migration rates estimated from microsatellites indicated that around 30% of fish collected in a specific location were immigrants from upstream and downstream sources. Such high migration rates probably contribute to the mosquitofish's invasive success and suggest that the consequences on the mosquitofish regional genetic structured of high levels of water toxicants could be mediated by immigration from other sites, but the effect of pollutants on local diversity might be higher than observed here.
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Affiliation(s)
- David Díez-Del-Molino
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain; Dept. of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 104 05 Stockholm, Sweden.
| | | | - Rosa-Maria Araguas
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain.
| | - Carles Alcaraz
- IRTA Marine and Continental Waters, Carretera Poble Nou, km 5.5, 43540 Sant Carles de la Ràpita, Spain.
| | - Oriol Vidal
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain.
| | - Nuria Sanz
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain.
| | - Jose-Luis García-Marín
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain.
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Cammen KM, Schultz TF, Don Bowen W, Hammill MO, Puryear WB, Runstadler J, Wenzel FW, Wood SA, Kinnison M. Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds. Ecol Evol 2018; 8:6599-6614. [PMID: 30038760 PMCID: PMC6053562 DOI: 10.1002/ece3.4143] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/30/2018] [Accepted: 04/04/2018] [Indexed: 12/13/2022] Open
Abstract
Population increases over the past several decades provide natural settings in which to study the evolutionary processes that occur during bottleneck, growth, and spatial expansion. We used parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species in the Northwest Atlantic, the gray seal (Halichoerus grypus atlantica) and harbor seal (Phoca vitulina vitulina), to study the impact of recent demographic change in genomic diversity. Using restriction site-associated DNA sequencing, we assessed genomic diversity at over 8,700 polymorphic gray seal loci and 3,700 polymorphic harbor seal loci in samples from multiple cohorts collected throughout recovery over the past half-century. Despite significant differences in the degree of genetic diversity assessed in the two species, we found signatures of historical bottlenecks in the contemporary genomes of both gray and harbor seals. We evaluated temporal trends in diversity across cohorts, as well as compared samples from sites at both the center and edge of a recent gray seal range expansion, but found no significant change in genomewide diversity following recovery. We did, however, find that the variance and degree of allele frequency change measured over the past several decades were significantly different from neutral expectations of drift under population growth. These two cases of well-described demographic history provide opportunities for critical evaluation of current approaches to simulating and understanding the genetic effects of historical demographic change in natural populations.
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Affiliation(s)
| | - Thomas F. Schultz
- Duke University Marine LabNicholas School of the EnvironmentBeaufortNCUSA
| | - W. Don Bowen
- Bedford Institute of OceanographyDartmouthNSCanada
| | - Michael O. Hammill
- Fisheries and Oceans CanadaMaurice Lamontagne InstituteMont‐JoliQCCanada
| | - Wendy B. Puryear
- Department of Infectious Disease and Global HealthCummings School of Veterinary MedicineTufts UniversityNorth GraftonMAUSA
| | - Jonathan Runstadler
- Department of Infectious Disease and Global HealthCummings School of Veterinary MedicineTufts UniversityNorth GraftonMAUSA
| | - Frederick W. Wenzel
- Protected Species Branch, NOAA, NMFSNortheast Fisheries Science CenterWoods HoleMAUSA
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Combe FJ, Taylor-Cox E, Fox G, Sandri T, Davis N, Jones MJ, Cain B, Mallon D, Harris WE. Rapid isolation and characterization of microsatellites in the critically endangered mountain bongo (Tragelaphus eurycerus isaaci). J Genet 2018. [DOI: 10.1007/s12041-018-0922-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hapeman P, Latch EK, Rhodes OE, Swanson B, Kilpatrick CW. Genetic population structure of fishers (Pekania pennanti) in the Great Lakes region: remnants and reintroductions. CAN J ZOOL 2017. [DOI: 10.1139/cjz-2016-0325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Reintroduction programs have been pivotal in augmenting populations of fishers (Pekania pennanti (Erxleben, 1777)) and re-establishing them to their former range in North America. The majority of reintroduction efforts in fishers have been considered demographically successful, but reintroductions can alter genetic population structure and success has rarely been evaluated in fishers from a genetic standpoint. We used microsatellite data (n = 169) to examine genetic population structure of fishers in the Great Lakes region and comment on the success of past reintroductions at two different spatial scales. We found significant genetic population structure among source and reintroduced populations within the Great Lakes region and large-scale genetic structure between fisher populations located in two geographically distant regions (Great Lakes and Northeast) in the eastern United States. Reintroductions associated with the Great Lakes produced results that were largely consistent with other studies of fisher reintroductions in the Northeast. However, our data are the first to support a measurable impact on genetic population structure in Pekania pennanti pennanti (Erxleben, 1777) from a reintroduction using geographically distant source and reintroduced populations. When feasible, we strongly recommend that reintroduction programs include an investigation of the underlying genetic structure to better define intended goals and supplement measures of demographic success.
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Affiliation(s)
- Paul Hapeman
- Department of Biology, Central Connecticut State University, New Britain, CT 06050, USA
| | - Emily K. Latch
- Department of Biological Sciences, University of Wisconsin–Milwaukee, 3209 North Maryland Avenue, Milwaukee, WI 53211-3102, USA
| | - Olin E. Rhodes
- Savannah River Ecology Laboratory P.O. Drawer E, Aiken, SC 29802, USA
| | - Brad Swanson
- Department of Biology, Central Michigan University, Mount Pleasant, MI 05405-0086, USA
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Geary B, Longest SM, Ottewell K, Lantz SM, Walter ST, Karubian J, Leberg PL. Genetic structure of brown pelicans (Pelecanus occidentalis) in the northern Gulf of Mexico in the context of human management and disturbance. PLoS One 2017; 12:e0185309. [PMID: 28977003 PMCID: PMC5627915 DOI: 10.1371/journal.pone.0185309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/11/2017] [Indexed: 11/19/2022] Open
Abstract
Environmental disturbances, both natural and anthropogenic, have the capacity to substantially impact animal behavior and abundance, which can in turn influence patterns of genetic diversity and gene flow. However, little empirical information is available on the nature and degree of such changes due to the relative rarity of longitudinal genetic sampling of wild populations at appropriate intervals. Addressing this knowledge gap is therefore of interest to evolutionary biologists, policy makers, and managers. In the past half century, populations of the brown pelican (Pelecanus occidentalis) in the southeastern United States have been exposed to regional extirpations, translocations, colony losses, and oil spills, but potential impacts on genetic diversity and population structure remain unknown. To investigate the cumulative impacts of recent disturbances and management actions, we analyzed seven microsatellite loci using genetic samples collected from 540 nestlings across twelve pelican colonies from two time periods, corresponding to before (n = 305) and after (n = 235) the 2010 Deepwater Horizon oil spill. Pre-2010 populations in Texas were significantly differentiated from Louisiana, Alabama, and Florida populations to the east, with reintroduced populations in southeastern Louisiana having less genetic diversity than sites in Texas, consistent with a recent bottleneck. In contrast, there was no evidence of a geographic component to genetic structure among colonies sampled after the spill, consistent with increased dispersal among sites following the event. This pattern may be associated with reduced philopatry in response to colony abandonment in the areas most heavily impacted by the Deepwater Horizon event, though other factors (e.g., rehabilitation and translocation of oiled birds or colony loss due to erosion and tropical storms) were likely also involved. Future monitoring is necessary to determine if bottlenecks and loss of genetic variation are associated with the oil spill over time, and is recommended for other systems in which disturbance effects may be inferred via repeated genetic sampling.
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Affiliation(s)
- Brock Geary
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail:
| | - Susan M. Longest
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, Louisiana, United States of America
| | - Kym Ottewell
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, Louisiana, United States of America
| | - Samantha M. Lantz
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, Louisiana, United States of America
| | - Scott T. Walter
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, Louisiana, United States of America
| | - Jordan Karubian
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, Louisiana, United States of America
| | - Paul L. Leberg
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, United States of America
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Bourgeois L, Beaman L. Tracking the Genetic Stability of a Honey Bee (Hymenoptera: Apidae) Breeding Program With Genetic Markers. JOURNAL OF ECONOMIC ENTOMOLOGY 2017; 110:1419-1423. [PMID: 28854659 DOI: 10.1093/jee/tox175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Indexed: 06/07/2023]
Abstract
A genetic stock identification (GSI) assay was developed in 2008 to distinguish Russian honey bees from other honey bee stocks that are commercially produced in the United States. Probability of assignment (POA) values have been collected and maintained since the stock release in 2008 to the Russian Honey Bee Breeders Association. These data were used to assess stability of the breeding program and the diversity levels of the contemporary breeding stock through comparison of POA values and genetic diversity parameters from the initial release to current values. POA values fluctuated throughout 2010-2016, but have recovered to statistically similar levels in 2016 (POA(2010) = 0.82, POA(2016) = 0.74; P = 0.33). Genetic diversity parameters (i.e., allelic richness and gene diversity) in 2016 also remained at similar levels when compared to those in 2010. Estimates of genetic structure revealed stability (FST(2009/2016) = 0.0058) with a small increase in the estimate of the inbreeding coefficient (FIS(2010) = 0.078, FIS(2016) = 0.149). The relationship among breeding lines, based on genetic distance measurement, was similar in 2008 and 2016 populations, but with increased homogeneity among lines (i.e., decreased genetic distance). This was expected based on the closed breeding system used for Russian honey bees. The successful application of the GSI assay in a commercial breeding program demonstrates the utility and stability of such technology to contribute to and monitor the genetic integrity of a breeding stock of an insect species.
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Affiliation(s)
- Lelania Bourgeois
- USDA-ARS, Honey Bee Breeding, Genetics, and Physiology Laboratory, 1157 Ben Hur Rd., Baton Rouge, LA 70820
| | - Lorraine Beaman
- USDA-ARS, Honey Bee Breeding, Genetics, and Physiology Laboratory, 1157 Ben Hur Rd., Baton Rouge, LA 70820
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Scicchitano V, Dedeine F, Bagnères AG, Luchetti A, Mantovani B. Genetic diversity and invasion history of the European subterranean termite Reticulitermes urbis (Blattodea, Termitoidae, Rhinotermitidae). Biol Invasions 2017. [DOI: 10.1007/s10530-017-1510-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Bock CH, Hotchkiss MW, Young CA, Charlton ND, Chakradhar M, Stevenson KL, Wood BW. Population Genetic Structure of Venturia effusa, Cause of Pecan Scab, in the Southeastern United States. PHYTOPATHOLOGY 2017; 107:607-619. [PMID: 28414611 DOI: 10.1094/phyto-10-16-0376-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Venturia effusa is the most important pathogen of pecan in the southeastern United States. Little information exists on the population biology and genetic diversity of the pathogen. A hierarchical sampling of 784 isolates from 63 trees in 11 pecan orchards in the southeastern United States were screened against a set of 30 previously characterized microsatellite markers. Populations were collected from Georgia (n = 2), Florida (n = 1), Alabama (n = 2), Mississippi (n = 1), Louisiana (n = 1), Illinois (n = 1), Oklahoma (n = 1), Texas (n = 1), and Kansas (n = 1). Clonality was low in all orchard populations (≤10.1% of isolates), and there were consistently high levels of genotypic diversity (Shannon-Weiner's index = 3.49 to 4.59) and gene diversity (Nei's measure = 0.513 to 0.713). Analysis of molecular variance showed that, although 81% of genetic diversity occurred at the scale of the individual tree, 16% occurred between orchards and only 3% between trees within orchards. All populations could be differentiated from each other (P = 0.01), and various cluster analyses indicated that some populations were more closely related compared with other pairs of populations. This is indicative of some limited population differentiation in V. effusa in the southeastern United States. Bayesian and nearest-neighbor methods suggested eight clusters, with orchards from Georgia and Florida being grouped together. A minimum spanning tree of all 784 isolates also indicated some isolate identification with source population. Linkage disequilibrium was detected in all but one population (Kansas), although 8 of the 11 populations had <20% of loci at disequilibrium. A Mantel test demonstrated a relationship between physical and genetic distance between populations (Z = 11.9, r = 0.559, P = 0.001). None of the populations were at mutation-drift equilibrium. All but 3 of the 11 populations had a deficiency of gene diversity compared with that expected at mutation-drift equilibrium (indicating population expansion); the remaining populations had an excess of gene diversity compared with that expected at mutation-drift equilibrium (indicating a recent bottleneck). These observations are consistent with the known history of pecan and pecan scab, which is that V. effusa became an issue on cultivated pecan in the last approximately 120 years (recent population expansion). Recently reported mating type genes and the sexual stage of this fungus may help explain the observed population characteristics, which bear a strong resemblance to those of other well-characterized sexually reproducing ascomycete pathogens.
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Affiliation(s)
- Clive H Bock
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Michael W Hotchkiss
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Carolyn A Young
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Nikki D Charlton
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Mattupalli Chakradhar
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Katherine L Stevenson
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Bruce W Wood
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
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Su Z, Richardson BA, Zhuo L, Jiang X, Li W, Kang X. Genetic diversity and structure of an endangered desert shrub and the implications for conservation. AOB PLANTS 2017; 9:plx016. [PMID: 28533899 PMCID: PMC5434794 DOI: 10.1093/aobpla/plx016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/21/2017] [Accepted: 04/17/2017] [Indexed: 06/07/2023]
Abstract
Population genetic information can provide valuable insight for the conservation and management of threatened and endangered plant species. Tamarix taklamakanensis is an endangered shrub endemic to arid basins of northwestern China. This species serves to stabilize soils in this region, but has seen substantial loss in its abundance due to depletion of ground water. The populations of this species have become small and fragmented, warranting conservation. Seven microsatellite loci were used to assess the genetic diversity and structure of 15 populations in the Tarim Basin, China. Among populations, the expected heterozygosity and total gene diversity were both moderate (HE = 0.392, hT = 0.432), however the allelic diversity was low (A = 2.4). Eleven populations were detected to have experienced recent bottlenecks using Wilcoxon's test and a model-shift test. Most populations of T. taklamakanensis in the centre of Tarim Basin showed low levels of genetic differentiation, but higher levels in geographically outlying populations. Genetic structure based on Bayesian assignment, the neighbour-joining network and principal coordinates analyses produced similar results, supporting five groups in the Tarim Basin. Gene flow was high among Bayesian groups based on historical gene flow estimated by private alleles. The genetic structure of T. taklamakanensis supports a pattern where gene flow principally occurs along river corridors through hydrochory of seeds and insect-mediated pollination. Populations upstream have contributed to a more diverse mixture of populations near the confluence of several rivers near the centre of Tarim Basin. This pattern of genetic structure could be influenced by the flow of water from different river systems. Conservation efforts should focus on fostering the regeneration of this species, maintaining genetic diversity and preserving the extant genetic structure. Conservation efforts are contingent upon maintaining ground water and streamflows in this arid basin.
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Affiliation(s)
- Zhihao Su
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, no. 818 South Beijing Road, Xinjiang, Urumqi 830011, China
| | - Bryce A. Richardson
- USDA Forest Service, Rocky Mountain Research Station, 735 North 500 East, Provo, UT 84606, USA
| | - Li Zhuo
- Library, Xinjiang Normal University, Urumqi 830054, China
| | - Xiaolong Jiang
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai 201602, China
| | - Wenjun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, no. 818 South Beijing Road, Xinjiang, Urumqi 830011, China
| | - Xiaoshan Kang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, no. 818 South Beijing Road, Xinjiang, Urumqi 830011, China
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Chen C, Lu RS, Zhu SS, Tamaki I, Qiu YX. Population structure and historical demography of Dipteronia dyeriana (Sapindaceae), an extremely narrow palaeoendemic plant from China: implications for conservation in a biodiversity hot spot. Heredity (Edinb) 2017; 119:95-106. [PMID: 28379211 DOI: 10.1038/hdy.2017.19] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/02/2017] [Accepted: 02/03/2017] [Indexed: 11/09/2022] Open
Abstract
Inferring past demography is a central question in evolutionary and conservation biology. It is, however, sometimes challenging to disentangle their roles of contemporary versus historical processes in shaping the current patterns of genetic variation in endangered species. In this study, we used both chloroplast microsatellite (cpSSR) loci and nuclear microsatellite (nSSR) loci to assess the levels of genetic differentiation, genetic effective population size, contemporary/historical levels of gene flow and demographic history for five populations sampled across the range of Dipteronia dyeriana, an endangered palaeoendemism from Southwestern China. We found that D. dyeriana had a mixed pattern of moderate genetic diversity and high inbreeding. Bayesian clustering divided D. dyeriana populations into two nSSR genetic clusters. Coalescent-based approximate Bayesian computation analyses suggest the western and eastern groups of D. dyeriana likely persisted in a long-term refuge in Southern China since the beginning of the last glacial period, whereas increasingly colder and arid climates at the onset of the last glacial maximum might have fostered the fragmentation of D. dyeriana within refugia. Following their divergence, the western group kept relatively stable effective population size, whereas the eastern group had experienced 500-fold population expansion during the Holocene. Although clear loss of genetic diversity by human activities was not suggested, recent habitat fragmentation has led to a reduction of population connectivity and increased genetic differentiation by ongoing genetic drift in isolated populations, possibly owing to decreased population size in recent dozen years. Finally, we discussed the implications of these results on conservation policies.
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Affiliation(s)
- C Chen
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China.,College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - R S Lu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - S S Zhu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - I Tamaki
- Gifu Academy of Forest Science and Culture, Mino, Japan
| | - Y X Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
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Miura O, Kanaya G, Nakai S, Itoh H, Chiba S, Makino W, Nishimura T, Kojima S, Urabe J. Ecological and genetic impact of the 2011 Tohoku Earthquake Tsunami on intertidal mud snails. Sci Rep 2017; 7:44375. [PMID: 28281698 PMCID: PMC5345064 DOI: 10.1038/srep44375] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/07/2017] [Indexed: 11/13/2022] Open
Abstract
Natural disturbances often destroy local populations and can considerably affect the genetic properties of these populations. The 2011 Tohoku Earthquake Tsunami greatly damaged local populations of various coastal organisms, including the mud snail Batillaria attramentaria, which was an abundant macroinvertebrate on the tidal flats in the Tohoku region. To evaluate the impact of the tsunami on the ecology and population genetic properties of these snails, we monitored the density, shell size, and microsatellite DNA variation of B. attramentaria for more than ten years (2005–2015) throughout the disturbance event. We found that the density of snails declined immediately after the tsunami. Bayesian inference of the genetically effective population size (Ne) demonstrated that the Ne declined by 60–99% at the study sites exposed to the tsunami. However, we found that their genetic diversity was not significantly reduced after the tsunami. The maintenance of genetic diversity is essential for long-term survival of local populations, and thus, the observed genetic robustness could play a key role in the persistence of snail populations in this region which has been devastated by similar tsunamis every 500–800 years. Our findings have significant implications for understanding the sustainability of populations damaged by natural disturbances.
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Affiliation(s)
- Osamu Miura
- Faculty of Agriculture and Marine Science, Kochi University, 200 Monobe, Nankoku, Kochi 783-8502, Japan
| | - Gen Kanaya
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Shizuko Nakai
- Department of Marine Science and Resources, College of Bioresource Sciences Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Hajime Itoh
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Satoshi Chiba
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Kawauchi 41, Aoba-ku, Sendai, Miyagi 980-0862, Japan
| | - Wataru Makino
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Tomohiro Nishimura
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Shigeaki Kojima
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Jotaro Urabe
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
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37
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Mimura M, Yahara T, Faith DP, Vázquez‐Domínguez E, Colautti RI, Araki H, Javadi F, Núñez‐Farfán J, Mori AS, Zhou S, Hollingsworth PM, Neaves LE, Fukano Y, Smith GF, Sato Y, Tachida H, Hendry AP. Understanding and monitoring the consequences of human impacts on intraspecific variation. Evol Appl 2017; 10:121-139. [PMID: 28127389 PMCID: PMC5253428 DOI: 10.1111/eva.12436] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/20/2016] [Indexed: 12/15/2022] Open
Abstract
Intraspecific variation is a major component of biodiversity, yet it has received relatively little attention from governmental and nongovernmental organizations, especially with regard to conservation plans and the management of wild species. This omission is ill-advised because phenotypic and genetic variations within and among populations can have dramatic effects on ecological and evolutionary processes, including responses to environmental change, the maintenance of species diversity, and ecological stability and resilience. At the same time, environmental changes associated with many human activities, such as land use and climate change, have dramatic and often negative impacts on intraspecific variation. We argue for the need for local, regional, and global programs to monitor intraspecific genetic variation. We suggest that such monitoring should include two main strategies: (i) intensive monitoring of multiple types of genetic variation in selected species and (ii) broad-brush modeling for representative species for predicting changes in variation as a function of changes in population size and range extent. Overall, we call for collaborative efforts to initiate the urgently needed monitoring of intraspecific variation.
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Affiliation(s)
- Makiko Mimura
- Department of Bioenvironmental SystemsTamagawa UniversityTokyoJapan
| | - Tetsukazu Yahara
- Department of Biology and Institute of Decision Science for a Sustainable SocietyKyushu UniversityFukuokaJapan
| | - Daniel P. Faith
- The Australian Museum Research InstituteThe Australian MuseumSydneyNSWAustralia
| | | | | | - Hitoshi Araki
- Research Faculty of AgricultureHokkaido UniversitySapporoHokkaidoJapan
| | - Firouzeh Javadi
- Department of Biology and Institute of Decision Science for a Sustainable SocietyKyushu UniversityFukuokaJapan
| | - Juan Núñez‐Farfán
- Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoMéxicoMéxico
| | - Akira S. Mori
- Graduate School of Environment and Information SciencesYokohama National UniversityYokohamaJapan
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
| | | | - Linda E. Neaves
- Royal Botanic Garden EdinburghEdinburghUK
- Australian Centre for Wildlife Genomics, Australian Museum Research InstituteAustralian MuseumSydneyNSWAustralia
| | - Yuya Fukano
- Department of Biology and Institute of Decision Science for a Sustainable SocietyKyushu UniversityFukuokaJapan
| | - Gideon F. Smith
- Department of BotanyNelson Mandela Metropolitan UniversityPort ElizabethSouth Africa
- Departamento de Ciências da VidaCentre for Functional EcologyUniversidade de CoimbraCoimbraPortugal
| | | | - Hidenori Tachida
- Department of Biology and Institute of Decision Science for a Sustainable SocietyKyushu UniversityFukuokaJapan
| | - Andrew P. Hendry
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
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Wilk RJ, Horth L. A genetically distinct hybrid zone occurs for two globally invasive mosquito fish species with striking phenotypic resemblance. Ecol Evol 2016; 6:8375-8388. [PMID: 28031790 PMCID: PMC5167044 DOI: 10.1002/ece3.2562] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 09/11/2016] [Accepted: 09/19/2016] [Indexed: 12/03/2022] Open
Abstract
Hybrid zones allow for the investigation of incipient speciation and related evolutionary processes of selection, gene flow, and migration. Interspecific dynamics, like competition, can impact the size, shape, and directional movement of species in hybrid zones. Hybrid zones contribute to a paradox for the biological species concept because interbreeding between species occurs while parental forms remain distinct. A long‐standing zone of intergradation or introgression exists for eastern and western mosquito fish (Gambusia holbrooki and G. affinis) around Mobile Bay, AL. The region has been studied episodically, over decades, making it perfect for addressing temporal dynamics and for providing a deeper understanding of the genetics of these periodically reclassified fishes (as species or subspecies). We used six microsatellite markers to assess the current population structure and gene flow patterns across 19 populations of mosquito fish and then compared our results with historical data. Genetic evidence demonstrates that the current hybrid zone is located in a similar geographic region as the historical one, even after three decades. Hybrid fish, however, demonstrate relatively low heterozygosity and are genetically distinct from western and eastern mosquito fish populations. Fin ray counts, sometimes used to distinguish the two species from one another, demonstrate more eastern (G. holbrooki) phenotype fish within the molecular genetic hybrid zone today. Mosquito fish are globally invasive, often found on the leading edge of flooded waters that they colonize, so the impact of hurricanes in the wake of climate change was also evaluated. An increase in the frequency and intensity of hurricanes in the hybrid region has occurred, and this point warrants further attention since hurricanes are known to move these aggressive, invasive species into novel territory. This work contributes to our classical understanding of hybrid zone temporal dynamics, refines our understanding of mosquito fish genetics in their native range, evaluates important genotype–phenotype relationships, and identifies a potential new impact of climate change.
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Affiliation(s)
- Rebecca J Wilk
- Department of Biological Sciences Old Dominion University Norfolk VA USA
| | - Lisa Horth
- Department of Biological Sciences Old Dominion University Norfolk VA USA
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39
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Connectivity rescues genetic diversity after a demographic bottleneck in a butterfly population network. Proc Natl Acad Sci U S A 2016; 113:10914-9. [PMID: 27621433 DOI: 10.1073/pnas.1600865113] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Demographic bottlenecks that occur when populations fluctuate in size erode genetic diversity, but that diversity can be recovered through immigration. Connectivity among populations and habitat patches in the landscape enhances immigration and should in turn facilitate recovery of genetic diversity after a sudden reduction in population size. For the conservation of genetic diversity, it may therefore be particularly important to maintain connectivity in the face of factors that increase demographic instability, such as climate change. However, a direct link between connectivity and recovery of genetic diversity after a demographic bottleneck has not been clearly demonstrated in an empirical system. Here, we show that connectivity of habitat patches in the landscape contributes to the maintenance of genetic diversity after a demographic bottleneck. We were able to monitor genetic diversity in a network of populations of the alpine butterfly, Parnassius smintheus, before, during, and after a severe reduction in population size that lasted two generations. We found that allelic diversity in the network declined after the demographic bottleneck but that less allelic diversity was lost from populations occupying habitat patches with higher connectivity. Furthermore, the effect of connectivity on allelic diversity was important during the demographic recovery phase. Our results demonstrate directly the ability of connectivity to mediate the rescue of genetic diversity in a natural system.
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Hudson MA, Young RP, D'Urban Jackson J, Orozco-terWengel P, Martin L, James A, Sulton M, Garcia G, Griffiths RA, Thomas R, Magin C, Bruford MW, Cunningham AA. Dynamics and genetics of a disease-driven species decline to near extinction: lessons for conservation. Sci Rep 2016; 6:30772. [PMID: 27485994 PMCID: PMC4971493 DOI: 10.1038/srep30772] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/07/2016] [Indexed: 12/05/2022] Open
Abstract
Amphibian chytridiomycosis has caused precipitous declines in hundreds of species worldwide. By tracking mountain chicken (Leptodactylus fallax) populations before, during and after the emergence of chytridiomycosis, we quantified the real-time species level impacts of this disease. We report a range-wide species decline amongst the fastest ever recorded, with a loss of over 85% of the population in fewer than 18 months on Dominica and near extinction on Montserrat. Genetic diversity declined in the wild, but emergency measures to establish a captive assurance population captured a representative sample of genetic diversity from Montserrat. If the Convention on Biological Diversity’s targets are to be met, it is important to evaluate the reasons why they appear consistently unattainable. The emergence of chytridiomycosis in the mountain chicken was predictable, but the decline could not be prevented. There is an urgent need to build mitigation capacity where amphibians are at risk from chytridiomycosis.
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Affiliation(s)
- M A Hudson
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK.,Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent CT2 7NR, UK.,Durrell Wildlife Conservation Trust, Les Augres Manor, Trinity, Jersey, Channel Islands, UK
| | - R P Young
- Durrell Wildlife Conservation Trust, Les Augres Manor, Trinity, Jersey, Channel Islands, UK.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
| | - J D'Urban Jackson
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK.,Department of Biology &Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - P Orozco-terWengel
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
| | - L Martin
- Department of Environment, Montserrat Ministry of Agriculture, Housing, Lands and Environment, Montserrat, West Indies
| | - A James
- Forestry, Wildlife and Parks Division, Dominica Ministry of Agriculture and Fisheries, Botanical Gardens, Roseau, Commonwealth of Dominica, West Indies
| | - M Sulton
- Forestry, Wildlife and Parks Division, Dominica Ministry of Agriculture and Fisheries, Botanical Gardens, Roseau, Commonwealth of Dominica, West Indies
| | - G Garcia
- Chester Zoo, Cedar House, Caughall Road, Upton by Chester, Chester CH2 1LH, UK
| | - R A Griffiths
- Durrell Wildlife Conservation Trust, Les Augres Manor, Trinity, Jersey, Channel Islands, UK
| | - R Thomas
- Division of Agriculture, Dominica Ministry of Agriculture and Fisheries, Botanical Gardens, Roseau, Commonwealth of Dominica, West Indies
| | - C Magin
- The Royal Society for the Protection of Birds, The Lodge, Sandy, Bedfordshire SG19 2DL, UK
| | - M W Bruford
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK.,Sustainable Places Research Institute, Cardiff University, Cardiff CF10 3BB, UK
| | - A A Cunningham
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
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Bryant JV, Gottelli D, Zeng X, Hong X, Chan BPL, Fellowes JR, Zhang Y, Luo J, Durrant C, Geissmann T, Chatterjee HJ, Turvey ST. Assessing current genetic status of the Hainan gibbon using historical and demographic baselines: implications for conservation management of species of extreme rarity. Mol Ecol 2016; 25:3540-56. [PMID: 27273107 DOI: 10.1111/mec.13716] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/13/2016] [Accepted: 05/31/2016] [Indexed: 12/30/2022]
Abstract
Evidence-based conservation planning is crucial for informing management decisions for species of extreme rarity, but collection of robust data on genetic status or other parameters can be extremely challenging for such species. The Hainan gibbon, possibly the world's rarest mammal, consists of a single population of ~25 individuals restricted to one protected area on Hainan Island, China, and has persisted for over 30 years at exceptionally low population size. Analysis of genotypes at 11 microsatellite loci from faecal samples for 36% of the current global population and tissue samples from 62% of existing historical museum specimens demonstrates limited current genetic diversity (Na = 2.27, Ar = 2.24, He = 0.43); diversity has declined since the 19th century and even further within the last 30 years, representing declines of ~30% from historical levels (Na = 3.36, Ar = 3.29, He = 0.63). Significant differentiation is seen between current and historical samples (FST = 0.156, P = 0.0315), and the current population exhibits extremely small Ne (current Ne = 2.16). There is evidence for both a recent population bottleneck and an earlier bottleneck, with population size already reasonably low by the late 19th century (historical Ne = 1162.96). Individuals in the current population are related at the level of half- to full-siblings between social groups, and full-siblings or parent-offspring within a social group, suggesting that inbreeding is likely to increase in the future. The species' current reduced genetic diversity must be considered during conservation planning, particularly for expectations of likely population recovery, indicating that intensive, carefully planned management is essential.
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Affiliation(s)
- J V Bryant
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.,Department of Genetics, Evolution & Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - D Gottelli
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - X Zeng
- Bawangling National Nature Reserve Management Office, Changjiang Lizu Autonomous County, Hainan, 572722, China
| | - X Hong
- Bawangling National Nature Reserve Management Office, Changjiang Lizu Autonomous County, Hainan, 572722, China
| | - B P L Chan
- Kadoorie Conservation China, Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - J R Fellowes
- The Kadoorie Institute, University of Hong Kong, Pokfulam Road, Hong Kong
| | - Y Zhang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,College of Life Sciences, Yunnan University, Kunming, 650091, China
| | - J Luo
- College of Life Sciences, Yunnan University, Kunming, 650091, China
| | - C Durrant
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - T Geissmann
- Anthropological Institute, University Zurich-Irchel, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland
| | - H J Chatterjee
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - S T Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
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Hinkson KM, Henry NL, Hensley NM, Richter SC. Initial founders of captive populations are genetically representative of natural populations in critically endangered dusky gopher frogs, Lithobates sevosus. Zoo Biol 2016; 35:378-384. [PMID: 27383748 DOI: 10.1002/zoo.21309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/11/2016] [Accepted: 06/28/2016] [Indexed: 11/11/2022]
Abstract
The rapid rate of decline in amphibian populations has urged many researchers and conservationists to establish captive, or ex situ, populations. Such populations are guarded against effects of habitat loss and degradation, and if actively managed, can serve as a reservoir for rare alleles that might be lost in the wild. Without proper management, ex situ population sizes can dwindle and will no longer perform this function. The dusky gopher frog, Lithobates sevosus, is a critically endangered species, imperiled by habitat loss and population isolation. To assist in recovery of the species and prevent further genetic erosion, a captive breeding program was initiated. We investigated how well natural genetic variation was captured within the ex situ population and determined relatedness within each ex situ population. We genotyped individuals from two natural populations and two founding, captive populations to compare metrics of genetic variation and relatedness. The data show the initial founder populations are genetically representative of the natural populations, although variation is low in each, and that relatedness values are similar. Therefore, founding captive populations were successful at capturing genetic variation in the wild. Future research should continue to compare genetic variation of captive and natural populations to monitor efficacy of their management programs. Zoo Biol. 35:378-384, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kristin M Hinkson
- Department of Biological Sciences, Eastern Kentucky University, Richmond, Kentucky
| | - Natochia L Henry
- Department of Biological Sciences, Eastern Kentucky University, Richmond, Kentucky
| | - Nina M Hensley
- Department of Biological Sciences, Eastern Kentucky University, Richmond, Kentucky
| | - Stephen C Richter
- Department of Biological Sciences, Eastern Kentucky University, Richmond, Kentucky. .,Division of Natural Areas, Eastern Kentucky University, Richmond, Kentucky.
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Graignic N, Tremblay F, Bergeron Y. Genetic consequences of selection cutting on sugar maple (Acer saccharum Marshall). Evol Appl 2016; 9:777-90. [PMID: 27330554 PMCID: PMC4908464 DOI: 10.1111/eva.12384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/10/2016] [Indexed: 11/30/2022] Open
Abstract
Selection cutting is a treatment that emulates tree-by-tree replacement for forests with uneven-age structures. It creates small openings in large areas and often generates a more homogenous forest structure (fewer large leaving trees and defective trees) that differs from old-growth forest. In this study, we evaluated whether this type of harvesting has an impact on genetic diversity of sugar maple (Acer saccharum Marshall). Genetic diversity among seedlings, saplings, and mature trees was compared between selection cut and old-growth forest stands in Québec, Canada. We found higher observed heterozygosity and a lower inbreeding coefficient in mature trees than in younger regeneration cohorts of both forest types. We detected a recent bottleneck in all stands undergoing selection cutting. Other genetic indices of diversity (allelic richness, observed and expected heterozygosity, and rare alleles) were similar between forest types. We concluded that the effect of selection cutting on the genetic diversity of sugar maple was recent and no evidence of genetic erosion was detectable in Québec stands after one harvest. However, the cumulative effect of recurring applications of selection cutting in bottlenecked stands could lead to fixation of deleterious alleles, and this highlights the need for adopting better forest management practices.
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Affiliation(s)
- Noémie Graignic
- Institut de Recherche sur les ForêtsUniversité du Québec en Abitibi‐TémiscamingueRouyn‐NorandaQCCanada
| | - Francine Tremblay
- Institut de Recherche sur les ForêtsUniversité du Québec en Abitibi‐TémiscamingueRouyn‐NorandaQCCanada
| | - Yves Bergeron
- Institut de Recherche sur les ForêtsUniversité du Québec en Abitibi‐TémiscamingueRouyn‐NorandaQCCanada
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Labuschagne C, Nupen L, Kotzé A, Grobler JP, Dalton DL. Genetic monitoring of ex situ African Penguin (Spheniscus demersus) populations in South Africa. AFRICAN ZOOLOGY 2016. [DOI: 10.1080/15627020.2016.1186499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Christiaan Labuschagne
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
- Inqaba Biotechnical Industries (Pty) Ltd, Pretoria, South Africa
- National Zoological Gardens of South Africa, Pretoria, South Africa
| | - Lisa Nupen
- National Zoological Gardens of South Africa, Pretoria, South Africa
| | - Antoinette Kotzé
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
- National Zoological Gardens of South Africa, Pretoria, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Desiré L Dalton
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
- National Zoological Gardens of South Africa, Pretoria, South Africa
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Sharma R, Kumar B, Arora R, Ahlawat S, Mishra A, Tantia M. Genetic diversity estimates point to immediate efforts for conserving the endangered Tibetan sheep of India. Meta Gene 2016; 8:14-20. [PMID: 27014586 PMCID: PMC4792857 DOI: 10.1016/j.mgene.2016.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/26/2015] [Accepted: 01/04/2016] [Indexed: 11/24/2022] Open
Abstract
Tibetan is a valuable Himalayan sheep breed classified as endangered. Knowledge of the level and distribution of genetic diversity in Tibetan sheep is important for designing conservation strategies for their sustainable survival and to preserve their evolutionary potential. Thus, for the first time, genetic variability in the Tibetan population was accessed with twenty five inter-simple sequence repeat markers. All the microsatellites were polymorphic and a total of 148 alleles were detected across these loci. The observed number of alleles across all the loci was more than the effective number of alleles and ranged from 3 (BM6506) to 11 (BM6526) with 5.920 ± 0.387 mean number of alleles per locus. The average observed heterozygosity was less than the expected heterozygosity. The observed and expected heterozygosity values ranged from 0.150 (BM1314) to 0.9 (OarCP20) with an overall mean of 0.473 ± 0.044 and from 0.329 (BM8125) to 0.885 (BM6526) with an overall mean 0.672 ± 0.030, respectively. The lower heterozygosity pointed towards diminished genetic diversity in the population. Thirteen microsatellite loci exhibited significant (P < 0.05) departures from the Hardy-Weinberg proportions in the population. The estimate of heterozygote deficiency varied from - 0.443 (OarCP20) to 0.668 (OarFCB128) with a mean positive value of 0.302 ± 0.057. A normal 'L' shaped distribution of mode-shift test and non-significant heterozygote excess on the basis of different models suggested absence of recent bottleneck in the existing Tibetan population. In view of the declining population of Tibetan sheep (less than 250) in the breeding tract, need of the hour is immediate scientific management of the population so as to increase the population hand in hand with retaining the founder alleles to the maximum possible extent.
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Affiliation(s)
- Rekha Sharma
- National Bureau of Animal Genetic Resources, Karnal 132 001, India
| | - Brijesh Kumar
- ICAR Research Complex for NEH Region, Sikkim Centre, Gangtok 737102, India
| | - Reena Arora
- National Bureau of Animal Genetic Resources, Karnal 132 001, India
| | - Sonika Ahlawat
- National Bureau of Animal Genetic Resources, Karnal 132 001, India
| | - A.K. Mishra
- National Bureau of Animal Genetic Resources, Karnal 132 001, India
| | - M.S. Tantia
- National Bureau of Animal Genetic Resources, Karnal 132 001, India
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Jacquet S, Huber K, Guis H, Setier-Rio ML, Goffredo M, Allène X, Rakotoarivony I, Chevillon C, Bouyer J, Baldet T, Balenghien T, Garros C. Spatio-temporal genetic variation of the biting midge vector species Culicoides imicola (Ceratopogonidae) Kieffer in France. Parasit Vectors 2016; 9:141. [PMID: 26968517 PMCID: PMC4788842 DOI: 10.1186/s13071-016-1426-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/04/2016] [Indexed: 11/10/2022] Open
Abstract
Background Introduction of vector species into new areas represents a main driver for the emergence and worldwide spread of vector-borne diseases. This poses a substantial threat to livestock economies and public health. Culicoides imicola Kieffer, a major vector species of economically important animal viruses, is described with an apparent range expansion in Europe where it has been recorded in south-eastern continental France, its known northern distribution edge. This questioned on further C. imicola population extension and establishment into new territories. Studying the spatio-temporal genetic variation of expanding populations can provide valuable information for the design of reliable models of future spread. Methods Entomological surveys and population genetic approaches were used to assess the spatio-temporal population dynamics of C. imicola in France. Entomological surveys (2–3 consecutive years) were used to evaluate population abundances and local spread in continental France (28 sites in the Var department) and in Corsica (4 sites). We also genotyped at nine microsatellite loci insects from 3 locations in the Var department over 3 years (2008, 2010 and 2012) and from 6 locations in Corsica over 4 years (2002, 2008, 2010 and 2012). Results Entomological surveys confirmed the establishment of C. imicola populations in Var department, but indicated low abundances and no apparent expansion there within the studied period. Higher population abundances were recorded in Corsica. Our genetic data suggested the absence of spatio-temporal genetic changes within each region but a significant increase of the genetic differentiation between Corsican and Var populations through time. The lack of intra-region population structure may result from strong gene flow among populations. We discussed the observed temporal variation between Corsica and Var as being the result of genetic drift following introduction, and/or the genetic characteristics of populations at their range edge. Conclusions Our results suggest that local range expansion of C. imicola in continental France may be slowed by the low population abundances and unsuitable climatic and environmental conditions. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1426-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stéphanie Jacquet
- Cirad, UMR15 Contrôle des Maladies Animales Exotiques et Emergentes, Campus International de Baillarguet, TA-A15/G, 34398, Montpellier, France. .,UMR 5290 Maladies Infectieuses & Vecteurs-Ecologie, Génétique, Ecologie, Contrôle (MIVEGEC), CNRS, Université de Montpellier, Montpellier, France. .,IRD, UR 224 MIVEGEC, Agropolis, BP 64501, 34 394, Montpellier cedex 5, France.
| | - Karine Huber
- Cirad, UMR15 Contrôle des Maladies Animales Exotiques et Emergentes, Campus International de Baillarguet, TA-A15/G, 34398, Montpellier, France.,INRA, UMR1309 CMAEE, 34398, Montpellier, France
| | - Hélène Guis
- Cirad, UMR15 Contrôle des Maladies Animales Exotiques et Emergentes, Campus International de Baillarguet, TA-A15/G, 34398, Montpellier, France
| | | | - Maria Goffredo
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise 'G. Caporale', 64100, Teramo, Italy
| | - Xavier Allène
- Cirad, UMR15 Contrôle des Maladies Animales Exotiques et Emergentes, Campus International de Baillarguet, TA-A15/G, 34398, Montpellier, France
| | - Ignace Rakotoarivony
- Cirad, UMR15 Contrôle des Maladies Animales Exotiques et Emergentes, Campus International de Baillarguet, TA-A15/G, 34398, Montpellier, France
| | - Christine Chevillon
- UMR 5290 Maladies Infectieuses & Vecteurs-Ecologie, Génétique, Ecologie, Contrôle (MIVEGEC), CNRS, Université de Montpellier, Montpellier, France.,IRD, UR 224 MIVEGEC, Agropolis, BP 64501, 34 394, Montpellier cedex 5, France
| | - Jérémy Bouyer
- Cirad, UMR15 Contrôle des Maladies Animales Exotiques et Emergentes, Campus International de Baillarguet, TA-A15/G, 34398, Montpellier, France
| | - Thierry Baldet
- Cirad, UMR15 Contrôle des Maladies Animales Exotiques et Emergentes, Campus International de Baillarguet, TA-A15/G, 34398, Montpellier, France
| | - Thomas Balenghien
- Cirad, UMR15 Contrôle des Maladies Animales Exotiques et Emergentes, Campus International de Baillarguet, TA-A15/G, 34398, Montpellier, France
| | - Claire Garros
- Cirad, UMR15 Contrôle des Maladies Animales Exotiques et Emergentes, Campus International de Baillarguet, TA-A15/G, 34398, Montpellier, France
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Exploring the legacy of goat grazing: signatures of habitat fragmentation on genetic patterns of endemic weevil populations in Northern Isabela Island, Galápagos (Ecuador). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0831-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kitavi M, Downing T, Lorenzen J, Karamura D, Onyango M, Nyine M, Ferguson M, Spillane C. The triploid East African Highland Banana (EAHB) genepool is genetically uniform arising from a single ancestral clone that underwent population expansion by vegetative propagation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:547-61. [PMID: 26743524 DOI: 10.1007/s00122-015-2647-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/30/2015] [Indexed: 05/04/2023]
Abstract
All East African Highland Banana varieties are genetically uniform having arisen from a single clone introduced to Africa. East African Highland bananas (EAHBs) are a subgroup of triploid (AAA genome) bananas of importance to food security in the Great Lakes region of Africa. Little is known about their genetic variation, population structure and evolutionary history. Ninety phenotypically diverse EAHB cultivars were genotyped at 100 SSR microsatellite markers to investigate population genetic diversity, the correlation of genetic variability with morphological classes, and evolutionary origins since introduction to Africa. Population-level statistics were compared to those for plantain (AAB) and dessert (AAA) cultivars representing other M. acuminata subgroups. EAHBs displayed minimal genetic variation and are largely genetically uniform, irrespective of whether they were derived from the distinct Ugandan or Kenyan germplasm collections. No association was observed between EAHB genetic diversity and currently employed morphological taxonomic systems for EAHB germplasm. Population size dynamics indicated that triploid EAHBs arose as a single hybridization event, which generated a genetic bottleneck during foundation of the EAHB genepool. As EAHB triploids are sterile, subsequent asexual vegetative propagation of EAHBs allowed a recent rapid expansion in population size. This provided a basis for emergence of genetically near-isogenic somatic mutants selected across farmers and environments in East Africa over the past 2000 years since EAHBs were first introduced to the African continent.
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Affiliation(s)
- Mercy Kitavi
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, C306 Aras de Brun, National University of Ireland Galway, University Road, Galway, Ireland
- International Institute for Tropical Agriculture (IITA), Biosciences Eastern and Central Africa (BecA-ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Tim Downing
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, University Road, Galway, Ireland
| | - Jim Lorenzen
- International Institute for Tropical Agriculture (IITA), Biosciences Eastern and Central Africa (BecA-ILRI), P.O. Box 30709-00100, Nairobi, Kenya
- Bill and Melinda Gates Foundation, 500 5th Ave N, Seattle, WA, 98102, USA
| | - Deborah Karamura
- Bioversity International, PLOT 106, Katalima Road, P.O. Box 24384, Kampala, Uganda
| | - Margaret Onyango
- Kenya Agricultural Research Institute (KARI), KARI, Kisii Centre, P.O. Box 523-40200, Kisii, Kenya
| | - Moses Nyine
- International Institute for Tropical Agriculture (IITA), Biosciences Eastern and Central Africa (BecA-ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Morag Ferguson
- International Institute for Tropical Agriculture (IITA), Biosciences Eastern and Central Africa (BecA-ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Charles Spillane
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, C306 Aras de Brun, National University of Ireland Galway, University Road, Galway, Ireland.
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Díez-del-Molino D, Araguas RM, Vera M, Vidal O, Sanz N, García-Marín JL. Temporal genetic dynamics among mosquitofish (Gambusia holbrooki) populations in invaded watersheds. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1055-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Xuereb ATJ, Rouse JD, Cunnington G, Lougheed SC. Population genetic structure at the northern range limit of the threatened eastern hog-nosed snake (Heterodon platirhinos). CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0737-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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