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Bruxaux J, Zhao W, Hall D, Curtu AL, Androsiuk P, Drouzas AD, Gailing O, Konrad H, Sullivan AR, Semerikov V, Wang XR. Scots pine - panmixia and the elusive signal of genetic adaptation. THE NEW PHYTOLOGIST 2024. [PMID: 38308133 DOI: 10.1111/nph.19563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/14/2024] [Indexed: 02/04/2024]
Abstract
Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.
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Affiliation(s)
- Jade Bruxaux
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - David Hall
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
- Forestry Research Institute of Sweden (Skogforsk), 918 21, Sävar, Sweden
| | | | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, 37077, Göttingen, Germany
| | - Heino Konrad
- Department of Forest Biodiversity and Nature Conservation, Unit of Ecological Genetics, Austrian Research Centre for Forests (BFW), 1140, Vienna, Austria
| | - Alexis R Sullivan
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - Vladimir Semerikov
- Institute of Plant and Animal Ecology, Ural Division of Russian Academy of Sciences, 620144, Ekaterinburg, Russia
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
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Danusevičius D, Rajora OP, Kavaliauskas D, Baliuckas V, Augustaitis A. Stronger genetic differentiation among within-population genetic groups than among populations in Scots pine provides new insights into within-population genetic structuring. Sci Rep 2024; 14:2713. [PMID: 38302512 PMCID: PMC10834436 DOI: 10.1038/s41598-024-52769-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
We investigated the presence of spatial genetic groups within forest tree populations and determined if the genetic divergence among these groups is greater than that between populations using Scots pine (Pinus sylvestris) as a model species. We genotyped 890 adult trees of Scots pine in six natural populations in Lithuania at 11 nuclear microsatellite loci. We used a Bayesian clustering approach to identify the within-population genetic groups within each of the six populations. We calculated the differentiation indexes among the genetic groups within each population and among the six populations by ignoring the genetic groups. The Bayesian clustering revealed 2 to 6 distinct genetic groups of varying size as the most likely genetic structures within populations. The genetic differentiation indexes among the genetic groups within populations were nearly tenfold greater (FST = 0.012-0.070) than those between the populations (FST = 0.003). We conclude on the existence of markedly stronger structuring of genetic variation within populations than between populations of Scots pine in large forest tracts of northern Europe. Such genetic structures serve as a contributing factor to large within population genetic diversity in northern conifers. We assume that within population mating in Scots pine is not completely random but rather is stratified into genetic clusters. Our study provides pioneering novel key insights into structuring of genetic variation within populations. Our findings have implications for examining within-population genetic diversity and genetic structure, conservation, and management of genetic resources.
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Affiliation(s)
- Darius Danusevičius
- Vytautas Magnus University, K. Donelaičio Str. 58, 44248, Kaunas, Lithuania.
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, PO Box 4400, 28 Dineen Drive, Fredericton, NB, E3B 5A3, Canada.
| | - Darius Kavaliauskas
- Vytautas Magnus University, K. Donelaičio Str. 58, 44248, Kaunas, Lithuania
- Lithuanian Research Centre for Agriculture and Forestry, Forestry Institute, Liepu Str. 1, 53101, Kaunas Reg., Lithuania
| | - Virgilijus Baliuckas
- Vytautas Magnus University, K. Donelaičio Str. 58, 44248, Kaunas, Lithuania
- Lithuanian Research Centre for Agriculture and Forestry, Forestry Institute, Liepu Str. 1, 53101, Kaunas Reg., Lithuania
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3
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Belton S, Cubry P, Roche JR, Kelleher CT. Molecular characterisation of Pinus sylvestris (L.) in Ireland at the western limit of the species distribution. BMC Ecol Evol 2024; 24:12. [PMID: 38262959 PMCID: PMC10807061 DOI: 10.1186/s12862-023-02181-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/26/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Scots pine (Pinus sylvestris L.) underwent significant population declines across much of northwest Europe during the mid-to-late Holocene and was thought to have become extirpated in Ireland from about 400 AD. However, most extant populations are plantations reintroduced from Scotland. Others are naturalised therefrom and one in Western Ireland is a putative relict. In this paper, Scots pine in Ireland are genetically described for the first time. RESULTS Using two mitochondrial (mtDNA) loci, eight chloroplast (cpSSR) and 18 nuclear (nSSR) loci, the genetic composition and diversity of 19 Irish Scots pine populations is described and compared to other European populations. All trees sampled in Ireland were fixed for mitotype a, which is the most common across northwest Europe. By contrast, cpSSR (HCP = 0.967) and nSSR (He = 0.540) variation was high, and comparable with estimates for other regions across the species range. Differentiation at both sets of loci were similarly low (cpSSR FST = 0.019; nSSR FST = 0.018), but populations from continental Europe were significantly differentiated from all Irish populations based on nSSR variation. CONCLUSIONS All Irish Scots pine are likely part of a common Irish-Scottish gene pool which diverged from continental Scots pine following post-glacial recolonisation. A high genetic diversity and an absence of evidence of inbreeding suggests the regional decline of Scots pine did not critically reduce allelic variation. The post-glacial relationship between Irish and Scottish pine is discussed, and a suggestion from recent palaeoecological work that reintroduced Scots pine be managed as a native species is now further supported by genetic data.
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Affiliation(s)
- Samuel Belton
- DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Glasnevin, Dublin, Ireland
| | - Philippe Cubry
- DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Glasnevin, Dublin, Ireland
- DIADE, Univ de Montpellier, CIRAD, IRD, Montpellier, F-34090, France
| | - Jenni R Roche
- National Parks and Wildlife Service, Department of Housing, Local Government and Heritage, 90 King Street North, Smithfield, Dublin, Ireland
| | - Colin T Kelleher
- DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Glasnevin, Dublin, Ireland.
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Cervantes S, Kesälahti R, Kumpula TA, Mattila TM, Helanterä H, Pyhäjärvi T. Strong Purifying Selection in Haploid Tissue-Specific Genes of Scots Pine Supports the Masking Theory. Mol Biol Evol 2023; 40:msad183. [PMID: 37565532 PMCID: PMC10457172 DOI: 10.1093/molbev/msad183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/16/2023] [Accepted: 08/10/2023] [Indexed: 08/12/2023] Open
Abstract
The masking theory states that genes expressed in a haploid stage will be under more efficient selection. In contrast, selection will be less efficient in genes expressed in a diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can be hidden from selection in heterozygous form. This difference can influence several evolutionary processes such as the maintenance of genetic variation, adaptation rate, and genetic load. Masking theory expectations have been confirmed in single-cell haploid and diploid organisms. However, in multicellular organisms, such as plants, the effects of haploid selection are not clear-cut. In plants, the great majority of studies indicating haploid selection have been carried out using male haploid tissues in angiosperms. Hence, evidence in these systems is confounded with the effects of sexual selection and intraspecific competition. Evidence from other plant groups is scarce, and results show no support for the masking theory. Here, we have used a gymnosperm Scots pine megagametophyte, a maternally derived seed haploid tissue, and four diploid tissues to test the strength of purifying selection on a set of genes with tissue-specific expression. By using targeted resequencing data of those genes, we obtained estimates of genetic diversity, the site frequency spectrum of 0-fold and 4-fold sites, and inferred the distribution of fitness effects of new mutations in haploid and diploid tissue-specific genes. Our results show that purifying selection is stronger for tissue-specific genes expressed in the haploid megagametophyte tissue and that this signal of strong selection is not an artifact driven by high expression levels.
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Affiliation(s)
- Sandra Cervantes
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Robert Kesälahti
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Timo A Kumpula
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Tiina M Mattila
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Heikki Helanterä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Tanja Pyhäjärvi
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
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5
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New Insight into Genetic Structure and Diversity of Scots Pine (Pinus sylvestris L.) Populations in Lithuania Based on Nuclear, Chloroplast and Mitochondrial DNA Markers. FORESTS 2022. [DOI: 10.3390/f13081179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
We studied the genetic differentiation, structure, and diversity of Scots pine populations in Lithuania based on nuclear, chloroplast microsatellite, and mitochondrial DNA markers. We focused on revealing evolutionary history, country-wide geneflow patterns, and structuring among the Scots pine populations. We genotyped 439 Scots pine individuals of mature age from 23 natural Scots pine stands in Lithuania and used the AMOVA and a set of genetic-clustering methods. The among-population differentiation was weak for nuclear microsatellite loci (nSSRs) (FST = 0.005) but much stronger for cpSSRs (PhiST = 0.240). The populations were structured into highland and lowland populations based on cpSSRs and eastern highland versus the rest for nSSRs. We detected two mtDNA mitotypes—the universal type A and northeastern type B, and the latter occurred at a markedly higher frequency in eastern Lithuania. Within-population genetic diversity was higher in large pine-dominated forest tracts in the eastern highlands than in fragmented forests in the western highlands. We concluded that phenology-based genetic networks following the temperature climate gradients have a strong effect on shaping the genetic structure of otherwise rather homogeneous gene pools of Scots pine populations in Lithuania. The possible effects of human interference with forests on genetic diversity of Scots pine populations in Lithuania are discussed.
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Kastally C, Niskanen AK, Perry A, Kujala ST, Avia K, Cervantes S, Haapanen M, Kesälahti R, Kumpula TA, Mattila TM, Ojeda DI, Tyrmi JS, Wachowiak W, Cavers S, Kärkkäinen K, Savolainen O, Pyhäjärvi T. Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1337-1350. [PMID: 34897859 PMCID: PMC9303803 DOI: 10.1111/tpj.15628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/05/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called 'PiSy50k'). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.
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Affiliation(s)
- Chedly Kastally
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Alina K. Niskanen
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Annika Perry
- UK Centre for Ecology & HydrologyBush EstatePenicuikMidlothianEH26 0QBUK
| | - Sonja T. Kujala
- Natural Resources Institute Finland (Luke)Paavo Havaksen tie 390570OuluFinland
| | - Komlan Avia
- Université de StrasbourgINRAESVQV UMR‐A 1131F‐68000ColmarFrance
| | - Sandra Cervantes
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Matti Haapanen
- Natural Resources Institute Finland (Luke)Latokartanonkaari 9FI‐00790HelsinkiFinland
| | - Robert Kesälahti
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Timo A. Kumpula
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Tiina M. Mattila
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
- Department of Organismal BiologyEBCUppsala UniversityNorbyvägen 18 AUppsala752 36Sweden
| | - Dario I. Ojeda
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
- Norwegian Institute of Bioeconomy ResearchP.O. Box 115Ås1431Norway
| | - Jaakko S. Tyrmi
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Witold Wachowiak
- Institute of Environmental BiologyFaculty of BiologyAdam Mickiewicz University in PoznańUniwersytetu Poznańskiego 661‐614PoznańPoland
| | - Stephen Cavers
- UK Centre for Ecology & HydrologyBush EstatePenicuikMidlothianEH26 0QBUK
| | - Katri Kärkkäinen
- Natural Resources Institute Finland (Luke)Paavo Havaksen tie 390570OuluFinland
| | - Outi Savolainen
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Tanja Pyhäjärvi
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
- Department of Forest SciencesUniversity of HelsinkiP.O. Box 2700014HelsinkiFinland
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7
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Takou M, Hämälä T, Koch EM, Steige KA, Dittberner H, Yant L, Genete M, Sunyaev S, Castric V, Vekemans X, Savolainen O, de Meaux J. Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population. Mol Biol Evol 2021; 38:1820-1836. [PMID: 33480994 PMCID: PMC8097302 DOI: 10.1093/molbev/msaa322] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
During range expansion, edge populations are expected to face increased genetic drift, which in turn can alter and potentially compromise adaptive dynamics, preventing the removal of deleterious mutations and slowing down adaptation. Here, we contrast populations of the European subspecies Arabidopsis lyrata ssp. petraea, which expanded its Northern range after the last glaciation. We document a sharp decline in effective population size in the range-edge population and observe that nonsynonymous variants segregate at higher frequencies. We detect a 4.9% excess of derived nonsynonymous variants per individual in the range-edge population, suggesting an increase of the genomic burden of deleterious mutations. Inference of the fitness effects of mutations and modeling of allele frequencies under the explicit demographic history of each population predicts a depletion of rare deleterious variants in the range-edge population, but an enrichment for fixed ones, consistent with the bottleneck effect. However, the demographic history of the range-edge population predicts a small net decrease in per-individual fitness. Consistent with this prediction, the range-edge population is not impaired in its growth and survival measured in a common garden experiment. We further observe that the allelic diversity at the self-incompatibility locus, which ensures strict outcrossing and evolves under negative frequency-dependent selection, has remained unchanged. Genomic footprints indicative of selective sweeps are broader in the Northern population but not less frequent. We conclude that the outcrossing species A. lyrata ssp. petraea shows a strong resilience to the effect of range expansion.
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Affiliation(s)
- Margarita Takou
- Institute of Botany, University of Cologne, Cologne, Germany
| | - Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Evan M Koch
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kim A Steige
- Institute of Botany, University of Cologne, Cologne, Germany
| | | | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Mathieu Genete
- CNRS, UMR 8198 – Evo-Eco-Paleo, University of Lille, Lille, France
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Vincent Castric
- CNRS, UMR 8198 – Evo-Eco-Paleo, University of Lille, Lille, France
| | - Xavier Vekemans
- CNRS, UMR 8198 – Evo-Eco-Paleo, University of Lille, Lille, France
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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8
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Imprints of selection in peripheral and ecologically marginal central-eastern European Scots pine populations. Gene 2021; 779:145509. [PMID: 33600955 DOI: 10.1016/j.gene.2021.145509] [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: 06/10/2020] [Revised: 11/04/2020] [Accepted: 02/05/2021] [Indexed: 11/21/2022]
Abstract
Knowledge of the molecular mechanisms underlying the stress response in plants is essential to understand evolutionary processes that result in long-term persistence of populations. Populations inhabiting marginal ecological conditions at the distribution range periphery may have preserved imprints of natural selection that have shaped functional genetic variation of the species. Our aim was to evaluate the extent of selection processes in the extremely fragmented, peripheral and isolated populations of Scots pine in central-eastern Europe. Autochthonous populations of the Carpathian Mts. and the Pannonian Basin were sampled and drought stress-related candidate genes were re-sequenced. Neutrality tests and outlier detection approaches were applied to infer the effect and direction of selection. Populations retained high genetic diversity by preserving a high number of alleles and haplotypes, many of them being population specific. Neutrality tests and outlier detection highlighted nucleotide positions that are under divergent selection and may be involved in local adaptation. The detected genetic pattern confirms that natural selection has played an important role in shaping modern-day genetic variation in marginal Scots pine populations, allowing for the long-term persistence of populations. Selection detected at functional regions possibly acts to maintain diversity and counteract the effect of genetic erosion.
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9
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Myers BM, Burns KJ, Clark CJ, Brelsford A. The population genetics of nonmigratory Allen's Hummingbird ( Selasphorus sasin sedentarius) following a recent mainland colonization. Ecol Evol 2021; 11:1850-1865. [PMID: 33614008 PMCID: PMC7882939 DOI: 10.1002/ece3.7174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/10/2020] [Accepted: 12/17/2020] [Indexed: 02/01/2023] Open
Abstract
Allen's Hummingbird comprises two subspecies, one migratory (Selasphorus sasin sasin) and one nonmigratory (S. s. sedentarius). The nonmigratory subspecies, previously endemic to the California Channel Islands, apparently colonized the California mainland on the Palos Verdes Peninsula some time before 1970 and now breeds throughout coastal southern California. We sequenced and compared populations of mainland nonmigratory Allen's Hummingbird to Channel Island populations from Santa Catalina, San Clemente, and Santa Cruz Island. We found no evidence of founder effects on the mainland population. Values of nucleotide diversity on the mainland were higher than on the Channel Islands. There were low levels of divergence between the Channel Islands and the mainland, and Santa Cruz Island was the most genetically distinct. Ecological niche models showed that rainfall and temperature variables on the Channel Islands are similar in the Los Angeles basin and predicted continued expansion of nonmigratory Allen's Hummingbird north along the coast and inland. We also reviewed previous genetic studies of vertebrate species found on the Channel Islands and mainland and showed that broad conclusions regarding island-mainland patterns remain elusive. Challenges include the idiosyncratic nature of colonization itself as well as the lack of a comprehensive approach that incorporates similar markers and sampling strategies across taxa, which, within the context of a comparative study of island-mainland relationships, may lead to inconsistent results.
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Affiliation(s)
- Brian M. Myers
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
| | - Kevin J. Burns
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
| | - Christopher J. Clark
- Department of Evolution, Ecology, and Organismal BiologySpeith HallUniversity of CaliforniaRiversideCAUSA
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal BiologySpeith HallUniversity of CaliforniaRiversideCAUSA
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10
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Ranade SS, García-Gil MR. Molecular signatures of local adaptation to light in Norway spruce. PLANTA 2021; 253:53. [PMID: 33511433 PMCID: PMC7843583 DOI: 10.1007/s00425-020-03517-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 12/02/2020] [Indexed: 05/12/2023]
Abstract
MAIN CONCLUSION Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light. The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
- Department of Plant Physiology, Umeå Plant Science Centre, University of Umeå, 901 87 Umeå, Sweden
| | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
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11
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Hall D, Olsson J, Zhao W, Kroon J, Wennström U, Wang XR. Divergent patterns between phenotypic and genetic variation in Scots pine. PLANT COMMUNICATIONS 2021; 2:100139. [PMID: 33511348 PMCID: PMC7816077 DOI: 10.1016/j.xplc.2020.100139] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 12/12/2020] [Accepted: 12/25/2020] [Indexed: 05/06/2023]
Abstract
In boreal forests, autumn frost tolerance in seedlings is a critical fitness component because it determines survival rates during regeneration. To understand the forces that drive local adaptation in this trait, we conducted freezing tests in a common garden setting for 54 Pinus sylvestris (Scots pine) populations (>5000 seedlings) collected across Scandinavia into western Russia, and genotyped 24 of these populations (>900 seedlings) at >10 000 SNPs. Variation in cold hardiness among populations, as measured by QST , was above 80% and followed a distinct cline along latitude and longitude, demonstrating significant adaptation to climate at origin. In contrast, the genetic differentiation was very weak (mean FST 0.37%). Despite even allele frequency distribution in the vast majority of SNPs among all populations, a few rare alleles appeared at very high or at fixation in marginal populations restricted to northwestern Fennoscandia. Genotype-environment associations showed that climate variables explained 2.9% of the genetic differentiation, while genotype-phenotype associations revealed a high marker-estimated heritability of frost hardiness of 0.56, but identified no major loci. Very extensive gene flow, strong local adaptation, and signals of complex demographic history across markers are interesting topics of forthcoming studies on this species to better clarify signatures of selection and demography.
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Affiliation(s)
- David Hall
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, Sweden
| | - Jenny Olsson
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, Sweden
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, Sweden
- Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Johan Kroon
- The Forestry Research Institute of Sweden (Skogforsk), Uppsala Sweden
| | | | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, Sweden
- Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Corresponding author
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12
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Wang X, Bernhardsson C, Ingvarsson PK. Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies). Genome Biol Evol 2020; 12:3803-3817. [PMID: 31958121 PMCID: PMC7046165 DOI: 10.1093/gbe/evaa005] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 12/13/2022] Open
Abstract
Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.
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Affiliation(s)
- Xi Wang
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Sweden.,Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Carolina Bernhardsson
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Sweden.,Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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13
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Genomics of Clinal Local Adaptation in Pinus sylvestris Under Continuous Environmental and Spatial Genetic Setting. G3-GENES GENOMES GENETICS 2020; 10:2683-2696. [PMID: 32546502 PMCID: PMC7407466 DOI: 10.1534/g3.120.401285] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic basis often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we identified several loci contributing to local adaptation, but only few with large allele frequency changes across latitude. We also discovered a very large (ca. 300 Mbp) putative inversion potentially under selection, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out the need for more attention toward multi-locus analysis of polygenic adaptation.
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14
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Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species. PLoS One 2020; 15:e0232201. [PMID: 32520936 PMCID: PMC7286500 DOI: 10.1371/journal.pone.0232201] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/08/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The presupposition of genomic selection (GS) is that predictive accuracies should be based on population-wide linkage disequilibrium (LD). However, in species with large, highly complex genomes the limitation of marker density may preclude the ability to resolve LD accurately enough for GS. Here we investigate such an effect in two conifer species with ~ 20 Gbp genomes, Douglas-fir (Pseudotsuga menziesii Mirb. (Franco)) and Interior spruce (Picea glauca (Moench) Voss x Picea engelmannii Parry ex Engelm.). Random sampling of markers was performed to obtain SNP sets with totals in the range of 200-50,000, this was replicated 10 times. Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) was deployed as the GS method to test these SNP sets, and 10-fold cross-validation was performed on 1,321 Douglas-fir trees, representing 37 full-sib F1 families and on 1,126 Interior spruce trees, representing 25 open-pollinated (half-sib) families. Both trials are located on 3 sites in British Columbia, Canada. RESULTS As marker number increased, so did GS predictive accuracy for both conifer species. However, a plateau in the gain of accuracy became apparent around 10,000-15,000 markers for both Douglas-fir and Interior spruce. Despite random marker selection, little variation in predictive accuracy was observed across replications. On average, Douglas-fir prediction accuracies were higher than those of Interior spruce, reflecting the difference between full- and half-sib families for Douglas-fir and Interior spruce populations, respectively, as well as their respective effective population size. CONCLUSIONS Although possibly advantageous within an advanced breeding population, reducing marker density cannot be recommended for carrying out GS in conifers. Significant LD between markers and putative causal variants was not detected using 50,000 SNPS, and GS was enabled only through the tracking of relatedness in the populations studied. Dramatically increasing marker density would enable said markers to better track LD with causal variants in these large, genetically diverse genomes; as well as providing a model that could be used across populations, breeding programs, and traits.
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15
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Hall D, Zhao W, Wennström U, Andersson Gull B, Wang XR. Parentage and relatedness reconstruction in Pinus sylvestris using genotyping-by-sequencing. Heredity (Edinb) 2020; 124:633-646. [PMID: 32123330 PMCID: PMC7171117 DOI: 10.1038/s41437-020-0302-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023] Open
Abstract
Estimating kinship is fundamental for studies of evolution, conservation, and breeding. Genotyping-by-sequencing (GBS) and other restriction based genotyping methods have become widely applied in these applications in non-model organisms. However, sequencing errors, depth, and reproducibility between library preps could potentially hinder accurate genetic inferences. In this study, we tested different sets of parameters in data filtering, different reference populations and eight estimation methods to obtain a robust procedure for relatedness estimation in Scots pine (Pinus sylvestris L.). We used a seed orchard as our study system, where candidate parents are known and pedigree reconstruction can be compared with theoretical expectations. We found that relatedness estimates were lower than expected for all categories of kinship estimated if the proportion of shared SNPs was low. However, estimates reached expected values if loci showing an excess of heterozygotes were removed and genotyping error rates were considered. The genetic variance-covariance matrix (G-matrix) estimation, however, performed poorly in kinship estimation. The reduced relatedness estimates are likely due to false heterozygosity calls. We analyzed the mating structure in the seed orchard and identified a selfing rate of 3% (including crosses between clone mates) and external pollen contamination of 33.6%. Little genetic structure was observed in the sampled Scots pine natural populations, and the degree of inbreeding in the orchard seed crop is comparable to natural stands. We illustrate that under our optimized data processing procedure, relatedness, and genetic composition, including level of pollen contamination within a seed orchard crop, can be established consistently by different estimators.
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Affiliation(s)
- David Hall
- Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå, Sweden
| | - Wei Zhao
- Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå, Sweden.,Advanced Innovation Center for Tree Breeding by Molecular Design; College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | | | | | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå, Sweden.
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16
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Pyhäjärvi T, Kujala ST, Savolainen O. 275 years of forestry meets genomics in Pinus sylvestris. Evol Appl 2020; 13:11-30. [PMID: 31988655 PMCID: PMC6966708 DOI: 10.1111/eva.12809] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/05/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022] Open
Abstract
Pinus sylvestris has a long history of basic and applied research that is relevant for both forestry and evolutionary studies. Its patterns of adaptive variation and role in forest economic and ecological systems have been studied extensively for nearly 275 years, detailed demography for a 100 years and mating system more than 50 years. However, its reference genome sequence is not yet available and genomic studies have been lagging compared to, for example, Pinus taeda and Picea abies, two other economically important conifers. Despite the lack of reference genome, many modern genomic methods are applicable for a more detailed look at its biological characteristics. For example, RNA-seq has revealed a complex transcriptional landscape and targeted DNA sequencing displays an excess of rare variants and geographically homogenously distributed molecular genetic diversity. Current DNA and RNA resources can be used as a reference for gene expression studies, SNP discovery, and further targeted sequencing. In the future, specific consequences of the large genome size, such as functional effects of regulatory open chromatin regions and transposable elements, should be investigated more carefully. For forest breeding and long-term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness estimates. Given the challenges of breeding (long generation time, no easy vegetative propagation) and the economic importance, application of genomic tools has a potential to have a considerable impact. Here, we explore how genomic characteristics of P. sylvestris, such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools.
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Affiliation(s)
- Tanja Pyhäjärvi
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
| | | | - Outi Savolainen
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
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17
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Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris. G3-GENES GENOMES GENETICS 2019; 9:3409-3421. [PMID: 31427456 PMCID: PMC6778806 DOI: 10.1534/g3.119.400357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.
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18
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Acosta JJ, Fahrenkrog AM, Neves LG, Resende MFR, Dervinis C, Davis JM, Holliday JA, Kirst M. Exome Resequencing Reveals Evolutionary History, Genomic Diversity, and Targets of Selection in the Conifers Pinus taeda and Pinus elliottii. Genome Biol Evol 2019; 11:508-520. [PMID: 30689841 PMCID: PMC6385631 DOI: 10.1093/gbe/evz016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2019] [Indexed: 12/22/2022] Open
Abstract
Loblolly pine (Pinus taeda) and slash pine (Pinus elliottii) are ecologically and economically important pine species that dominate many forest ecosystems in the southern United States, but like all conifers, the study of their genetic diversity and demographic history has been hampered by their large genome size. A small number of studies mainly based on candidate-gene sequencing have been reported for P. taeda to date, whereas none are available for P. elliottii. Targeted exome resequencing has recently enabled population genomics studies for conifers, approach used here to assess genomic diversity, signatures of selection, population structure, and demographic history of P. elliottii and P. taeda. Extensive similarities were revealed between these species: both species feature rapid linkage disequilibrium decay and high levels of genetic diversity. Moreover, genome-wide positive correlations for measures of genetic diversity between the species were also observed, likely due to shared structural genomic constraints. Also, positive selection appears to be targeting a common set of genes in both pines. Demographic history differs between both species, with only P. taeda being affected by a dramatic bottleneck during the last glacial period. The ability of P. taeda to recover from a dramatic reduction in population size while still retaining high levels of genetic diversity shows promise for other pines facing environmental stressors associated with climate change, indicating that these too may be able to adapt successfully to new future conditions even after a drastic population size contraction.
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Affiliation(s)
- Juan J Acosta
- School of Forest Resources and Conservation, University of Florida.,University of Florida Genetics Institute, University of Florida.,Camcore, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC
| | - Annette M Fahrenkrog
- School of Forest Resources and Conservation, University of Florida.,Plant Molecular and Cellular Biology Graduate Program, University of Florida
| | - Leandro G Neves
- School of Forest Resources and Conservation, University of Florida.,Plant Molecular and Cellular Biology Graduate Program, University of Florida.,RAPiD Genomics, Gainesville, FL
| | | | | | - John M Davis
- School of Forest Resources and Conservation, University of Florida
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida.,Plant Molecular and Cellular Biology Graduate Program, University of Florida.,University of Florida Genetics Institute, University of Florida
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19
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Wachowiak W, Zaborowska J, Łabiszak B, Perry A, Zucca GM, González-Martínez SC, Cavers S. Molecular signatures of divergence and selection in closely related pine taxa. TREE GENETICS & GENOMES 2018; 14:83. [PMID: 30930708 PMCID: PMC6404648 DOI: 10.1007/s11295-018-1296-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/01/2018] [Accepted: 10/10/2018] [Indexed: 06/09/2023]
Abstract
Efforts to detect loci under selection in plants have mostly focussed on single species. However, assuming that intraspecific divergence may lead to speciation, comparisons of genetic variation within and among recently diverged taxa can help to locate such genes. In this study, coalescent and outlier detection methods were used to assess nucleotide polymorphism and divergence at 79 nuclear gene fragments (1212 SNPs) in 16 populations (153 individuals) of the closely related, but phenotypically and ecologically distinct, pine taxa Pinus mugo, P. uliginosa and P. uncinata across their European distributions. Simultaneously, mitochondrial DNA markers, which are maternally inherited in pines and distributed by seeds at short geographic distance, were used to assess genetic relationships of the focal populations and taxa. The majority of nuclear loci showed homogenous patterns of variation between the taxa due to a high number of shared SNPs and haplotypes, similar levels of polymorphism, and low net divergence. However, against this common genetic background and an overall low population structure within taxa at mitochondrial markers, we identified several genes showing signatures of selection, accompanied by significant intra- and interspecific divergence. Our results indicate that loci involved in species divergence may be involved in intraspecific local adaptation.
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Affiliation(s)
- Witold Wachowiak
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB UK
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Julia Zaborowska
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Bartosz Łabiszak
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Annika Perry
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB UK
| | - Giovanni M. Zucca
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB UK
| | | | - Stephen Cavers
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB UK
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20
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Grivet D, Avia K, Vaattovaara A, Eckert AJ, Neale DB, Savolainen O, González-Martínez SC. High rate of adaptive evolution in two widespread European pines. Mol Ecol 2017; 26:6857-6870. [PMID: 29110402 DOI: 10.1111/mec.14402] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 09/14/2017] [Accepted: 09/25/2017] [Indexed: 12/18/2022]
Abstract
Comparing related organisms with differing ecological requirements and evolutionary histories can shed light on the mechanisms and drivers underlying genetic adaptation. Here, by examining a common set of hundreds of loci, we compare patterns of nucleotide diversity and molecular adaptation of two European conifers (Scots pine and maritime pine) living in contrasted environments and characterized by distinct population genetic structure (low and clinal in Scots pine, high and ecotypic in maritime pine) and demographic histories. We found higher nucleotide diversity in Scots pine than in maritime pine, whereas rates of new adaptive substitutions (ωa ), as estimated from the distribution of fitness effects, were similar across species and among the highest found in plants. Sample size and population genetic structure did not appear to have resulted in significant bias in estimates of ωa . Moreover, population contraction-expansion dynamics for each species did not affect differentially the rate of adaptive substitution in these two pines. Several methodological and biological factors may underlie the unusually high rate of adaptive evolution of Scots pine and maritime pine. By providing two new case studies with contrasting evolutionary histories, we contribute to disentangling the multiple factors potentially affecting adaptive evolution in natural plant populations.
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Affiliation(s)
- Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain.,Sustainable Forest Management Research Institute, INIA - University of Valladolid, Palencia, Spain
| | - Komlan Avia
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland.,Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, Roscoff, France.,UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, Roscoff, France
| | - Aleksia Vaattovaara
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland.,Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, USA
| | - David B Neale
- Department of Plant Sciences, University of California at Davis, Davis, CA, USA
| | - Outi Savolainen
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain.,Sustainable Forest Management Research Institute, INIA - University of Valladolid, Palencia, Spain.,BIOGECO, INRA, Univ. Bordeaux, Cestas, France
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21
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Fahrenkrog AM, Neves LG, Resende MFR, Dervinis C, Davenport R, Barbazuk WB, Kirst M. Population genomics of the eastern cottonwood ( Populus deltoides). Ecol Evol 2017; 7:9426-9440. [PMID: 29187979 PMCID: PMC5696417 DOI: 10.1002/ece3.3466] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/30/2022] Open
Abstract
Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood (Populus deltoides). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms (SNPs). This natural P. deltoides population showed low levels of subpopulation differentiation (FST = 0.022–0.106), high genetic diversity (θW = 0.00100, π = 0.00170), a large effective population size (Ne ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's D), subpopulation differentiation (XTX), and environmental association analyses with eleven climate variables carried out with two different methods (LFMM and BAYENV2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species, Populus trichocarpa, indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in P. deltoides throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change.
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Affiliation(s)
- Annette M Fahrenkrog
- School of Forest Resources and Conservation University of Florida Gainesville FL USA.,Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA
| | - Leandro G Neves
- School of Forest Resources and Conservation University of Florida Gainesville FL USA.,Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA.,Present address: RAPiD Genomics LLC756 2nd Avenue Gainesville FL 32601 USA
| | - Márcio F R Resende
- Horticultural Sciences Department University of Florida Gainesville FL USA
| | - Christopher Dervinis
- School of Forest Resources and Conservation University of Florida Gainesville FL USA
| | - Ruth Davenport
- Biology Department University of Florida Gainesville FL USA
| | - W Brad Barbazuk
- Biology Department University of Florida Gainesville FL USA.,University of Florida Genetics Institute University of Florida Gainesville FL USA
| | - Matias Kirst
- School of Forest Resources and Conservation University of Florida Gainesville FL USA.,University of Florida Genetics Institute University of Florida Gainesville FL USA
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22
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Chanroj V, Rattanawong R, Phumichai T, Tangphatsornruang S, Ukoskit K. Genome-wide association mapping of latex yield and girth in Amazonian accessions of Hevea brasiliensis grown in a suboptimal climate zone. Genomics 2017; 109:475-484. [PMID: 28751185 DOI: 10.1016/j.ygeno.2017.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/07/2017] [Accepted: 07/21/2017] [Indexed: 12/29/2022]
Abstract
Latex yield and growth are the key complex traits in commercial rubber production. The present study is the first to report genome-wide association mapping of latex yield and girth, for 170 Amazonian accessions grown in a suboptimal area characterized by limited rainfall and a lengthy dry season. Targeted sequence enrichment to capture gene transcripts generated 14,155 high quality filtered single nucleotide polymorphisms (SNPs) of which 94.3% resided in coding regions. The rapid decay of linkage disequilibrium over physical and genetic distance found in the accessions was comparable to those previously reported for several outcrossing species. A mixed linear model detected three significant SNPs in three candidate genes involved in plant adaptation to drought stress, individually explaining 12.7-15.7% of the phenotypic variance. The SNPs identified in the study will help to extend understanding, and to support genetic improvement of rubber trees grown in drought-affected regions.
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Affiliation(s)
- Vipavee Chanroj
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand
| | - Ratchanee Rattanawong
- Nong Khai Rubber Research Center, Rubber Research Institute of Thailand, Rattanawapi District, Nong Khai, 43120, Thailand
| | | | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand.
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23
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Nechaeva YS, Julanov AA, Boronnikova SV, Prishnivskaya YV. Nucleotide polymorphisms of candidate genes of adaptive significance in the ural populations of Larix sibirica Ledeb. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417050064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Barthe S, Binelli G, Hérault B, Scotti-Saintagne C, Sabatier D, Scotti I. Tropical rainforests that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana shield. Mol Ecol 2017; 26:1161-1174. [PMID: 27926985 DOI: 10.1111/mec.13949] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 11/29/2022]
Abstract
How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rainfall and temperature changes during and/or immediately after the last glacial maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil records in Neotropical forests prevents a direct reconstruction of such processes. To describe community-level historical trends in forest composition, we turned therefore to inferential methods based on the reconstruction of past demographic changes. In particular, we modelled the history of rainforests in the eastern Guiana Shield over a timescale of several thousand generations, through the application of approximate Bayesian computation and maximum-likelihood methods to diversity data at nuclear and chloroplast loci in eight species or subspecies of rainforest trees. Depending on the species and on the method applied, we detected population contraction, expansion or stability, with a general trend in favour of stability or expansion, with changes presumably having occurred during or after the LGM. These findings suggest that Guiana Shield rainforests have globally persisted, while expanding, through the Quaternary, but that different species have experienced different demographic events, with a trend towards the increase in frequency of light-demanding, disturbance-associated species.
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Affiliation(s)
- Stéphanie Barthe
- UMR EcoFoG ("Ecologie des forêts de Guyane"), UAG, Campus Agronomique, BP 709, 97387, Kourou, French Guiana.,UMR EcoFoG ("Ecologie des forêts de Guyane"), INRA, Campus Agronomique, BP 709, 97387, Kourou, French Guiana
| | - Giorgio Binelli
- DBSV ("Dipartimento di Biotecnologie e Scienze della Vita"), Università degli Studi dell'Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | - Bruno Hérault
- UMR EcoFoG ("Ecologie des forêts de Guyane"), CIRAD, Campus Agronomique, BP 709, 97387, Kourou, French Guiana
| | - Caroline Scotti-Saintagne
- URFM ("Écologie des Forêts Méditerranéennes"), INRA, Domaine Saint_Paul, Site Agroparc, 84914, Avignon, France
| | - Daniel Sabatier
- UMR AMAP ("Botanique et modélisation de l'architecture des plantes et des végétations"), IRD, Boulevard de la Lironde, Parc Scientifique 2, 34398, Montpellier, France
| | - Ivan Scotti
- URFM ("Écologie des Forêts Méditerranéennes"), INRA, Domaine Saint_Paul, Site Agroparc, 84914, Avignon, France
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25
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Lowry DB, Hoban S, Kelley JL, Lotterhos KE, Reed LK, Antolin MF, Storfer A. Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation. Mol Ecol Resour 2016; 17:142-152. [PMID: 27860289 DOI: 10.1111/1755-0998.12635] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/23/2016] [Accepted: 09/02/2016] [Indexed: 12/26/2022]
Abstract
Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site-associated DNA sequencing (RADseq), a popular reduced representation method, has ushered in a new era of genome-scale research for assessing population structure, hybridization, demographic history, phylogeography and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation. To understand what proportion of the genome is missed by RADseq studies, we developed a simple model using different numbers of RAD-tags, genome sizes and extents of linkage disequilibrium (length of haplotype blocks). Under the best-case modelling scenario, we found that RADseq using six- or eight-base pair cutting restriction enzymes would fail to sample many regions of the genome, especially for species with short linkage disequilibrium. We then surveyed recent studies that have used RADseq for genome scans and found that the median density of markers across these studies was 4.08 RAD-tag markers per megabase (one marker per 245 kb). The length of linkage disequilibrium for many species is one to three orders of magnitude less than density of the typical recent RADseq study. Thus, we conclude that genome scans based on RADseq data alone, while useful for studies of neutral genetic variation and genetic population structure, will likely miss many loci under selection in studies of local adaptation.
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Affiliation(s)
- David B Lowry
- Plant Biology Laboratories, Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Sean Hoban
- The Morton Arboretum, Lisle, IL, USA.,National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, TN, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, 430 Nahant Rd., Nahant, MA, 01908, USA
| | - Laura K Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35406, USA
| | - Michael F Antolin
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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26
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Wójkiewicz B, Litkowiec M, Wachowiak W. Contrasting patterns of genetic variation in core and peripheral populations of highly outcrossing and wind pollinated forest tree species. AOB PLANTS 2016; 8:plw054. [PMID: 27497422 PMCID: PMC5018396 DOI: 10.1093/aobpla/plw054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/10/2016] [Indexed: 06/06/2023]
Abstract
Gene flow tends to have a homogenising effect on a species' background genetic variation over large geographical areas. However, it is usually unknown to what extent the genetic structure of populations is influenced by gene exchange between core and peripheral populations that may represent stands of different evolutionary and demographic history. In this study, we looked at the patterns of population differentiation in Scots pine-a highly outcrossing and wind pollinated conifer species that forms large ecosystems of great ecological and economic importance in Europe and Asia. A set of 13 polymorphic nuclear microsatellite loci was analysed to infer the genetic relationships among 24 populations (676 individuals) from Europe and Asia Minor. The study included specimens from the primary continuous range and from isolated, marginal stands that are considered to be autochthonous populations representative of the species' putative refugial areas. Despite their presumably different histories, a similar level of genetic variation and no evidence of a population bottleneck was found across the populations. Differentiation among populations was relatively low (average FST = 0.035); however, the population structure was not homogenous, which was clearly evident from the allelic frequency spectra and Bayesian assignment analysis. Significant differentiation over short geographical distances was observed between isolated populations within the Iberian and Anatolian Peninsulas (Asia Minor), which contrasted with the absence of genetic differentiation observed between distant populations e.g., between central and northern Europe. The analysed populations were assigned to several groups that corresponded to the geographical regions of their occurrence. These results will be useful in genetics studies in Scots pine that aim to link nucleotide and phenotypic variation across the species distribution range and for development of sustainable breeding and management programs.
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Affiliation(s)
- Błażej Wójkiewicz
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, Kórnik 62-035, Poland
| | - Monika Litkowiec
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, Kórnik 62-035, Poland
| | - Witold Wachowiak
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, Kórnik 62-035, Poland Faculty of Biology, Adam Mickiewicz University, Institute of Environmental Biology, Umultowska 89, Poznań 61-614, Poland
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27
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Marí-Mena N, Lopez-Vaamonde C, Naveira H, Auger-Rozenberg MA, Vila M. Phylogeography of the Spanish Moon Moth Graellsia isabellae (Lepidoptera, Saturniidae). BMC Evol Biol 2016; 16:139. [PMID: 27342978 PMCID: PMC4919910 DOI: 10.1186/s12862-016-0708-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 06/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Geographic and demographic factors as well as specialisation to a new host-plant may lead to host-associated differentiation in plant-feeding insects. We explored the phylogeography of a protected moth, Graellsia isabellae, and its two recognised host-plant species (Pinus sylvestris and P. nigra) in order to seek for any concordance useful to disentangle the evolutionary history of this iconic lepidopteran. RESULTS DNA variation in one mitochondrial marker and nine nuclear microsatellite loci revealed a strong phylogeographic pattern across 28 populations of G. isabellae studied in Spain and France comprising six groups mostly distributed along different mountain ranges. Reanalysis of a previously published chloroplast microsatellite dataset revealed a three and two-group structure for Spanish P. sylvestris and P. nigra, respectively. Overall, the population groupings of this protected moth did not match the ones of P. sylvestris and P. nigra. CONCLUSIONS There was no evidence of host-associated differentiation between populations using P. sylvestris and the ones inhabiting P. nigra. The two major mitochondrial clades of G. isabellae likely diverged before the Last Glacial Maximum and geographically separated the species into a "southern" (Central and Southern Iberian clusters) and a "northern" lineage (Eastern Iberian, Pyrenean and French Alpine clusters). The Eastern Iberian System, where this insect uses both host-plants, harboured the highest level of genetic diversity. Such a group independently colonised the West and East parts of the Pyrenees. Our results point to a native origin for the French populations occurring in the Alps, genetically related to the Eastern Iberian and Pyrenean sites. The Central Iberian group derived from Southern Iberian ancestors. Secondary contacts were inferred between the Southern/Central Iberian populations and Eastern Iberian cluster as well as between the two Pyrenean ones. The mito-nuclear discordance observed with regard to the Eastern Iberian cluster is congruent with a secondary contact after the evolution of mito-nuclear incompatibilities in geographically isolated areas.
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Affiliation(s)
- Neus Marí-Mena
- Department of Molecular and Cell Biology, Evolutionary Biology Group (GIBE), Universidade da Coruña, A Fraga 10, E-15008, A Coruña, Spain
- AllGenetics & Biology, SL, Edificio de Servizos Centrais de Investigación, Campus de Elviña, E-15008, A Coruña, Spain
| | - Carlos Lopez-Vaamonde
- INRA, UR633 Zoologie Forestière, F-45075, Orléans, France
- IRBI, UMR 7261, CNRS/Université François-Rabelais de Tours, 37200, Tours, France
| | - Horacio Naveira
- Department of Molecular and Cell Biology, Evolutionary Biology Group (GIBE), Universidade da Coruña, A Fraga 10, E-15008, A Coruña, Spain
| | | | - Marta Vila
- Department of Molecular and Cell Biology, Evolutionary Biology Group (GIBE), Universidade da Coruña, A Fraga 10, E-15008, A Coruña, Spain.
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28
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Yang YX, Wang ML, Liu ZL, Zhu J, Yan MY, Li ZH. Nucleotide polymorphism and phylogeographic history of an endangered conifer species Pinus bungeana. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2015.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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29
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Guerrero J, Gallo-Reynoso JP, Biek R. Mitochondrial DNA diversity, genetic structure, and demographic history of the Neotropical otter (Lontra longicaudis) in Mexico. J Mammal 2015. [DOI: 10.1093/jmammal/gyv124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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30
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Mosaic genetic differentiation along environmental and geographic gradients indicate divergent selection in a white pine species complex. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9785-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Rodríguez-Robles JA, Jezkova T, Fujita MK, Tolson PJ, García MA. Genetic divergence and diversity in the Mona and Virgin Islands Boas, Chilabothrus monensis (Epicrates monensis) (Serpentes: Boidae), West Indian snakes of special conservation concern. Mol Phylogenet Evol 2015; 88:144-53. [PMID: 25837733 DOI: 10.1016/j.ympev.2015.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 02/24/2015] [Accepted: 03/20/2015] [Indexed: 10/23/2022]
Abstract
Habitat fragmentation reduces the extent and connectivity of suitable habitats, and can lead to changes in population genetic structure. Limited gene flow among isolated demes can result in increased genetic divergence among populations, and decreased genetic diversity within demes. We assessed patterns of genetic variation in the Caribbean boa Chilabothrus monensis (Epicrates monensis) using two mitochondrial and seven nuclear markers, and relying on the largest number of specimens of these snakes examined to date. Two disjunct subspecies of C. monensis are recognized: the threatened C. m. monensis, endemic to Mona Island, and the rare and endangered C. m. granti, which occurs on various islands of the Puerto Rican Bank. Mitochondrial and nuclear markers revealed unambiguous genetic differences between the taxa, and coalescent species delimitation methods indicated that these snakes likely are different evolutionary lineages, which we recognize at the species level, C. monensis and C. granti. All examined loci in C. monensis (sensu stricto) are monomorphic, which may indicate a recent bottleneck event. Each population of C. granti exclusively contains private mtDNA haplotypes, but five of the seven nuclear genes assayed are monomorphic, and nucleotide diversity is low in the two remaining markers. The faster pace of evolution of mtDNA possibly reflects the present-day isolation of populations of C. granti, whereas the slower substitution rate of nuDNA may instead mirror the relatively recent episodes of connectivity among the populations facilitated by the lower sea level during the Pleistocene. The small degree of overall genetic variation in C. granti suggests that demes of this snake could be managed as a single unit, a practice that would significantly increase their effective population size.
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Affiliation(s)
- Javier A Rodríguez-Robles
- School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154-4004, USA.
| | - Tereza Jezkova
- School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154-4004, USA.
| | - Matthew K Fujita
- Department Biology, University of Texas at Arlington, 501 S. Nedderman Drive, Arlington, TX 76019, USA.
| | - Peter J Tolson
- Department of Conservation and Research, The Toledo Zoo, P.O. Box 140130, Toledo, OH 43614-0130, USA.
| | - Miguel A García
- Bureau of Fisheries and Wildlife, Department of Natural and Environmental Resources, P.O. Box 366147, San Juan, PR 00936-6147, USA; Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, P.O. Box 23341, Río Piedras, PR 00931-3341, USA.
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32
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Wachowiak W, Trivedi U, Perry A, Cavers S. Comparative transcriptomics of a complex of four European pine species. BMC Genomics 2015; 16:234. [PMID: 25887584 PMCID: PMC4458023 DOI: 10.1186/s12864-015-1401-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/24/2015] [Indexed: 11/25/2022] Open
Abstract
Background Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis of the species, transcriptome sequence was generated for 17 samples collected across the European distribution range using Illumina paired-end sequencing technology. Results De novo transcriptome assembly of a reference sample of P. sylvestris contained 40968 unigenes, of which fewer than 0.5% were identified as putative retrotransposon sequences. Based on gene annotation approaches, 19659 contigs were identified and assigned to unique genes covering a broad range of gene ontology categories. About 80% of the reads from each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms were identified in 22041-24096 of the unigenes providing a set of ~220-262 k SNPs identified for each species. Very similar levels of nucleotide polymorphism were observed across species (π=0.0044-0.0053) and highest pairwise nucleotide divergence (0.006) was found between P. mugo and P. sylvestris at a common set of unigenes. Conclusions The study provides whole transcriptome sequence and a large set of SNPs to advance population and association genetic studies in pines. Our study demonstrates that transcriptome sequencing can be a very useful approach for development of novel genomic resources in species with large and complex genomes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1401-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Witold Wachowiak
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK. .,Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland.
| | - Urmi Trivedi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3JT, UK.
| | - Annika Perry
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK.
| | - Stephen Cavers
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK.
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33
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Wang B, Khalili Mahani M, Ng WL, Kusumi J, Phi HH, Inomata N, Wang XR, Szmidt AE. Extremely low nucleotide polymorphism in Pinus krempfii Lecomte, a unique flat needle pine endemic to Vietnam. Ecol Evol 2014; 4:2228-38. [PMID: 25360263 PMCID: PMC4201436 DOI: 10.1002/ece3.1091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/21/2014] [Accepted: 04/02/2014] [Indexed: 11/07/2022] Open
Abstract
Pinus krempfii Lecomte is a morphologically and ecologically unique pine, endemic to Vietnam. It is regarded as vulnerable species with distribution limited to just two provinces: Khanh Hoa and Lam Dong. Although a few phylogenetic studies have included this species, almost nothing is known about its genetic features. In particular, there are no studies addressing the levels and patterns of genetic variation in natural populations of P. krempfii. In this study, we sampled 57 individuals from six natural populations of P. krempfii and analyzed their sequence variation in ten nuclear gene regions (approximately 9 kb) and 14 mitochondrial (mt) DNA regions (approximately 10 kb). We also analyzed variation at seven chloroplast (cp) microsatellite (SSR) loci. We found very low haplotype and nucleotide diversity at nuclear loci compared with other pine species. Furthermore, all investigated populations were monomorphic across all mitochondrial DNA (mtDNA) regions included in our study, which are polymorphic in other pine species. Population differentiation at nuclear loci was low (5.2%) but significant. However, structure analysis of nuclear loci did not detect genetically differentiated groups of populations. Approximate Bayesian computation (ABC) using nuclear sequence data and mismatch distribution analysis for cpSSR loci suggested recent expansion of the species. The implications of these findings for the management and conservation of P. krempfii genetic resources were discussed.
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Affiliation(s)
- Baosheng Wang
- Department of Ecology and Environmental Science, Umeå University Umeå, Sweden
| | | | - Wei Lun Ng
- Department of Biology, Kyushu University Fukuoka, Japan
| | - Junko Kusumi
- Department of Biology, Kyushu University Fukuoka, Japan
| | - Hai Hong Phi
- Vietnamese Academy of Forest Sciences Hanoi, Vietnam
| | - Nobuyuki Inomata
- Department of Biology, Kyushu University Fukuoka, Japan ; Department of Environmental Science, International College of Arts and Sciences, Fukuoka Women's University Fukuoka, Japan
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University Umeå, Sweden
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34
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Functional multi-locus QTL mapping of temporal trends in Scots pine wood traits. G3-GENES GENOMES GENETICS 2014; 4:2365-79. [PMID: 25305041 PMCID: PMC4267932 DOI: 10.1534/g3.114.014068] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals.
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35
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Zhou Y, Zhang L, Liu J, Wu G, Savolainen O. Climatic adaptation and ecological divergence between two closely related pine species in Southeast China. Mol Ecol 2014; 23:3504-22. [PMID: 24935279 DOI: 10.1111/mec.12830] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 05/09/2014] [Accepted: 05/21/2014] [Indexed: 02/04/2023]
Abstract
Climate is one of the most important drivers for adaptive evolution in forest trees. Climatic selection contributes greatly to local adaptation and intraspecific differentiation, but this kind of selection could also have promoted interspecific divergence through ecological speciation. To test this hypothesis, we examined intra- and interspecific genetic variation at 25 climate-related candidate genes and 12 reference loci in two closely related pine species, Pinus massoniana Lamb. and Pinus hwangshanensis Hisa, using population genetic and landscape genetic approaches. These two species occur in Southeast China but have contrasting ecological preferences in terms of several environmental variables, notably altitude, although hybrids form where their distributions overlap. One or more robust tests detected signals of recent and/or ancient selection at two-thirds (17) of the 25 candidate genes, at varying evolutionary timescales, but only three of the 12 reference loci. The signals of recent selection were species specific, but signals of ancient selection were mostly shared by the two species likely because of the shared evolutionary history. FST outlier analysis identified six SNPs in five climate-related candidate genes under divergent selection between the two species. In addition, a total of 24 candidate SNPs representing nine candidate genes showed significant correlation with altitudinal divergence in the two species based on the covariance matrix of population history derived from reference SNPs. Genetic differentiation between these two species was higher at the candidate genes than at the reference loci. Moreover, analysis using the isolation-with-migration model indicated that gene flow between the species has been more restricted for climate-related candidate genes than the reference loci, in both directions. Taken together, our results suggest that species-specific and divergent climatic selection at the candidate genes might have counteracted interspecific gene flow and played a key role in the ecological divergence of these two closely related pine species.
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Affiliation(s)
- Yongfeng Zhou
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China; Plant Genetics Group, Department of Biology, University of Oulu, 90014, Oulu, Finland
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36
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Mamidi S, Lee RK, Goos JR, McClean PE. Genome-wide association studies identifies seven major regions responsible for iron deficiency chlorosis in soybean (Glycine max). PLoS One 2014; 9:e107469. [PMID: 25225893 PMCID: PMC4166409 DOI: 10.1371/journal.pone.0107469] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/14/2014] [Indexed: 01/08/2023] Open
Abstract
Iron deficiency chlorosis (IDC) is a yield limiting problem in soybean (Glycine max (L.) Merr) production regions with calcareous soils. Genome-wide association study (GWAS) was performed using a high density SNP map to discover significant markers, QTL and candidate genes associated with IDC trait variation. A stepwise regression model included eight markers after considering LD between markers, and identified seven major effect QTL on seven chromosomes. Twelve candidate genes known to be associated with iron metabolism mapped near these QTL supporting the polygenic nature of IDC. A non-synonymous substitution with the highest significance in a major QTL region suggests soybean orthologs of FRE1 on Gm03 is a major gene responsible for trait variation. NAS3, a gene that encodes the enzyme nicotianamine synthase which synthesizes the iron chelator nicotianamine also maps to the same QTL region. Disease resistant genes also map to the major QTL, supporting the hypothesis that pathogens compete with the plant for Fe and increase iron deficiency. The markers and the allelic combinations identified here can be further used for marker assisted selection.
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Affiliation(s)
- Sujan Mamidi
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota, United States of America
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Rian K. Lee
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota, United States of America
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Jay R. Goos
- Department of Soil Science, North Dakota State University, Fargo, North Dakota, United States of America
| | - Phillip E. McClean
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota, United States of America
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
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Zhou L, Bawa R, Holliday JA. Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa). Mol Ecol 2014; 23:2486-99. [PMID: 24750333 DOI: 10.1111/mec.12752] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 12/11/2022]
Abstract
Extant variation in temperate and boreal plant species has been influenced by both demographic histories associated with Pleistocene glacial cycles and adaptation to local climate. We used sequence capture to investigate the role of these neutral and adaptive processes in shaping diversity in black cottonwood (Populus trichocarpa). Nucleotide diversity and Tajima's D were lowest at replacement sites and highest at intergenic sites, while LD showed the opposite pattern. With samples grouped into three populations arrayed latitudinally, effective population size was highest in the north, followed by south and centre, and LD was highest in the south followed by the north and centre, suggesting a possible northern glacial refuge. FST outlier analysis revealed that promoter, 5'-UTR and intronic sites were enriched for outliers compared with coding regions, while no outliers were found among intergenic sites. Codon usage bias was evident, and genes with synonymous outliers had 30% higher average expression compared with genes containing replacement outliers. These results suggest divergent selection related to regulation of gene expression is important to local adaptation in P. trichocarpa. Finally, within-population selective sweeps were much more pronounced in the central population than in putative northern and southern refugia, which may reflect the different demographic histories of the populations and concomitant effects on signatures of genetic hitchhiking from standing variation.
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Affiliation(s)
- L Zhou
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, 304 Cheatham Hall, Blacksburg, VA, 24061, USA
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38
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Patterns of nucleotide diversity at photoperiod related genes in Norway spruce [Picea abies (L.) Karst]. PLoS One 2014; 9:e95306. [PMID: 24810273 PMCID: PMC4014479 DOI: 10.1371/journal.pone.0095306] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 03/26/2014] [Indexed: 11/20/2022] Open
Abstract
The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populations are adapted to local light conditions, but data on the genes underlying this adaptation are more limited. Here we present nucleotide diversity data from 19 genes putatively involved in photoperiodic response in Norway spruce (Picea abies). Based on similarity to model plants the genes were grouped into three categories according to their presumed position in the photoperiod pathway: photoreceptors, circadian clock genes, and downstream targets. An HKA (Hudson, Kreitman and Aquade) test showed a significant excess of diversity at photoreceptor genes, but no departure from neutrality at circadian genes and downstream targets. Departures from neutrality were also tested with Tajima's D and Fay and Wu's H statistics under three demographic scenarios: the standard neutral model, a population expansion model, and a more complex population split model. Only one gene, the circadian clock gene PaPRR3 with a highly positive Tajima's D value, deviates significantly from all tested demographic scenarios. As the PaPRR3 gene harbours multiple non-synonymous variants it appears as an excellent candidate gene for control of photoperiod response in Norway spruce.
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Li L, Abbott RJ, Liu B, Sun Y, Li L, Zou J, Wang X, Miehe G, Liu J. Pliocene intraspecific divergence and Plio-Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai-Tibet Plateau. Mol Ecol 2014; 22:5237-55. [PMID: 24118118 DOI: 10.1111/mec.12466] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 07/04/2013] [Accepted: 07/17/2013] [Indexed: 11/30/2022]
Abstract
A knowledge of intraspecific divergence and range dynamics of dominant forest trees in response to past geological and climate change is of major importance to an understanding of their recent evolution and demography. Such knowledge is informative of how forests were affected by environmental factors in the past and may provide pointers to their response to future environmental change. However, genetic signatures of such historical events are often weak at individual loci due to large effective population sizes and long generation times of forest trees. This problem can be overcome by analysing genetic variation across multiple loci. We used this approach to examine intraspecific divergence and past range dynamics in the conifer Picea likiangensis, a dominant tree of forests occurring in eastern and southern areas of the Qinghai-Tibet Plateau (QTP). We sequenced 13 nuclear loci, two mitochondrial DNA regions and three plastid (chloroplast) DNA regions in 177 individuals sampled from 22 natural populations of this species, and tested the hypothesis that its evolutionary history was markedly affected by Pliocene QTP uplifts and Quaternary climatic oscillations. Consistent with the taxonomic delimitation of the three morphologically divergent varieties examined, all individuals clustered into three genetic groups with intervariety admixture detected in regions of geographical overlap. Divergence between varieties was estimated to have occurred within the Pliocene and ecological niche modelling based on 20 ecological variables suggested that niche differentiation was high. Furthermore, modelling of population-genetic data indicated that two of the varieties (var. rubescens and var. linzhiensis) expanded their population sizes after the largest Quaternary glaciation in the QTP, while expansion of the third variety (var. likiangensis) began prior to this, probably following the Pliocene QTP uplift. These findings point to the importance of geological and climatic changes during the Pliocene and Pleistocene as causes of intraspecific diversification and range shifts of dominant tree species in the QTP biodiversity hot spot region.
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Affiliation(s)
- Long Li
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Science, Lanzhou University, Lanzhou 730000, Gansu, China
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Saxena RK, von Wettberg E, Upadhyaya HD, Sanchez V, Songok S, Saxena K, Kimurto P, Varshney RK. Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs. PLoS One 2014; 9:e88568. [PMID: 24533111 PMCID: PMC3922937 DOI: 10.1371/journal.pone.0088568] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 01/07/2014] [Indexed: 11/22/2022] Open
Abstract
Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively.
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Affiliation(s)
- Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | - Eric von Wettberg
- Department of Biological Sciences, Florida International University, Miami, Florida, United States of America
- Fairchild Tropical Botanic Garden, Kushlan Institute for Tropical Science, Miami, Florida, United States of America
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | - Vanessa Sanchez
- Florida International University, Department of Earth and Environment, Miami, Florida, United States of America
| | - Serah Songok
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
- Egerton University, Egerton, Kenya
| | - Kulbhushan Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
- * E-mail:
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Mamidi S, Lee RK, Goos JR, McClean PE. Genome-wide association studies identifies seven major regions responsible for iron deficiency chlorosis in soybean (Glycine max). PLoS One 2014; 9:e107469. [PMID: 25225893 DOI: 10.1371journal.pone.0107469/journal.pone.0107469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/14/2014] [Indexed: 05/20/2023] Open
Abstract
Iron deficiency chlorosis (IDC) is a yield limiting problem in soybean (Glycine max (L.) Merr) production regions with calcareous soils. Genome-wide association study (GWAS) was performed using a high density SNP map to discover significant markers, QTL and candidate genes associated with IDC trait variation. A stepwise regression model included eight markers after considering LD between markers, and identified seven major effect QTL on seven chromosomes. Twelve candidate genes known to be associated with iron metabolism mapped near these QTL supporting the polygenic nature of IDC. A non-synonymous substitution with the highest significance in a major QTL region suggests soybean orthologs of FRE1 on Gm03 is a major gene responsible for trait variation. NAS3, a gene that encodes the enzyme nicotianamine synthase which synthesizes the iron chelator nicotianamine also maps to the same QTL region. Disease resistant genes also map to the major QTL, supporting the hypothesis that pathogens compete with the plant for Fe and increase iron deficiency. The markers and the allelic combinations identified here can be further used for marker assisted selection.
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Affiliation(s)
- Sujan Mamidi
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota, United States of America; Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Rian K Lee
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota, United States of America; Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Jay R Goos
- Department of Soil Science, North Dakota State University, Fargo, North Dakota, United States of America
| | - Phillip E McClean
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota, United States of America; Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
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Uchiyama K, Iwata H, Moriguchi Y, Ujino-Ihara T, Ueno S, Taguchi Y, Tsubomura M, Mishima K, Iki T, Watanabe A, Futamura N, Shinohara K, Tsumura Y. Demonstration of genome-wide association studies for identifying markers for wood property and male strobili traits in Cryptomeria japonica. PLoS One 2013; 8:e79866. [PMID: 24260312 PMCID: PMC3833940 DOI: 10.1371/journal.pone.0079866] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 09/26/2013] [Indexed: 12/02/2022] Open
Abstract
Genome-wide association studies (GWAS) are an alternative to bi-parental QTL mapping in long-lived perennials. In the present study, we examined the potential of GWAS in conifers using 367 unrelated plus trees of Cryptomeria japonica D. Don, which is the most widely planted and commercially important tree species in Japan, and tried to detect significant associations between wood property traits and quantity of male strobili on the one hand, and 1,032 single nucleotide polymorphisms (SNPs) assigned to 1,032 genes on the other. Association analysis was performed with the mixed linear model taking into account kinship relationships and subpopulation structure. In total, 6 SNPs were found to have significant associations with the variations in phenotype. These SNPs were not associated with the positions of known genes and QTLs that have been reported to date, thus they may identify novel QTLs. These 6 SNPs were all found in sequences showing similarities with known genes, although further analysis is required to dissect the ways in which they affect wood property traits and abundance of male strobili. These presumptive QTL loci provide opportunities for improvement of C. japonica, based on a marker approach. The results suggest that GWAS has potential for use in future breeding programs in C. japonica.
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Affiliation(s)
- Kentaro Uchiyama
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Yoshinari Moriguchi
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Tokuko Ujino-Ihara
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Saneyoshi Ueno
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Yuriko Taguchi
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Miyoko Tsubomura
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Ibaraki, Japan
| | - Kentaro Mishima
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Ibaraki, Japan
| | - Taiichi Iki
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Ibaraki, Japan
| | - Atsushi Watanabe
- Faculty of Agriculture, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Norihiro Futamura
- Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Kenji Shinohara
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Yoshihiko Tsumura
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
- * E-mail:
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Chang Y, Tang R, Sun X, Liang L, Chen J, Huang J, Dou X, Tao R. Genetic analysis of population differentiation and adaptation in Leuciscus waleckii. Genetica 2013; 141:417-29. [PMID: 24154703 DOI: 10.1007/s10709-013-9741-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 10/09/2013] [Indexed: 01/05/2023]
Abstract
Demographic events and natural selection both influence animal phenotypic and genetic variation; exploring the effects of demography and selection on population divergence is of great significance in evolutionary biology. To uncover the causes behind the patterns of genetic differentiation and adaptation among six populations of Leuciscus waleckii from Dali Basin (two populations, alkaline vs. freshwater) and Amur Basin (four populations, freshwater rivers vs. alkaline lake), a set of 21 unlinked polymorphic microsatellite markers and two mitochondrial DNA sequences (Cytb and D-loop) were applied to examine whether populations from different environments or habitats have distinct genetic differentiation and whether alkalinity is the major factor that caused population divergence. Bayesian analysis and principal component analysis as well as haplotype network analysis showed that these populations are primarily divided into two groups, which are congruent with geographic separation but not inconsistent with the habitat environment (alkalinity). Using three different approaches, outlier detection indicated that one locus, HLJYL017, may be under directional selection and involved in local adaptation processes. Overall, this study suggested that demographic events and selection of local environmental conditions including of alkalinity are jointly responsible for population divergence. These findings constitute an important step towards the understanding of the genetic basis of differentiation and adaptation, as well as towards the conservation of L. waleckii.
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Affiliation(s)
- Yumei Chang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Rd 232 Hesong, Daoli District, Harbin, 150070, China
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Semerikov VL, Semerikova SA, Polezhaeva MA. Nucleotide diversity and linkage disequilibrium of adaptive significant genes in Larix (Pinaceae). RUSS J GENET+ 2013. [DOI: 10.1134/s102279541309007x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Semerikov VL, Semerikova SA, Polezhaeva MA, Kosintsev PA, Lascoux M. Southern montane populations did not contribute to the recolonization of West Siberian Plain by Siberian larch (Larix sibirica): a range-wide analysis of cytoplasmic markers. Mol Ecol 2013; 22:4958-71. [DOI: 10.1111/mec.12433] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 06/26/2013] [Accepted: 06/29/2013] [Indexed: 02/06/2023]
Affiliation(s)
- Vladimir L. Semerikov
- Institute of Plant and Animal Ecology; Ural Branch of Russian Academy of Science; 8 Marta Str., 202 620144 Ekaterinburg Russia
| | - Svetlana A. Semerikova
- Institute of Plant and Animal Ecology; Ural Branch of Russian Academy of Science; 8 Marta Str., 202 620144 Ekaterinburg Russia
| | - Maria A. Polezhaeva
- Institute of Plant and Animal Ecology; Ural Branch of Russian Academy of Science; 8 Marta Str., 202 620144 Ekaterinburg Russia
| | - Pavel A. Kosintsev
- Institute of Plant and Animal Ecology; Ural Branch of Russian Academy of Science; 8 Marta Str., 202 620144 Ekaterinburg Russia
| | - Martin Lascoux
- Department of Ecology & Genetics; EBC; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
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Purifying selection after episodes of recurrent adaptive diversification in fungal pathogens. INFECTION GENETICS AND EVOLUTION 2013; 17:123-31. [DOI: 10.1016/j.meegid.2013.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 02/26/2013] [Accepted: 03/07/2013] [Indexed: 11/20/2022]
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Gugerli F, Brandl R, Castagneyrol B, Franc A, Jactel H, Koelewijn HP, Martin F, Peter M, Pritsch K, Schröder H, Smulders MJM, Kremer A, Ziegenhagen B. Community genetics in the time of next-generation molecular technologies. Mol Ecol 2013; 22:3198-207. [DOI: 10.1111/mec.12300] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 01/30/2013] [Accepted: 02/16/2013] [Indexed: 02/03/2023]
Affiliation(s)
- Felix Gugerli
- WSL Swiss Federal Research Institute; 8903 Birmensdorf Switzerland
| | - Roland Brandl
- Fachbereich Biologie; Philipps-Universität Marburg; 35032 Marburg Germany
| | - Bastien Castagneyrol
- UMR1202 Biodiversity, Genes & Communities; INRA Pierroton; 33612 Cestas Cedex France
| | - Alain Franc
- UMR1202 Biodiversity, Genes & Communities; INRA Pierroton; 33612 Cestas Cedex France
| | - Hervé Jactel
- UMR1202 Biodiversity, Genes & Communities; INRA Pierroton; 33612 Cestas Cedex France
| | - Hans-Peter Koelewijn
- ALTERRA Centre for Ecosystem Studies; Wageningen UR; 6700 AA Wageningen The Netherlands
| | - Francis Martin
- UMR “Interactions Arbres/Micro-Organismes”; INRA Nancy; 54280 Champenoux France
| | - Martina Peter
- WSL Swiss Federal Research Institute; 8903 Birmensdorf Switzerland
| | - Karin Pritsch
- Institute of Soil Ecology; Helmholtz Zentrum München; 85764 Neuherberg Germany
| | - Hilke Schröder
- Institute for Forest Genetics; Johann Heinrich von Thuenen-Institute; 22927 Grosshansdorf Germany
| | | | - Antoine Kremer
- UMR1202 Biodiversity, Genes & Communities; INRA Pierroton; 33612 Cestas Cedex France
| | - Birgit Ziegenhagen
- Fachbereich Biologie; Philipps-Universität Marburg; 35032 Marburg Germany
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Alberto FJ, Aitken SN, Alía R, González-Martínez SC, Hänninen H, Kremer A, Lefèvre F, Lenormand T, Yeaman S, Whetten R, Savolainen O. Potential for evolutionary responses to climate change - evidence from tree populations. GLOBAL CHANGE BIOLOGY 2013; 19:1645-61. [PMID: 23505261 PMCID: PMC3664019 DOI: 10.1111/gcb.12181] [Citation(s) in RCA: 373] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/01/2013] [Accepted: 02/03/2013] [Indexed: 05/18/2023]
Abstract
Evolutionary responses are required for tree populations to be able to track climate change. Results of 250 years of common garden experiments show that most forest trees have evolved local adaptation, as evidenced by the adaptive differentiation of populations in quantitative traits, reflecting environmental conditions of population origins. On the basis of the patterns of quantitative variation for 19 adaptation-related traits studied in 59 tree species (mostly temperate and boreal species from the Northern hemisphere), we found that genetic differentiation between populations and clinal variation along environmental gradients were very common (respectively, 90% and 78% of cases). Thus, responding to climate change will likely require that the quantitative traits of populations again match their environments. We examine what kind of information is needed for evaluating the potential to respond, and what information is already available. We review the genetic models related to selection responses, and what is known currently about the genetic basis of the traits. We address special problems to be found at the range margins, and highlight the need for more modeling to understand specific issues at southern and northern margins. We need new common garden experiments for less known species. For extensively studied species, new experiments are needed outside the current ranges. Improving genomic information will allow better prediction of responses. Competitive and other interactions within species and interactions between species deserve more consideration. Despite the long generation times, the strong background in quantitative genetics and growing genomic resources make forest trees useful species for climate change research. The greatest adaptive response is expected when populations are large, have high genetic variability, selection is strong, and there is ecological opportunity for establishment of better adapted genotypes.
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Affiliation(s)
- Florian J Alberto
- Department of Biology and Biocenter Oulu, University of OuluFIN-90014, Oulu, Finland
- UMR1202 Biodiversité Gènes et Communautés, INRAF-33610, Cestas, France
- UMR1202 Biodiversité Gènes et Communautés, Université de BordeauxF-33410, Talence, France
| | - Sally N Aitken
- Department of Forest and Conservation Sciences and Centre for Forest Conservation Genetics, University of British ColumbiaVancouver, BC V6T 1Z4, Canada
| | - Ricardo Alía
- Department of Forest Ecology and Genetics, INIA - Forest Research CentreE-28040, Madrid, Spain
| | | | - Heikki Hänninen
- Department of Biosciences, University of HelsinkiFIN-00014, Helsinki, Finland
| | - Antoine Kremer
- UMR1202 Biodiversité Gènes et Communautés, INRAF-33610, Cestas, France
- UMR1202 Biodiversité Gènes et Communautés, Université de BordeauxF-33410, Talence, France
| | - François Lefèvre
- URFM, UR629 Ecologie des Forêts Méditerranéennes, INRAF-84914, Avignon, France
| | - Thomas Lenormand
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de MontpellierUMR 5175, F-34293, Montpellier, France
| | - Sam Yeaman
- Department of Forest and Conservation Sciences and Centre for Forest Conservation Genetics, University of British ColumbiaVancouver, BC V6T 1Z4, Canada
- Institute of Biology, Université de NeuchâtelCH-2000, Neuchâtel, Switzerland
| | - Ross Whetten
- Department of Forestry & Environmental Resources, NC State UniversityRaleigh, NC, 27695-8008, USA
| | - Outi Savolainen
- Department of Biology and Biocenter Oulu, University of OuluFIN-90014, Oulu, Finland
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Distribution of long-range linkage disequilibrium and Tajima's D values in Scandinavian populations of Norway Spruce (Picea abies). G3-GENES GENOMES GENETICS 2013; 3:795-806. [PMID: 23550126 PMCID: PMC3656727 DOI: 10.1534/g3.112.005462] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The site frequency spectrum of mutations (SFS) and linkage disequilibrium (LD) are the two major sources of information in population genetics studies. In this study we focus on the levels of LD and the SFS and on the effect of sample size on summary statistics in 10 Scandinavian populations of Norway spruce. We found that previous estimates of a low level of LD were highly influenced by both sampling strategy and the fact that data from multiple loci were analyzed jointly. Estimates of LD were in fact heterogeneous across loci and increased within individual populations compared with the estimate from the total data. The variation in levels of LD among populations most likely reflects different demographic histories, although we were unable to detect population structure by using standard approaches. As in previous studies, we also found that the SFS-based test Tajima’s D was highly sensitive to sample size, revealing that care should be taken to draw strong conclusions from this test when sample size is small. In conclusion, the results from this study are in line with recent studies in other conifers that have revealed a more complex and variable pattern of LD than earlier studies suggested and with studies in trees and humans that suggest that Tajima’s D is sensitive to sample size. This has large consequences for the design of future association and population genetic studies in Norway spruce.
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Mamidi S, Rossi M, Moghaddam SM, Annam D, Lee R, Papa R, McClean PE. Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L. Heredity (Edinb) 2013; 110:267-76. [PMID: 23169559 PMCID: PMC3668653 DOI: 10.1038/hdy.2012.82] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 05/31/2012] [Accepted: 06/29/2012] [Indexed: 11/09/2022] Open
Abstract
Wild common bean (Phaseolus vulgaris L.) is distributed throughout the Americas from Mexico to northern Argentina. Within this range, the species is divided into two gene pools (Andean and Middle American) along a latitudinal gradient. The diversity of 24 wild common bean genotypes from throughout the geographic range of the species was described by using sequence data from 13 loci. An isolation-migration model was evaluated using a coalescent analysis to estimate multiple demographic parameters. Using a Bayesian approach, Andean and Middle American subpopulations with high percentage of parentages were observed. Over all loci, the Middle American gene pool was more diverse than the Andean gene pool (π(sil)=0.0089 vs 0.0068). The two subpopulations were strongly genetically differentiated over all loci (F(st)=0.29). It is estimated that the two current wild gene pools diverged from a common ancestor ∼111 000 years ago. Subsequently, each gene pool underwent a bottleneck immediately after divergence and lasted ∼40 000 years. The Middle American bottleneck population size was ∼46% of the ancestral population size, whereas the Andean was 26%. Continuous asymmetric gene flow was detected between the two gene pools with a larger number of migrants entering Middle American gene pool from the Andean gene pool. These results suggest that because of the complex population structure associated with the ancestral divergence, subsequent bottlenecks in each gene pool, gene pool-specific domestication and intense selection within each gene pool by breeders; association mapping would best be practised within each common bean gene pool.
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Affiliation(s)
- S Mamidi
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - M Rossi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - S M Moghaddam
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - D Annam
- Department of Statistics, North Dakota State University, Fargo, ND, USA
| | - R Lee
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - R Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
- Cereal Research Centre, Agricultural Research Council (CRA-CER), Foggia, Italy
| | - P E McClean
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
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