1
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Simon A, Coop G. The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change. Proc Natl Acad Sci U S A 2024; 121:e2312377121. [PMID: 38363870 PMCID: PMC10907250 DOI: 10.1073/pnas.2312377121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/09/2024] [Indexed: 02/18/2024] Open
Abstract
Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 y, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.
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Affiliation(s)
- Alexis Simon
- Center for Population Biology, University of California, Davis, CA95616
- Department of Evolution and Ecology, University of California, Davis, CA95616
| | - Graham Coop
- Center for Population Biology, University of California, Davis, CA95616
- Department of Evolution and Ecology, University of California, Davis, CA95616
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2
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Hipp AL, Lazic D. Ancient tree genomes for old questions. Mol Ecol 2024; 33:e17259. [PMID: 38179684 DOI: 10.1111/mec.17259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/19/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024]
Abstract
Most foundational work on the evolution and migration of plant species relies on genomic data from contemporary samples. Ancient plant samples can give us access to allele sequences and distributions on the landscape dating back to the mid Holocene or earlier (Gugerli et al., 2005). Nuclear DNA from ancient wood, however, has been mostly inaccessible until now. In a From the Cover article in this issue of Molecular Ecology, Wagner et al. (2023) present the first resequenced nuclear genomes from ancient oak wood, including two samples dated to the 15th century and one that dates to more than 3500 years ago. These ancient tree genomes open the possibility for investigating species adaptation, migration, divergence, and hybridisation in the deep past. They pave the way for what we hope will be a new era in the use of paleogenomics to study Holocene tree histories.
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Affiliation(s)
- Andrew L Hipp
- Herbarium and Center for Tree Science, The Morton Arboretum, Lisle, Illinois, USA
- Botany Department, The Field Museum, Chicago, Illinois, USA
| | - Desanka Lazic
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
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3
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Wagner S, Seguin-Orlando A, Leplé JC, Leroy T, Lalanne C, Labadie K, Aury JM, Poirier S, Wincker P, Plomion C, Kremer A, Orlando L. Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood. Mol Ecol 2024; 33:e16859. [PMID: 36748324 PMCID: PMC7615563 DOI: 10.1111/mec.16859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 12/08/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023]
Abstract
Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.
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Affiliation(s)
- Stefanie Wagner
- Plant Genomic Resources Center (CNRGV), INRAE, Castanet-Tolosan, France
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| | - Andaine Seguin-Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| | | | - Thibault Leroy
- IRHS UMR1345, Université d’Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | | | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Patrick Wincker
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | | | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
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4
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Simon A, Coop G. The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.11.548607. [PMID: 37503227 PMCID: PMC10370008 DOI: 10.1101/2023.07.11.548607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 years, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.
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Affiliation(s)
- Alexis Simon
- Center for Population Biology, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
| | - Graham Coop
- Center for Population Biology, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
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5
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Frei T, Espelta JM, Górriz-Mifsud E, Hampe A, Lefèvre F, Martín-Forés I, Winkel G. Can natural forest expansion contribute to Europe's restoration policy agenda? An interdisciplinary assessment. AMBIO 2024; 53:34-45. [PMID: 37775713 PMCID: PMC10692052 DOI: 10.1007/s13280-023-01924-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 10/01/2023]
Abstract
Natural forest expansion (NFE), that is, the establishment of secondary forest on non-forested land through natural succession, has substantially contributed to the widespread expansion of forests in Europe over the last few decades. So far, EU policies have largely neglected the potential of NFE for meeting policy objectives on restoration. Synthesising recent interdisciplinary research, this paper assesses the challenges and opportunities of NFE in view of contributing to European forest and ecosystem restoration. Specifically, we discuss the potential for supporting climate change mitigation and adaptation, biodiversity conservation, and forestry and economic use, summarize the current knowledge about societal perceptions and the policymaking on NFE, and make policy recommendations to better use the potential of NFE. We conclude that NFE has the potential to contribute to the European restoration policy agenda if local contexts and possible trade-offs are properly considered.
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Affiliation(s)
- Theresa Frei
- European Forest Institute, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Josep Maria Espelta
- CREAF, E08193 Bellaterra (Cerdanyola del Vallès), 08193, Barcelona, Catalonia, Spain
| | - Elena Górriz-Mifsud
- Forest Science and Technology Center of Catalonia (CTFC), Ctra. St. Llorenç de Morunys km.2, 25280, Solsona, Spain
| | - Arndt Hampe
- BIOGECO, INRAE, University Bordeaux, Cestas, Bordeaux, France.
| | - François Lefèvre
- INRAE, URFM, 228 route de l'aérodrome AgroParc, 84914, Avignon, France
| | - Irene Martín-Forés
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Georg Winkel
- Wageningen University, 6708 PB, Wageningen, The Netherlands.
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6
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Kapoor B, Jenkins J, Schmutz J, Zhebentyayeva T, Kuelheim C, Coggeshall M, Heim C, Lasky JR, Leites L, Islam-Faridi N, Romero-Severson J, DeLeo VL, Lucas SM, Lazic D, Gailing O, Carlson J, Staton M. A haplotype-resolved chromosome-scale genome for Quercus rubra L. provides insights into the genetics of adaptive traits for red oak species. G3 (BETHESDA, MD.) 2023; 13:jkad209. [PMID: 37708394 PMCID: PMC10627279 DOI: 10.1093/g3journal/jkad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023]
Abstract
Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Quercus lobata and Quercus mongolica revealed high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubra genome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the 9 species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfamily, similar to Quercus robur. Phylogenetic analysis also identified 4 subfamilies of the IGT/LAZY gene family in Q. rubra important for plant structure. Single major QTL regions were identified for vegetative bud break and marcescence, which contain candidate genes for further research, including a putative ortholog of the circadian clock constituent cryptochrome (CRY2) and 8 tandemly duplicated genes for serine protease inhibitors, respectively. Genome-environment associations across natural populations identified candidate abiotic stress tolerance genes and predicted performance in a common garden. This high-quality red oak genome represents an essential resource to the oak genomic community, which will expedite comparative genomics and biological studies in Quercus species.
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Affiliation(s)
- Beant Kapoor
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Tatyana Zhebentyayeva
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40506, USA
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Carsten Kuelheim
- College of Forest Resources and Environmental Science, Michigan Tech University, Houghton, MI 49931, USA
| | - Mark Coggeshall
- College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Chris Heim
- Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Leites
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Nurul Islam-Faridi
- Forest Tree Molecular Cytogenetics Laboratory, USDA-FS, SRS-4160, Department of Ecology & Conservation Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Victoria L DeLeo
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah M Lucas
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Desanka Lazic
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Lower Saxony 37077, Germany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Lower Saxony 37077, Germany
| | - John Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
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7
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Abstract
AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of genetic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural populations. The 2022 Vice Presidential Symposium of the American Society of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse organisms, and addressed distinct aspects of how genetic variation influences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fitness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful introduction to the field.
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8
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Scotti I, Lalagüe H, Oddou-Muratorio S, Scotti-Saintagne C, Ruiz Daniels R, Grivet D, Lefevre F, Cubry P, Fady B, González-Martínez SC, Roig A, Lesur-Kupin I, Bagnoli F, Guerin V, Plomion C, Rozenberg P, Vendramin GG. Common microgeographical selection patterns revealed in four European conifers. Mol Ecol 2023; 32:393-411. [PMID: 36301304 DOI: 10.1111/mec.16750] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/06/2022] [Accepted: 10/11/2022] [Indexed: 01/11/2023]
Abstract
Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computation inferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains within-population diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions.
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Affiliation(s)
| | - Hadrien Lalagüe
- UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université des Antilles, Université de Guyane, Campus Agronomique, Kourou, France
| | | | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | | | | | - Philippe Cubry
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
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9
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Snead AA, Clark RD. The Biological Hierarchy, Time, and Temporal 'Omics in Evolutionary Biology: A Perspective. Integr Comp Biol 2022; 62:1872-1886. [PMID: 36057775 DOI: 10.1093/icb/icac138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 01/05/2023] Open
Abstract
Sequencing data-genomics, transcriptomics, epigenomics, proteomics, and metabolomics-have revolutionized biological research, enabling a more detailed study of processes, ranging from subcellular to evolutionary, that drive biological organization. These processes, collectively, are responsible for generating patterns of phenotypic variation and can operate over dramatically different timescales (milliseconds to billions of years). While researchers often study phenotypic variation at specific levels of biological organization to isolate processes operating at that particular scale, the varying types of sequence data, or 'omics, can also provide complementary inferences to link molecular and phenotypic variation to produce an integrated view of evolutionary biology, ranging from molecular pathways to speciation. We briefly describe how 'omics has been used across biological levels and then demonstrate the utility of integrating different types of sequencing data across multiple biological levels within the same study to better understand biological phenomena. However, single-time-point studies cannot evaluate the temporal dynamics of these biological processes. Therefore, we put forward temporal 'omics as a framework that can better enable researchers to study the temporal dynamics of target processes. Temporal 'omics is not infallible, as the temporal sampling regime directly impacts inferential ability. Thus, we also discuss the role the temporal sampling regime plays in deriving inferences about the environmental conditions driving biological processes and provide examples that demonstrate the impact of the sampling regime on biological inference. Finally, we forecast the future of temporal 'omics by highlighting current methodological advancements that will enable temporal 'omics to be extended across species and timescales. We extend this discussion to using temporal multi-omics to integrate across the biological hierarchy to evaluate and link the temporal dynamics of processes that generate phenotypic variation.
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Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - René D Clark
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
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Tiret M, Olsson L, Grahn T, Karlsson B, Milesi P, Lascoux M, Lundqvist S, García‐Gil MR. Divergent selection predating the Last Glacial Maximum mainly acted on macro-phenotypes in Norway spruce. Evol Appl 2022; 16:163-172. [PMID: 36699125 PMCID: PMC9850012 DOI: 10.1111/eva.13519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/27/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in and postglacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density, and tracheid traits at breast height. Data from 4461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of Q ST vs. F ST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly preadapted, mainly through growth-related traits.
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Affiliation(s)
- Mathieu Tiret
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala UniversityUppsalaSweden,Department of Forest Genetics and Plant PhysiologySLU, Umeå Plant Science Centre (UPSC)UmeåSweden,IGEPP, INRAE, Institut Agro, Université de RennesDomaine de la MotteLe RheuFrance
| | | | | | | | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala UniversityUppsalaSweden
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala UniversityUppsalaSweden
| | | | - Maria Rosario García‐Gil
- Department of Forest Genetics and Plant PhysiologySLU, Umeå Plant Science Centre (UPSC)UmeåSweden
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11
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Li L, Milesi P, Tiret M, Chen J, Sendrowski J, Baison J, Chen Z, Zhou L, Karlsson B, Berlin M, Westin J, Garcia‐Gil MR, Wu HX, Lascoux M. Teasing apart the joint effect of demography and natural selection in the birth of a contact zone. THE NEW PHYTOLOGIST 2022; 236:1976-1987. [PMID: 36093739 PMCID: PMC9828440 DOI: 10.1111/nph.18480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/23/2022] [Indexed: 05/26/2023]
Abstract
Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. During glacial periods species were confined to low-latitude refugia from which they recolonized higher latitudes as the climate improved. This multipronged recolonization led to many lineages that later met and formed large contact zones. We utilize genomic data from 5000 Picea abies trees to test for the presence of natural selection during recolonization and establishment of a contact zone in Scandinavia. Scandinavian P. abies is today made up of a southern genetic cluster originating from the Baltics, and a northern one originating from Northern Russia. The contact zone delineating them closely matches the limit between two major climatic regions. We show that natural selection contributed to its establishment and maintenance. First, an isolation-with-migration model with genome-wide linked selection fits the data better than a purely neutral one. Second, many loci show signatures of selection or are associated with environmental variables. These loci, regrouped in clusters on chromosomes, are often related to phenology. Altogether, our results illustrate how climatic cycles, recolonization and selection can establish strong local adaptation along contact zones and affect the genetic architecture of adaptive traits.
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Affiliation(s)
- Lili Li
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Mathieu Tiret
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Jun Chen
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
- College of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Janek Sendrowski
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - John Baison
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Zhi‐qiang Chen
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Linghua Zhou
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | | | - Mats Berlin
- SkogforskUppsala Science Park751 83UppsalaSweden
| | - Johan Westin
- Unit for Field‐Based Forest ResearchSwedish University of Agricultural SciencesSE‐922 91VindelnSweden
| | - Maria Rosario Garcia‐Gil
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Harry X. Wu
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
- CSIRO National Collection Research AustraliaBlack Mountain LaboratoryCanberraACT2601Australia
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
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12
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Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How. Int J Mol Sci 2022; 23:ijms23179980. [PMID: 36077370 PMCID: PMC9456323 DOI: 10.3390/ijms23179980] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors’ group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.
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