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Bolte CE, Phannareth T, Zavala-Paez M, Sutara BN, Can MF, Fitzpatrick MC, Holliday JA, Keller SR, Hamilton JA. Genomic insights into hybrid zone formation: The role of climate, landscape, and demography in the emergence of a novel hybrid lineage. Mol Ecol 2024; 33:e17430. [PMID: 38867593 DOI: 10.1111/mec.17430] [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: 02/21/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024]
Abstract
Population demographic changes, alongside landscape, geographic and climate heterogeneity, can influence the timing, stability and extent of introgression where species hybridise. Thus, quantifying interactions across diverged lineages, and the relative contributions of interspecific genetic exchange and selection to divergence at the genome-wide level is needed to better understand the drivers of hybrid zone formation and maintenance. We used seven latitudinally arrayed transects to quantify the contributions of climate, geography and landscape features to broad patterns of genetic structure across the hybrid zone of Populus trichocarpa and P. balsamifera and evaluated the demographic context of hybridisation over time. We found genetic structure differed among the seven transects. While ancestry was structured by climate, landscape features influenced gene flow dynamics. Demographic models indicated a secondary contact event may have influenced contemporary hybrid zone formation with the origin of a putative hybrid lineage that inhabits regions with higher aridity than either of the ancestral groups. Phylogenetic relationships based on chloroplast genomes support the origin of this hybrid lineage inferred from demographic models based on the nuclear data. Our results point towards the importance of climate and landscape patterns in structuring the contact zones between P. trichocarpa and P. balsamifera and emphasise the value whole genome sequencing can have to advancing our understanding of how neutral processes influence divergence across space and time.
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Affiliation(s)
- Constance E Bolte
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tommy Phannareth
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia, USA
| | - Michelle Zavala-Paez
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Brianna N Sutara
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Matthew C Fitzpatrick
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, Maryland, USA
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia, USA
| | - Stephen R Keller
- Department of Plant Biology, University of Vermont, Burlington, Vermont, USA
| | - Jill A Hamilton
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
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2
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Tumas H, Ilska JJ, Gérardi S, Laroche J, A’Hara S, Boyle B, Janes M, McLean P, Lopez G, Lee SJ, Cottrell J, Gorjanc G, Bousquet J, Woolliams JA, MacKay JJ. High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers. G3 (BETHESDA, MD.) 2024; 14:jkae020. [PMID: 38366548 PMCID: PMC10989875 DOI: 10.1093/g3journal/jkae020] [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: 12/04/2023] [Accepted: 01/03/2024] [Indexed: 02/18/2024]
Abstract
In species with large and complex genomes such as conifers, dense linkage maps are a useful resource for supporting genome assembly and laying the genomic groundwork at the structural, populational, and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 single nucleotide polymorphism (SNP) markers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-seq and genotyping array SNP data for 528 individuals from 2 full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for P. sitchensis and Picea glauca based on 27,052 markers and 11,609 gene sequences. Altogether, these 2 linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed, herein, open new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.
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Affiliation(s)
- Hayley Tumas
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Joana J Ilska
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Sebastien Gérardi
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC GIV 0A6, Canada
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - Jerome Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - Stuart A’Hara
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - Mateja Janes
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Paul McLean
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Gustavo Lopez
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Steve J Lee
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Joan Cottrell
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Gregor Gorjanc
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC GIV 0A6, Canada
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - John A Woolliams
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - John J MacKay
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
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3
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Firneno TJ, Semenov G, Dopman EB, Taylor SA, Larson EL, Gompert Z. Quantitative Analyses of Coupling in Hybrid Zones. Cold Spring Harb Perspect Biol 2023; 15:a041434. [PMID: 37739809 PMCID: PMC10691479 DOI: 10.1101/cshperspect.a041434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
In hybrid zones, whether barrier loci experience selection mostly independently or as a unit depends on the ratio of selection to recombination as captured by the coupling coefficient. Theory predicts a sharper transition between an uncoupled and coupled system when more loci affect hybrid fitness. However, the extent of coupling in hybrid zones has rarely been quantified. Here, we use simulations to characterize the relationship between the coupling coefficient and variance in clines across genetic loci. We then reanalyze 25 hybrid zone data sets and find that cline variances and estimated coupling coefficients form a smooth continuum from high variance and weak coupling to low variance and strong coupling. Our results are consistent with low rates of hybridization and a strong genome-wide barrier to gene flow when the coupling coefficient is much greater than 1, but also suggest that this boundary might be approached gradually and at a near constant rate over time.
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Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Georgy Semenov
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erik B Dopman
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erica L Larson
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah 84321, USA
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4
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Guo JF, Zhao W, Andersson B, Mao JF, Wang XR. Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau. PLANT COMMUNICATIONS 2023:100574. [PMID: 36906801 PMCID: PMC10363505 DOI: 10.1016/j.xplc.2023.100574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/09/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Most species have clearly defined distribution ranges and ecological niches. The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are, however, less clearly defined. This study investigated the genetic structure and clines in Pinus densata, a pine of hybrid origin on the southeastern Tibetan Plateau, to gain an understanding of the contemporary dynamics of species barriers. We analyzed genetic diversity in a range-wide collection of P. densata and representative populations of its progenitors, Pinus tabuliformis and Pinus yunnanensis, using exome capture sequencing. We detected four distinct genetic groups within P. densata that reflect its migration history and major gene-flow barriers across the landscape. The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories. Interestingly, population sizes rebounded rapidly during interglacial periods, suggesting persistence and resilience of the species during the Quaternary ice age. In the contact zone between P. densata and P. yunnanensis, 3.36% of the analyzed loci (57 849) showed exceptional patterns of introgression, suggesting their potential roles in either adaptive introgression or reproductive isolation. These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation. This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition. Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.
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Affiliation(s)
- Jing-Fang Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration; State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, 90187 Umeå, Sweden
| | - Bea Andersson
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, 90187 Umeå, Sweden
| | - Jian-Feng Mao
- National Engineering Research Center of Tree Breeding and Ecological Restoration; State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, 90187 Umeå, Sweden.
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5
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Wang Y, Jiang Z, Qin A, Wang F, Chang E, Liu Y, Nie W, Tan C, Yuan Y, Dong Y, Huang R, Jia Z, Wang J. Population Structure, Genetic Diversity and Candidate Genes for the Adaptation to Environmental Stress in Picea koraiensis. PLANTS (BASEL, SWITZERLAND) 2023; 12:1266. [PMID: 36986954 PMCID: PMC10055018 DOI: 10.3390/plants12061266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Picea koraiensis is major silvicultural and timber species in northeast China, and its distribution area is an important transition zone for genus spruce migration. The degree of intraspecific differentiation of P. koraiensis is high, but population structure and differentiation mechanisms are not clear. In this study, 523,761 single nucleotide polymorphisms (SNPs) were identified in 113 individuals from 9 populations of P. koraiensis by genotyping-by-sequencing (GBS). Population genomic analysis showed that P. koraiensis was divided into three geoclimatic regions: Great Khingan Mountains climatic region, Lesser Khingan Mountains climatic region, and Changbai Mountain climatic region. Mengkeshan (MKS) population on the northern edge of the distribution area and Wuyiling (WYL) population located in the mining area are two highly differentiated groups. Selective sweep analysis showed that MKS and WYL populations had 645 and 1126 selected genes, respectively. Genes selected in the MKS population were associated with flowering and photomorphogenesis, cellular response to water deficit, and glycerophospholipid metabolism; genes selected in the WYL population were associated with metal ion transport, biosynthesis of macromolecules, and DNA repair. Climatic factors and heavy metal stress drives divergence in MKS and WYL populations, respectively. Our findings provide insights into adaptive divergence mechanisms in Picea and will contribute to molecular breeding studies.
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Affiliation(s)
- Ya Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Zeping Jiang
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Aili Qin
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Fude Wang
- Forestry Research Institute in Heilongjiang Province, Harbin 150081, China
| | - Ermei Chang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yifu Liu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Wen Nie
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Cancan Tan
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Yanchao Yuan
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Yao Dong
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Ruizhi Huang
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Zirui Jia
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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6
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Giles‐Pérez GI, Aguirre‐Planter E, Eguiarte LE, Jaramillo‐Correa JP. Demographic modelling helps track the rapid and recent divergence of a conifer species pair from Central Mexico. Mol Ecol 2022; 31:5074-5088. [PMID: 35951172 PMCID: PMC9804182 DOI: 10.1111/mec.16646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 01/05/2023]
Abstract
Secondary contact of recently diverged species may have several outcomes, ranging from rampant hybridization to reinforced reproductive isolation. In plants, selfing tolerance and disjunct reproductive phenology may lead to reproductive isolation at contact zones. However, they may also evolve under both allopatric or parapatric frameworks and originate from adaptive and/or neutral forces. Inferring the historical demography of diverging taxa is thus a crucial step to identify factors that may have led to putative reproductive isolation. We explored various competing demographypotheses to account for the rapid divergence of a fir species complex (Abies flinckii-A. religiosa) distributed in "sky-islands" across central Mexico (i.e., along the Trans-Mexican Volcanic Belt; TMVB). Despite co-occurring in two independent sympatric regions (west and centre), these taxa rarely interbreed because of disjunct reproductive phenologies. We genotyped 1147 single nucleotide polymorphisms, generated by GBS (genotyping by sequencing), across 23 populations, and compared multiple scenarios based on the geological history of the TMVB. The best-fitting model revealed one of the most rapid and complete speciation cases for a conifer species-pair, dating back to ~1.2 million years ago. Coupled with the lack of support for stepwise colonization, our coalescent inferences point to an early cessation of interspecific gene flow under parapatric speciation; ancestral gene flow during divergence was asymmetrical (mostly from western firs into A. religiosa) and exclusive to the most ancient (i.e., central) contact zone. Factors promoting rapid reproductive isolation should be explored in other slowly evolving species complexes as they may account for the large tropical and subtropical diversity.
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Affiliation(s)
- Gustavo I. Giles‐Pérez
- Programa de Doctorado en Ciencias BiomédicasUniversidad Nacional Autónoma de MéxicoCDMXMexico,Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCDMXMexico
| | - Erika Aguirre‐Planter
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCDMXMexico
| | - Luis E. Eguiarte
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCDMXMexico
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7
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VanWallendael A, Lowry DB, Hamilton JA. One hundred years into the study of ecotypes, new advances are being made through large-scale field experiments in perennial plant systems. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102152. [PMID: 35065527 DOI: 10.1016/j.pbi.2021.102152] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
A hundred years after Turesson first clearly described how locally adaptive variation is distributed within species, plant biologists are making major breakthroughs in our understanding of mechanisms underlying adaptation from local populations to the scale of continents. Although the genetics of local adaptation has typically been studied in smaller reciprocal transplant experiments, it is now being evaluated with whole genomes in large-scale networks of common garden experiments with perennial switchgrass and poplar trees. These studies support the hypothesis that a complex combination of loci, both with and without adaptive trade-offs, underlies local adaptation and that hybridization and adaptive introgression play a key role in the evolution of these species. Future studies incorporating high-throughput phenotyping, gene expression, and modeling will be used to predict responses of these species to climate change.
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Affiliation(s)
- Acer VanWallendael
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA; Program in Ecology, Evolution, and Behaviour, Michigan State University, East Lansing, MI, 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA; Program in Ecology, Evolution, and Behaviour, Michigan State University, East Lansing, MI, 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA.
| | - Jill A Hamilton
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16801, USA
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8
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O'Donnell ST, Fitz-Gibbon ST, Sork VL. Ancient Introgression Between Distantly Related White Oaks (Quercus sect. Quercus) Shows Evidence of Climate-Associated Asymmetric Gene Exchange. J Hered 2021; 112:663-670. [PMID: 34508641 DOI: 10.1093/jhered/esab053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 09/10/2021] [Indexed: 12/14/2022] Open
Abstract
Ancient introgression can be an important source of genetic variation that shapes the evolution and diversification of many taxa. Here, we estimate the timing, direction, and extent of gene flow between two distantly related oak species in the same section (Quercus sect. Quercus). We estimated these demographic events using genotyping by sequencing data, which generated 25 702 single nucleotide polymorphisms for 24 individuals of California scrub oak (Quercus berberidifolia) and 23 individuals of Engelmann oak (Quercus engelmannii). We tested several scenarios involving gene flow between these species using the diffusion approximation-based population genetic inference framework and model-testing approach of the Python package DaDi. We found that the most likely demographic scenario includes a bottleneck in Q. engelmannii that coincides with asymmetric gene flow from Q. berberidifolia into Q. engelmannii. Given that the timing of this gene flow coincides with the advent of a Mediterranean-type climate in the California Floristic Province, we propose that changing precipitation patterns and seasonality may have favored the introgression of climate-associated genes from the endemic into the non-endemic California oak.
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Affiliation(s)
- Scott T O'Donnell
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Sorel T Fitz-Gibbon
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Victoria L Sork
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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9
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Shastry V, Adams PE, Lindtke D, Mandeville EG, Parchman TL, Gompert Z, Buerkle CA. Model-based genotype and ancestry estimation for potential hybrids with mixed-ploidy. Mol Ecol Resour 2021; 21:1434-1451. [PMID: 33482035 DOI: 10.1111/1755-0998.13330] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/11/2020] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
Non-random mating among individuals can lead to spatial clustering of genetically similar individuals and population stratification. This deviation from panmixia is commonly observed in natural populations. Consequently, individuals can have parentage in single populations or involving hybridization between differentiated populations. Accounting for this mixture and structure is important when mapping the genetics of traits and learning about the formative evolutionary processes that shape genetic variation among individuals and populations. Stratified genetic relatedness among individuals is commonly quantified using estimates of ancestry that are derived from a statistical model. Development of these models for polyploid and mixed-ploidy individuals and populations has lagged behind those for diploids. Here, we extend and test a hierarchical Bayesian model, called entropy, which can use low-depth sequence data to estimate genotype and ancestry parameters in autopolyploid and mixed-ploidy individuals (including sex chromosomes and autosomes within individuals). Our analysis of simulated data illustrated the trade-off between sequencing depth and genome coverage and found lower error associated with low-depth sequencing across a larger fraction of the genome than with high-depth sequencing across a smaller fraction of the genome. The model has high accuracy and sensitivity as verified with simulated data and through analysis of admixture among populations of diploid and tetraploid Arabidopsis arenosa.
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Affiliation(s)
| | - Paula E Adams
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Dorothea Lindtke
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | | | | | | | - C Alex Buerkle
- Department of Botany, University of Wyoming, Laramie, WY, USA
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10
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Menon M, Bagley JC, Page GFM, Whipple AV, Schoettle AW, Still CJ, Wehenkel C, Waring KM, Flores-Renteria L, Cushman SA, Eckert AJ. Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants. Commun Biol 2021; 4:160. [PMID: 33547394 PMCID: PMC7864969 DOI: 10.1038/s42003-020-01632-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 11/18/2020] [Indexed: 01/30/2023] Open
Abstract
Extant conifer species may be susceptible to rapid environmental change owing to their long generation times, but could also be resilient due to high levels of standing genetic diversity. Hybridisation between closely related species can increase genetic diversity and generate novel allelic combinations capable of fuelling adaptive evolution. Our study unravelled the genetic architecture of adaptive evolution in a conifer hybrid zone formed between Pinus strobiformis and P. flexilis. Using a multifaceted approach emphasising the spatial and environmental patterns of linkage disequilibrium and ancestry enrichment, we identified recently introgressed and background genetic variants to be driving adaptive evolution along different environmental gradients. Specifically, recently introgressed variants from P. flexilis were favoured along freeze-related environmental gradients, while background variants were favoured along water availability-related gradients. We posit that such mosaics of allelic variants within conifer hybrid zones will confer upon them greater resilience to ongoing and future environmental change and can be a key resource for conservation efforts.
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Affiliation(s)
- Mitra Menon
- grid.27860.3b0000 0004 1936 9684Department of Evolution and Ecology, University of California, Davis, CA USA
| | - Justin C. Bagley
- grid.257992.20000 0001 0019 1845Department of Biology, Jacksonville State University, Jacksonville, AL USA
| | - Gerald F. M. Page
- grid.4391.f0000 0001 2112 1969Forest Ecosystems and Society, Oregon State University, Corvallis, OR USA
| | - Amy V. Whipple
- grid.261120.60000 0004 1936 8040Department of Biological Sciences and Merriam Powel Center for Environmental Research, Northern Arizona University, Flagstaff, AZ USA
| | - Anna W. Schoettle
- grid.497401.f0000 0001 2286 5230Rocky Mountain Research Station, USDA Forest Service, Fort Collins, CO USA
| | - Christopher J. Still
- grid.4391.f0000 0001 2112 1969Forest Ecosystems and Society, Oregon State University, Corvallis, OR USA
| | - Christian Wehenkel
- grid.412198.70000 0000 8724 8383Instituto de Silvicultura e Industria de la Madera, Universidad Juarez del Estado de Durango, Durango, Mexico
| | - Kristen M. Waring
- grid.261120.60000 0004 1936 8040School of Forestry, Northern Arizona University, Flagstaff, AZ USA
| | - Lluvia Flores-Renteria
- grid.263081.e0000 0001 0790 1491Department of Biology, San Diego State University, San Diego, CA USA
| | - Samuel A. Cushman
- grid.472551.00000 0004 0404 3120Rocky Mountain Research Station, USDA Forest Service, Flagstaff, AZ USA
| | - Andrew J. Eckert
- grid.224260.00000 0004 0458 8737Department of Biology, Virginia Commonwealth University, Richmond, VA USA
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11
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Linan AG, Lowry PP, Miller AJ, Schatz GE, Sevathian JC, Edwards CE. RAD-sequencing reveals patterns of diversification and hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees. Mol Ecol 2020; 30:4520-4537. [PMID: 33210759 DOI: 10.1111/mec.15736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 12/31/2022]
Abstract
A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus Diospyros in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene Diospyros species, generated genome-wide single nucleotide polymorphism data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene Diospyros species diverged millions of years ago and are today largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression has occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now coexist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role that introgression may have played in adaptation and diversification of Mascarene Diospyros, and its relevance for conservation.
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Affiliation(s)
- Alexander G Linan
- Department of Biology, Saint Louis University, St. Louis, MO, USA.,Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, USA
| | - Porter P Lowry
- Africa and Madagascar Program, Missouri Botanical Garden, St. Louis, MO, USA.,Institut de Systématique, Évolution et Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, Paris, France
| | - Allison J Miller
- Department of Biology, Saint Louis University, St. Louis, MO, USA.,Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - George E Schatz
- Africa and Madagascar Program, Missouri Botanical Garden, St. Louis, MO, USA
| | - Jean-Claude Sevathian
- Botanist, Sustainability Consultant and Landscape Care and Maintenance Service, Beau Bassin-Rose Hill, Mauritius
| | - Christine E Edwards
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, USA
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12
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Mimura M, Suga M. Ambiguous species boundaries: Hybridization and morphological variation in two closely related Rubus species along altitudinal gradients. Ecol Evol 2020; 10:7476-7486. [PMID: 32760542 PMCID: PMC7391560 DOI: 10.1002/ece3.6473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 11/23/2022] Open
Abstract
Although hybridization frequently occurs among plant species, hybrid zones of divergent lineages formed at species boundaries are less common and may not be apparent in later generations of hybrids with more parental-like phenotypes, as a consequence of backcrossing. To determine the effects of dispersal and selection on species boundaries, we compared clines in leaf traits and molecular hybrid index along two hybrid zones on Yakushima Island, Japan, in which a temperate (Rubus palmatus) and subtropical (Rubus grayanus) species of wild raspberry are found. Leaf sinus depth in the two hybrid zones had narrower clines at 600 m a.s.l. than the molecular hybrid index and common garden tests confirmed that some leaf traits, including leaf sinus depth that is a major trait used in species identification, are genetically divergent between these closely related species. The sharp transition in leaf phenotypic traits compared to molecular markers indicated divergent selection pressure on the hybrid zone structure. We suggest that species boundaries based on neutral molecular data may differ from those based on observed morphological traits.
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Affiliation(s)
- Makiko Mimura
- Department of BiologyGraduate School of Natural Science and TechnologyOkayama UniversityOkayamaJapan
| | - Mihoko Suga
- Graduate School of AgricultureTamagawa UniversityTokyoJapan
- Present address:
Sacred Heart SchoolTokyoJapan
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13
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Reutimann O, Gugerli F, Rellstab C. A species-discriminatory single-nucleotide polymorphism set reveals maintenance of species integrity in hybridizing European white oaks (Quercus spp.) despite high levels of admixture. ANNALS OF BOTANY 2020; 125:663-676. [PMID: 31912148 PMCID: PMC7102958 DOI: 10.1093/aob/mcaa001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/04/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND AIMS Hybridization and introgression play an important role in the evolution and diversification of plants. To assess the degree of past and current hybridization, the level of genetic admixture in populations needs to be investigated. Ongoing hybridization and blurred species separation have made it challenging to assign European white oak taxa based on leaf morphology and/or genetic markers and to assess the level of admixture. Therefore, there is a need for powerful markers that differentiate between taxa. Here, we established a condensed set of single-nucleotide polymorphism (SNP) markers to reliably differentiate between the three most common oak species in temperate European forests (Quercus robur, Q. petraea, Q. pubescens) and to assess the degree of admixture in a large set of selected Swiss populations. METHODS A training set of 194 presumably pure reference samples from Switzerland and Europe was used to assign 633 test individuals with two different approaches (population genetic-based/Bayesian vs. assumption-free/discriminative classifier) using 58 selected SNPs from coding regions. Admixture was calculated at the individual and population level with the Shannon diversity index based on individual assignment probabilities. KEY RESULTS Depending on the approach, 97.5-100 % of training individuals were assigned correctly, and additional analyses showed that the established SNP set could be further reduced while maintaining its discriminatory power. The two assignment approaches showed high overlap (99 %) in assigning training individuals and slightly less overlap in test individuals (84 %). Levels of admixture varied widely among populations. Mixed stands of Q. petraea and Q. pubescens revealed much higher degrees of admixture than mixed stands of the other two taxon pairs, accentuating high levels of gene flow between these two taxa in Switzerland. CONCLUSIONS Our set of SNPs warrants reliable taxon discrimination with great potential for further applications. We show that the three European white oak taxa have largely retained their species integrity in Switzerland despite high levels of admixture.
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Affiliation(s)
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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14
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Ebrahimi A, Lawson SS, McKenna JR, Jacobs DF. Morpho-Physiological and Genomic Evaluation of Juglans Species Reveals Regional Maladaptation to Cold Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:229. [PMID: 32210997 PMCID: PMC7077431 DOI: 10.3389/fpls.2020.00229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/14/2020] [Indexed: 05/02/2023]
Abstract
Climate change may have unpredictable effects on the cold hardiness of woody species planted outside of their range of origin. Extreme undulations in temperatures may exacerbate susceptibility to cold stress, thereby interfering with productivity and ecosystem functioning. Juglans L. and their naturally occurring interspecific F1 hybrids, are distributed natively across many temperate regions, and J. regia has been extensively introduced. Cold hardiness, an environmental and genetic factor yet to be evaluated in many native and introduced Juglans species, may be a limiting factor under future climate change and following species introductions. We evaluated cold hardiness of native North American and Eastern Asian Juglans along with J. regia genotypes using field data from the Midwestern United States (Indiana), controlled freezing tests, and genome sequencing with close assessment of Juglans cold hardy genes. Many Juglans species previously screened for cold-hardiness were genotypes derived from the Midwest, California, and Europe. In 2014, despite general climate adaptation, Midwestern winter temperatures of -30°C killed J. regia originating from California; however, naturalized Midwestern J. regia survived and displayed low damage. Hybridization of J. regia with black walnut (J. nigra) and butternut (J. cinerea) produced F1s displaying greater cold tolerance than pure J. regia. Cold hardiness and growth are variable in Midwestern J. regia compared to native Juglans, East Asian Juglans, and F1 hybrids. Phylogeny analyses revealed that J. cinerea sorted with East Asian species using the nuclear genome but with North American species using the organellar genome. Investigation of selected cold hardy genes revealed that J. regia was distinct from other species and exhibited less genetic diversity than native Juglans species Average whole genome heterozygosity and Tajima's D for cold hardy genes was low within J. regia samples and significantly higher for hybrid as well as J. nigra. We confirmed that molecular and morpho-physiological data were highly correlated and thus can be used effectively to characterize cold hardiness in Juglans species. We conclude that the genetic diversity within local J. regia populations is low and additional germplasm is needed for development of more regionally adapted J. regia varieties.
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Affiliation(s)
- Aziz Ebrahimi
- Hardwood Tree Improvement and Regeneration Center, Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, United States
| | - Shaneka S. Lawson
- USDA Forest Service, Northern Research Station, Hardwood Tree Improvement and Regeneration Center, West Lafayette, IN, United States
| | - James R. McKenna
- USDA Forest Service, Northern Research Station, Hardwood Tree Improvement and Regeneration Center, West Lafayette, IN, United States
| | - Douglass F. Jacobs
- Hardwood Tree Improvement and Regeneration Center, Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, United States
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15
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Forcina G, Guerrini M, Barbanera F. Non-native and hybrid in a changing environment: conservation perspectives for the last Italian red-legged partridge (Alectoris rufa) population with long natural history. ZOOLOGY 2019; 138:125740. [PMID: 31935616 DOI: 10.1016/j.zool.2019.125740] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 11/16/2022]
Abstract
The ever-increasing biotic homogenization - especially when associated with introgressive hybridization - raises concern for the reduction of the spatial component of diversity in wildlife worldwide. Nonetheless, there is a growing attention to the potential conservation value of hybridization in fastening the adaptive evolutionary responses to rapidly changing selective pressures. Under these premises, we investigated the genetic affinity of the red-legged partridge (Alectoris rufa) population inhabiting Elba Island (Italy) in the context of the overall species phylogeography and particularly of the nominate subspecies it is traditionally ascribed to. Although notoriously hybrid with the congeneric A. chukar, this island population is of undisputedly value because of its long natural history and self-sustainability. As such, its adaptive conservation management calls for a comprehensive knowledge including the assessment of its geographic origin. For this purpose, 110 fecal samples were collected across Elba, genotyped at their joint Cytochrome-b and Control Region genes (2,249 characters), and compared with 149 conspecifics from all over the species distribution range. We confirmed a widespread A. chukar mitochondrial DNA introgression in Elba partridges, whereas their expected formal assignment to the nominate subspecies from Italy and France was rejected, since these turned out to be closely related to conspecifics from the Iberian Peninsula. This counterintuitive result found support in a large variety of literary sources and compelling evidences from personal testimonies revealing recent intense management with farm-reared birds of Spanish origin. Although the nativeness of Elba partridges was disproved, we advise local authorities to keep warranting the ongoing conservation efforts - and especially restore the connectivity between the western and eastern island sub-populations - as this resource may still be conceived as the ultimate repository for part of the otherwise extinct Italian A. r. rufa genome. Indeed, the admixture with conspecifics from the Iberian Peninsula does not necessarily mean that the entirety of the native nuclear genome of Elba partridges has been wiped out. Furthermore, these latter represent an interesting case study in conservation biology to investigate the possible role played by introgressive hybridization in the adaptation to recent land use and vegetation cover changes associated with rural abandonment in an insular yet heavily anthropized context.
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Affiliation(s)
- Giovanni Forcina
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Department of Biology, University of Pisa, Via A. Volta 4, 56126 Pisa, Italy
| | - Monica Guerrini
- Department of Biology, University of Pisa, Via A. Volta 4, 56126 Pisa, Italy
| | - Filippo Barbanera
- Department of Biology, University of Pisa, Via A. Volta 4, 56126 Pisa, Italy.
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16
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Shen TT, Ran JH, Wang XQ. Phylogenomics disentangles the evolutionary history of spruces (Picea) in the Qinghai-Tibetan Plateau: Implications for the design of population genetic studies and species delimitation of conifers. Mol Phylogenet Evol 2019; 141:106612. [DOI: 10.1016/j.ympev.2019.106612] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 12/13/2022]
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17
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Kastally C, Trasoletti M, Mardulyn P. Limited gene exchange between two sister species of leaf beetles within a hybrid zone in the Alps. J Evol Biol 2019; 32:1406-1417. [DOI: 10.1111/jeb.13538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 08/02/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Chedly Kastally
- Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium
| | - Marta Trasoletti
- Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium
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18
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Haselhorst MSH, Parchman TL, Buerkle CA. Genetic evidence for species cohesion, substructure and hybrids in spruce. Mol Ecol 2019; 28:2029-2045. [DOI: 10.1111/mec.15056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 12/18/2022]
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19
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Azaiez A, Pavy N, Gérardi S, Laroche J, Boyle B, Gagnon F, Mottet MJ, Beaulieu J, Bousquet J. A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies). BMC Genomics 2018; 19:942. [PMID: 30558528 PMCID: PMC6296092 DOI: 10.1186/s12864-018-5247-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species. RESULTS Targeted sequencing was achieved by capturing P. abies exome with probes previously designed from the sequenced transcriptome of white spruce (Picea glauca (Moench) Voss). Capture efficiency was high (74.5%) given a high level of exome conservation between the two species. Using stringent criteria, we delimited a set of 61,771 high-confidence SNPs across 13,543 genes. To validate SNPs, a high-throughput genotyping array was developed for a subset of 5571 predicted SNPs representing as many different gene loci, and was used to genotype over 1000 trees. The estimated true positive rate of the resource was 84.2%, which was comparable with the genotyping success rate obtained for P. abies control SNPs recycled from previous genotyping efforts. We also analyzed SNP abundance across various gene functional categories. Several GO terms and gene families involved in stress response were found over-represented in highly polymorphic genes. CONCLUSION The annotated high-confidence SNP catalog developed herein represents a valuable genomic resource, being representative of over 13 K genes distributed across the P. abies genome. This resource should serve a variety of population genomics and breeding applications in Norway spruce.
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Affiliation(s)
- Aïda Azaiez
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jérôme Laroche
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Brian Boyle
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - France Gagnon
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Marie-Josée Mottet
- Direction de la recherche forestière, Ministère des Forêts, de la Faune et des Parcs du Québec, 2700 Einstein, Québec, Québec G1P 3W8 Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
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20
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Menon M, Bagley JC, Friedline CJ, Whipple AV, Schoettle AW, Leal‐Sàenz A, Wehenkel C, Molina‐Freaner F, Flores‐Rentería L, Gonzalez‐Elizondo MS, Sniezko RA, Cushman SA, Waring KM, Eckert AJ. The role of hybridization during ecological divergence of southwestern white pine (
Pinus strobiformis
) and limber pine (
P. flexilis
). Mol Ecol 2018; 27:1245-1260. [DOI: 10.1111/mec.14505] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Mitra Menon
- Integrative Life Sciences Virginia Commonwealth University Richmond VA USA
- Department of Biology Virginia Commonwealth University Richmond VA USA
| | - Justin C. Bagley
- Department of Biology Virginia Commonwealth University Richmond VA USA
- Departamento de Zoologia Universidade de Brasília Brasília DF Brazil
| | | | - Amy V. Whipple
- Department of Biological Sciences and Merriam Powel Center for Environmental Research Northern Arizona University Flagstaff AZ USA
| | - Anna W. Schoettle
- Rocky Mountain Research Station USDA Forest Service Ft. Collins CO USA
| | - Alejandro Leal‐Sàenz
- Programa Institucional de Doctorado en Ciencias Agropecuarias y Forestales Universidad Juárez del Estado de Durango Durango Mexico
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera Universidad Juarez del Estado de Durango Durango Mexico
| | - Francisco Molina‐Freaner
- Institutos de Geologia y Ecologia Universidad Nacional Autónoma de Mexico, Estación Regional del Noroeste Hermosillo Sonora Mexico
| | | | | | | | - Samuel A. Cushman
- Rocky Mountain Research Station USDA Forest Service Flagstaff AZ USA
| | | | - Andrew J. Eckert
- Department of Biology Virginia Commonwealth University Richmond VA USA
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21
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Gompert Z, Mandeville EG, Buerkle CA. Analysis of Population Genomic Data from Hybrid Zones. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2017. [DOI: 10.1146/annurev-ecolsys-110316-022652] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zachariah Gompert
- Department of Biology and Ecology Center, Utah State University, Logan, Utah 84322
| | - Elizabeth G. Mandeville
- Department of Botany and Wyoming Cooperative Fish and Wildlife Research Unit, University of Wyoming, Laramie, Wyoming 82071
| | - C. Alex Buerkle
- Department of Botany and Program in Ecology, University of Wyoming, Laramie, Wyoming 82071
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22
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Fouet C, Kamdem C, Gamez S, White BJ. Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group. Evol Appl 2017; 10:897-906. [PMID: 29151881 PMCID: PMC5680430 DOI: 10.1111/eva.12492] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/27/2017] [Indexed: 01/16/2023] Open
Abstract
Ongoing speciation in the most important African malaria vectors gives rise to cryptic populations, which differ remarkably in their behavior, ecology, and capacity to vector malaria parasites. Understanding the population structure and the drivers of genetic differentiation among mosquitoes is crucial for effective disease control because heterogeneity within vector species contributes to variability in malaria cases and allow fractions of populations to escape control efforts. To examine population structure and the potential impacts of recent large-scale control interventions, we have investigated the genomic patterns of differentiation in mosquitoes belonging to the Anopheles nili group-a large taxonomic group that diverged ~3 Myr ago. Using 4,343 single nucleotide polymorphisms (SNPs), we detected strong population structure characterized by high-FST values between multiple divergent populations adapted to different habitats within the Central African rainforest. Delineating the cryptic species within the Anopheles nili group is challenging due to incongruence between morphology, ribosomal DNA, and SNP markers consistent with incomplete lineage sorting and/or interspecific gene flow. A very high proportion of loci are fixed (FST = 1) within the genome of putative species, which suggests that ecological and/or reproductive barriers are maintained by strong selection on a substantial number of genes.
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Affiliation(s)
- Caroline Fouet
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Colince Kamdem
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Stephanie Gamez
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Bradley J. White
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
- Center for Disease Vector ResearchInstitute for Integrative Genome BiologyUniversity of CaliforniaRiversideCAUSA
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23
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Scordato ESC, Wilkins MR, Semenov G, Rubtsov AS, Kane NC, Safran RJ. Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry. Mol Ecol 2017; 26:5676-5691. [DOI: 10.1111/mec.14276] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
| | - Matthew R. Wilkins
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - Georgy Semenov
- Department of Ecology & Evolutionary Biology University of Arizona Tucson AZ USA
- Institute of Systematics and Ecology of Animals Novosibirsk Russia
| | | | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
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24
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Hamilton JA, Royauté R, Wright JW, Hodgskiss P, Ledig FT. Genetic conservation and management of the California endemic, Torrey pine ( Pinus torreyana Parry): Implications of genetic rescue in a genetically depauperate species. Ecol Evol 2017; 7:7370-7381. [PMID: 28944023 PMCID: PMC5606898 DOI: 10.1002/ece3.3306] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 06/04/2017] [Accepted: 07/13/2017] [Indexed: 01/15/2023] Open
Abstract
Rare species present a challenge under changing environmental conditions as the genetic consequences of rarity may limit species ability to adapt to environmental change. To evaluate the evolutionary potential of a rare species, we assessed variation in traits important to plant fitness using multigenerational common garden experiments. Torrey pine, Pinus torreyana Parry, is one of the rarest pines in the world, restricted to one mainland and one island population. Morphological differentiation between island and mainland populations suggests adaptation to local environments may have contributed to trait variation. The distribution of phenotypic variances within the common garden suggests distinct population-specific growth trajectories underlay genetic differences, with the island population exhibiting substantially reduced genetic variance for growth relative to the mainland population. Furthermore, F1 hybrids, representing a cross between mainland and island trees, exhibit increased height accumulation and fecundity relative to mainland and island parents. This may indicate genetic rescue via intraspecific hybridization could provide the necessary genetic variation to persist in environments modified as a result of climate change. Long-term common garden experiments, such as these, provide invaluable resources to assess the distribution of genetic variance that may inform conservation strategies to preserve evolutionary potential of rare species, including genetic rescue.
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Affiliation(s)
- Jill A. Hamilton
- Department of Biological SciencesNorth Dakota State UniversityFargoNDUSA
| | - Raphaël Royauté
- Department of Biological SciencesNorth Dakota State UniversityFargoNDUSA
| | | | - Paul Hodgskiss
- Pacific Southwest Research StationUSDA‐Forest ServiceDavisCAUSA
| | - F. Thomas Ledig
- Department of Plant ScienceUniversity of CaliforniaDavisCAUSA
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25
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Mixing It Up: The Role of Hybridization in Forest Management and Conservation under Climate Change. FORESTS 2017. [DOI: 10.3390/f8070237] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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26
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de Lafontaine G, Bousquet J. Asymmetry matters: A genomic assessment of directional biases in gene flow between hybridizing spruces. Ecol Evol 2017; 7:3883-3893. [PMID: 28616185 PMCID: PMC5468134 DOI: 10.1002/ece3.2682] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 11/16/2016] [Accepted: 11/20/2016] [Indexed: 01/08/2023] Open
Abstract
Assessing directional bias in interspecific gene flow might be important in determining the evolutionary trajectory of closely related species pairs. Using a set of 300 single nucleotide polymorphisms (SNPs) having variable propensity to cross species boundary, we evaluated the genomic extent and direction of interspecific gene flow in a progenitor‐derivative spruce species pair (black spruce and red spruce). A higher rate of gene flow was found from black spruce toward red spruce purebreds than vice versa. This asymmetry could reflect the historical gene flow between the two taxa at the time of species inception and during postglacial colonization. A clear asymmetry in introgression was depicted by a greater gene flow between red spruce and hybrids than between black spruce and hybrids. While backcrossing toward red spruce was invariably high across the genome, the actual species boundary is between hybrids and black spruce where gene flow is impeded at those genomic regions impermeable to introgression. Associations between hybrid index and climatic variables (total annual precipitation and mean annual temperature) were tested, as these might indicate a role for exogenous selection in maintaining the species boundary. While an apparent association was found between the hybrid index and precipitation, it collapsed when considered in light of the directional bias in interspecific gene flow. Hence, considering asymmetrical patterns of introgression allowed us to falsify an apparent role for exogenous selection. Although this was not formerly tested here, we suggest that this pattern could result from asymmetrical endogenous selection, a contention that deserves further investigations.
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Affiliation(s)
- Guillaume de Lafontaine
- Canada Research Chair in Forest Genomics Centre for Forest Research and Institute of Systems and Integrative Biology Université Laval Québec QC Canada.,Department of Plant Biology University of Illinois Urbana IL USA
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics Centre for Forest Research and Institute of Systems and Integrative Biology Université Laval Québec QC Canada
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27
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Temporal shifts in the saltmarsh–Nelson’s sparrow hybrid zone revealed by replicated demographic and genetic surveys. CONSERV GENET 2017. [DOI: 10.1007/s10592-016-0920-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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28
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Hamilton JA, El Kayal W, Hart AT, Runcie DE, Arango-Velez A, Cooke JEK. The joint influence of photoperiod and temperature during growth cessation and development of dormancy in white spruce (Picea glauca). TREE PHYSIOLOGY 2016; 36:1432-1448. [PMID: 27449791 DOI: 10.1093/treephys/tpw061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 05/23/2016] [Indexed: 06/06/2023]
Abstract
Timely responses to environmental cues enable the synchronization of phenological life-history transitions essential for the health and survival of north-temperate and boreal tree species. While photoperiodic cues will remain persistent under climate change, temperature cues may vary, contributing to possible asynchrony in signals influencing developmental and physiological transitions essential to forest health. Understanding the relative contribution of photoperiod and temperature as determinants of the transition from active growth to dormancy is important for informing adaptive forest management decisions that consider future climates. Using a combination of photoperiod (long = 20 h or short = 8 h day lengths) and temperature (warm = 22 °C/16 °C and cool = 8 °C/4 °C day/night, respectively) treatments, we used microscopy, physiology and modeling to comprehensively examine hallmark traits of the growth-dormancy transition-including bud formation, growth cessation, cold hardiness and gas exchange-within two provenances of white spruce [Picea glauca (Moench) Voss] spanning a broad latitude in Alberta, Canada. Following exposure to experimental treatments, seedlings were transferred to favorable conditions, and the depth of dormancy was assessed by determining the timing and ability of spruce seedlings to resume growth. Short photoperiods promoted bud development and growth cessation, whereas longer photoperiods extended the growing season through the induction of lammas growth. In contrast, cool temperatures under both photoperiodic conditions delayed bud development. Photoperiod strongly predicted the development of cold hardiness, whereas temperature predicted photosynthetic rates associated with active growth. White spruce was capable of attaining endodormancy, but its release was environmentally determined. Dormancy depth varied substantially across experimental treatments suggesting that environmental cues experienced within one season could affect growth in the following season, which is particularly important for a determinate species such as white spruce. The joint influence of these environmental cues points toward the importance of including local constant photoperiod and shifting temperature cues into predictive models that consider how climate change may affect northern forests.
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Affiliation(s)
- Jill A Hamilton
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
- Department of Biological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Walid El Kayal
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Ashley T Hart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Daniel E Runcie
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Adriana Arango-Velez
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
- Department of Forestry and Horticulture, The Connecticut Agricultural Experiment Station, New Haven, CT 06504, USA
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
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29
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Gompert Z, Buerkle CA. What, if anything, are hybrids: enduring truths and challenges associated with population structure and gene flow. Evol Appl 2016; 9:909-23. [PMID: 27468308 PMCID: PMC4947152 DOI: 10.1111/eva.12380] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/27/2016] [Indexed: 01/17/2023] Open
Abstract
Hybridization is a potent evolutionary process that can affect the origin, maintenance, and loss of biodiversity. Because of its ecological and evolutionary consequences, an understanding of hybridization is important for basic and applied sciences, including conservation biology and agriculture. Herein, we review and discuss ideas that are relevant to the recognition of hybrids and hybridization. We supplement this discussion with simulations. The ideas we present have a long history, particularly in botany, and clarifying them should have practical consequences for managing hybridization and gene flow in plants. One of our primary goals is to illustrate what we can and cannot infer about hybrids and hybridization from molecular data; in other words, we ask when genetic analyses commonly used to study hybridization might mislead us about the history or nature of gene flow and selection. We focus on patterns of variation when hybridization is recent and populations are polymorphic, which are particularly informative for applied issues, such as contemporary hybridization following recent ecological change. We show that hybridization is not a singular process, but instead a collection of related processes with variable outcomes and consequences. Thus, it will often be inappropriate to generalize about the threats or benefits of hybridization from individual studies, and at minimum, it will be important to avoid categorical thinking about what hybridization and hybrids are. We recommend potential sampling and analytical approaches that should help us confront these complexities of hybridization.
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30
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Tsuda Y, Chen J, Stocks M, Källman T, Sønstebø JH, Parducci L, Semerikov V, Sperisen C, Politov D, Ronkainen T, Väliranta M, Vendramin GG, Tollefsrud MM, Lascoux M. The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west? Mol Ecol 2016; 25:2773-89. [PMID: 27087633 DOI: 10.1111/mec.13654] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/23/2016] [Accepted: 04/09/2016] [Indexed: 01/17/2023]
Abstract
Boreal species were repeatedly exposed to ice ages and went through cycles of contraction and expansion while sister species alternated periods of contact and isolation. The resulting genetic structure is consequently complex, and demographic inferences are intrinsically challenging. The range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata) covers most of northern Eurasia; yet their geographical limits and histories remain poorly understood. To delineate the hybrid zone between the two species and reconstruct their joint demographic history, we analysed variation at nuclear SSR and mitochondrial DNA in 102 and 88 populations, respectively. The dynamics of the hybrid zone was analysed with approximate Bayesian computation (ABC) followed by posterior predictive structure plot reconstruction and the presence of barriers across the range tested with estimated effective migration surfaces. To estimate the divergence time between the two species, nuclear sequences from two well-separated populations of each species were analysed with ABC. Two main barriers divide the range of the two species: one corresponds to the hybrid zone between them, and the other separates the southern and northern domains of Norway spruce. The hybrid zone is centred on the Urals, but the genetic impact of Siberian spruce extends further west. The joint distribution of mitochondrial and nuclear variation indicates an introgression of mitochondrial DNA from Norway spruce into Siberian spruce. Overall, our data reveal a demographic history where the two species interacted frequently and where migrants originating from the Urals and the West Siberian Plain recolonized northern Russia and Scandinavia using scattered refugial populations of Norway spruce as stepping stones towards the west.
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Affiliation(s)
- Yoshiaki Tsuda
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.,CNR, Institute of Biosciences and Bioresources, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy
| | - Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Michael Stocks
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Thomas Källman
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | | | - Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Vladimir Semerikov
- Urals Division of the Russian Academy of Sciences, Institute of Plant and Animal Ecology, 8 Marta Str., 202, 620144, Ekaterinburg, Russia
| | - Christoph Sperisen
- Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Zürcherstrasse 111, CH-8903, Birmendsdorf, Switzerland
| | - Dmitry Politov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin str. 3, 119991, Moscow, Russia
| | - Tiina Ronkainen
- Environmental Change Research Unit (ECRU), Department of Environmental Sciences, University of Helsinki, PO Box 65, FI-00014, Helsinki, Finland
| | - Minna Väliranta
- Environmental Change Research Unit (ECRU), Department of Environmental Sciences, University of Helsinki, PO Box 65, FI-00014, Helsinki, Finland
| | - Giovanni Giuseppe Vendramin
- CNR, Institute of Biosciences and Bioresources, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy
| | | | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
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31
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Dai B, Guo H, Huang C, Zhang X, Lin Z. Genomic heterozygosity and hybrid breakdown in cotton (Gossypium): different traits, different effects. BMC Genet 2016; 17:58. [PMID: 27072350 PMCID: PMC4830075 DOI: 10.1186/s12863-016-0366-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/07/2016] [Indexed: 11/25/2022] Open
Abstract
Background Hybrid breakdown has been well documented in various species. Relationships between genomic heterozygosity and traits-fitness have been extensively explored especially in the natural populations. But correlations between genomic heterozygosity and vegetative and reproductive traits in cotton interspecific populations have not been studied. In the current study, two reciprocal F2 populations were developed using Gossypium hirsutum cv. Emian 22 and G. barbadense acc. 3–79 as parents to study hybrid breakdown in cotton. A total of 125 simple sequence repeat (SSR) markers were used to genotype the two F2 interspecific populations. Results To guarantee mutual independence among the genotyped markers, the 125 SSR markers were checked by the linkage disequilibrium analysis. To our knowledge, this is a novel approach to evaluate the individual genomic heterozygosity. After marker checking, 83 common loci were used to assess the extent of genomic heterozygosity. Hybrid breakdown was found extensively in the two interspecific F2 populations particularly on the reproductive traits because of the infertility and the bare seeds. And then, the relationships between the genomic heterozygosity and the vegetative reproductive traits were investigated. The only relationships between hybrid breakdown and heterozygosity were observed in the (Emian22 × 3–79) F2 population for seed index (SI) and boll number per plant (BN). The maternal cytoplasmic environment may have a significant effect on genomic heterozygosity and on correlations between heterozygosity and reproductive traits. Conclusions A novel approach was used to evaluate genomic heterozygosity in cotton; and hybrid breakdown was observed in reproductive traits in cotton. These findings may offer new insight into hybrid breakdown in allotetraploid cotton interspecific hybrids, and may be useful for the development of interspecific hybrids for cotton genetic improvement. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0366-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Baosheng Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Huanle Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Cong Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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32
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Miller JM, Hamilton JA. Interspecies hybridization in the conservation toolbox: response to Kovach et al. (2016). CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:431-433. [PMID: 26918380 DOI: 10.1111/cobi.12677] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 12/30/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Joshua M Miller
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem St. New Haven, CT, 06520, U.S.A
| | - Jill A Hamilton
- Department of Biological Sciences, North Dakota State University, Fargo, ND, 58102, U.S.A
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Walsh J, Shriver WG, Olsen BJ, Kovach AI. Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone. BMC Evol Biol 2016; 16:65. [PMID: 27000833 PMCID: PMC4802838 DOI: 10.1186/s12862-016-0635-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/10/2016] [Indexed: 12/31/2022] Open
Abstract
Background Evolutionary processes, including selection and differential fitness, shape the introgression of genetic material across a hybrid zone, resulting in the exchange of some genes but not others. Differential introgression of molecular or phenotypic markers can thus provide insight into factors contributing to reproductive isolation. We characterized patterns of genetic variation across a hybrid zone between two tidal marsh birds, Saltmarsh (Ammodramus caudacutus) and Nelson’s (A. nelsoni) sparrows (n = 286), and compared patterns of introgression among multiple genetic markers and phenotypic traits. Results Geographic and genomic cline analyses revealed variable patterns of introgression among marker types. Most markers exhibited gradual clines and indicated that introgression exceeds the spatial extent of the previously documented hybrid zone. We found steeper clines, indicating strong selection for loci associated with traits related to tidal marsh adaptations, including for a marker linked to a gene region associated with metabolic functions, including an osmotic regulatory pathway, as well as for a marker related to melanin-based pigmentation, supporting an adaptive role of darker plumage (salt marsh melanism) in tidal marshes. Narrow clines at mitochondrial and sex-linked markers also offer support for Haldane’s rule. We detected patterns of asymmetrical introgression toward A. caudacutus, which may be driven by differences in mating strategy or differences in population density between the two species. Conclusions Our findings offer insight into the dynamics of a hybrid zone traversing a unique environmental gradient and provide evidence for a role of ecological divergence in the maintenance of pure species boundaries despite ongoing gene flow. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0635-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer Walsh
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA. .,Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA.
| | - W Gregory Shriver
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA
| | - Brian J Olsen
- School of Biology and Ecology, University of Maine, Orono, ME, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
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34
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Harrison RG, Larson EL. Heterogeneous genome divergence, differential introgression, and the origin and structure of hybrid zones. Mol Ecol 2016; 25:2454-66. [PMID: 26857437 DOI: 10.1111/mec.13582] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 12/16/2022]
Abstract
Hybrid zones have been promoted as windows on the evolutionary process and as laboratories for studying divergence and speciation. Patterns of divergence between hybridizing species can now be characterized on a genomewide scale, and recent genome scans have focused on the presence of 'islands' of divergence. Patterns of heterogeneous genomic divergence may reflect differential introgression following secondary contact and provide insights into which genome regions contribute to local adaptation, hybrid unfitness and positive assortative mating. However, heterogeneous genome divergence can also arise in the absence of any gene flow, as a result of variation in selection and recombination across the genome. We suggest that to understand hybrid zone origins and dynamics, it is essential to distinguish between genome regions that are divergent between pure parental populations and regions that show restricted introgression where these populations interact in hybrid zones. The latter, more so than the former, reveal the likely genetic architecture of reproductive isolation. Mosaic hybrid zones, because of their complex structure and multiple contacts, are particularly good subjects for distinguishing primary intergradation from secondary contact. Comparisons among independent hybrid zones or transects that involve the 'same' species pair can also help to distinguish between divergence with gene flow and secondary contact. However, data from replicate hybrid zones or replicate transects do not reveal consistent patterns; in a few cases, patterns of introgression are similar across independent transects, but for many taxa, there is distinct lack of concordance, presumably due to variation in environmental context and/or variation in the genetics of the interacting populations.
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Affiliation(s)
- Richard G Harrison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Erica L Larson
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
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35
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Hamilton JA, Miller JM. Adaptive introgression as a resource for management and genetic conservation in a changing climate. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:33-41. [PMID: 26096581 DOI: 10.1111/cobi.12574] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 05/22/2023]
Abstract
Current rates of climate change require organisms to respond through migration, phenotypic plasticity, or genetic changes via adaptation. We focused on questions regarding species' and populations' ability to respond to climate change through adaptation. Specifically, the role adaptive introgression, movement of genetic material from the genome of 1 species into the genome of another through repeated interbreeding, may play in increasing species' ability to respond to a changing climate. Such interspecific gene flow may mediate extinction risk or consequences of limited adaptive potential that result from standing genetic variation and mutation alone, enabling a quicker demographic recovery in response to changing environments. Despite the near dismissal of the potential benefits of hybridization by conservation practitioners, we examined a number of case studies across different taxa that suggest gene flow between sympatric or parapatric sister species or within species that exhibit strong ecotypic differentiation may represent an underutilized management option to conserve evolutionary potential in a changing environment. This will be particularly true where advanced-generation hybrids exhibit adaptive traits outside the parental phenotypic range, a phenomenon known as transgressive segregation. The ideas presented in this essay are meant to provoke discussion regarding how we maintain evolutionary potential, the conservation value of natural hybrid zones, and consideration of their important role in adaptation to climate.
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Affiliation(s)
- Jill A Hamilton
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, U.S.A..
- Department of Biological Sciences, North Dakota State University, Fargo, ND, 58102, U.S.A..
| | - Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
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36
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Walsh J, Rowe RJ, Olsen BJ, Shriver WG, Kovach AI. Genotype-environment associations support a mosaic hybrid zone between two tidal marsh birds. Ecol Evol 2015; 6:279-94. [PMID: 26811792 PMCID: PMC4716509 DOI: 10.1002/ece3.1864] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 01/19/2023] Open
Abstract
Local environmental features can shape hybrid zone dynamics when hybrids are bounded by ecotones or when patchily distributed habitat types lead to a corresponding mosaic of genotypes. We investigated the role of marsh-level characteristics in shaping a hybrid zone between two recently diverged avian taxa - Saltmarsh (Ammodramus caudacutus) and Nelson's (A. nelsoni) sparrows. These species occupy different niches where allopatric, with caudacutus restricted to coastal marshes and nelsoni found in a broader array of wetland and grassland habitats and co-occur in tidal marshes in sympatry. We determined the influence of habitat types on the distribution of pure and hybrid sparrows and assessed the degree of overlap in the ecological niche of each taxon. To do this, we sampled and genotyped 305 sparrows from 34 marshes across the hybrid zone and from adjacent regions. We used linear regression to test for associations between marsh characteristics and the distribution of pure and admixed sparrows. We found a positive correlation between genotype and environmental variables with a patchy distribution of genotypes and habitats across the hybrid zone. Ecological niche models suggest that the hybrid niche was more similar to that of A. nelsoni and habitat suitability was influenced strongly by distance from coastline. Our results support a mosaic model of hybrid zone maintenance, suggesting a role for local environmental features in shaping the distribution and frequency of pure species and hybrids across space.
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Affiliation(s)
- Jennifer Walsh
- Department of Natural Resources and the Environment University of New Hampshire Durham New Hampshire
| | - Rebecca J Rowe
- Department of Natural Resources and the Environment University of New Hampshire Durham New Hampshire
| | - Brian J Olsen
- School of Biology and Ecology University of Maine Orono Maine
| | - W Gregory Shriver
- Department of Entomology and Wildlife Ecology University of Delaware Newark Delaware
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment University of New Hampshire Durham New Hampshire
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37
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de Lafontaine G, Prunier J, Gérardi S, Bousquet J. Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana×P. rubens). Mol Ecol 2015; 24:5229-47. [DOI: 10.1111/mec.13377] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/05/2015] [Accepted: 09/01/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Guillaume de Lafontaine
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Julien Prunier
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
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38
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Taylor SA, Larson EL, Harrison RG. Hybrid zones: windows on climate change. Trends Ecol Evol 2015; 30:398-406. [PMID: 25982153 DOI: 10.1016/j.tree.2015.04.010] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 12/16/2022]
Abstract
Defining the impacts of anthropogenic climate change on biodiversity and species distributions is currently a high priority. Niche models focus primarily on predicted changes in abiotic factors; however, species interactions and adaptive evolution will impact the ability of species to persist in the face of changing climate. Our review focuses on the use of hybrid zones to monitor responses of species to contemporary climate change. Monitoring hybrid zones provides insight into how range boundaries shift in response to climate change by illuminating the combined effects of species interactions and physiological sensitivity. At the same time, the semipermeable nature of species boundaries allows us to document adaptive introgression of alleles associated with response to climate change.
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Affiliation(s)
- Scott A Taylor
- Cornell Lab of Ornithology, Fuller Evolutionary Biology Program, Ithaca, NY 14850, USA; Cornell University, Department of Ecology and Evolutionary Biology, Ithaca, NY 14853, USA.
| | - Erica L Larson
- University of Montana, Division of Biological Sciences, Missoula, MT 59812, USA
| | - Richard G Harrison
- Cornell University, Department of Ecology and Evolutionary Biology, Ithaca, NY 14853, USA
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39
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Stillman JH, Armstrong E. Genomics Are Transforming Our Understanding of Responses to Climate Change. Bioscience 2015. [DOI: 10.1093/biosci/biu219] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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40
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Mimura M, Mishima M, Lascoux M, Yahara T. Range shift and introgression of the rear and leading populations in two ecologically distinct Rubus species. BMC Evol Biol 2014; 2014:209. [PMID: 25344198 PMCID: PMC4221717 DOI: 10.1186/s12862-014-0209-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 09/23/2014] [Indexed: 11/15/2022] Open
Abstract
Background The margins of a species’ range might be located at the margins of a species’ niche, and in such cases, can be highly vulnerable to climate changes. They, however, may also undergo significant evolutionary changes due to drastic population dynamics in response to climate changes, which may increase the chances of isolation and contact among species. Such species interactions induced by climate changes could then regulate or facilitate further responses to climatic changes. We hypothesized that climate changes lead to species contacts and subsequent genetic exchanges due to differences in population dynamics at the species boundaries. We sampled two closely related Rubus species, one temperate (Rubus palmatus) and the other subtropical (R. grayanus) near their joint species boundaries in southern Japan. Coalescent analysis, based on molecular data and ecological niche modelling during the Last Glacial Maximum (LGM), were used to infer past population dynamics. At the contact zones on Yakushima (Yaku Island), where the two species are parapatrically distributed, we tested hybridization along altitudinal gradients. Results Coalescent analysis suggested that the southernmost populations of R. palmatus predated the LGM (~20,000 ya). Conversely, populations at the current northern limit of R. grayanus diverged relatively recently and likely represent young outposts of a northbound range shift. These population dynamics were partly supported by the ensemble forecasting of six different species distribution models. Both past and ongoing hybridizations were detected near and on Yakushima. Backcrosses and advanced-generation hybrids likely generated the clinal hybrid zones along altitudinal gradients on the island where the two species are currently parapatrically distributed. Conclusions Climate oscillations during the Quaternary Period and the response of a species in range shifts likely led to repeated contacts with the gene pools of ecologically distinct relatives. Such species interactions, induced by climate changes, may bring new genetic material to the marginal populations where species tend to experience more extreme climatic conditions at the margins of the species distribution. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0209-9) contains supplementary material, which is available to authorized users.
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Harrison RG, Larson EL. Hybridization, Introgression, and the Nature of Species Boundaries. J Hered 2014; 105 Suppl 1:795-809. [DOI: 10.1093/jhered/esu033] [Citation(s) in RCA: 418] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers. DIVERSITY-BASEL 2014. [DOI: 10.3390/d6020283] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Rieseberg L, Vines T, Gow J, Kane N. Molecular Ecology continues to perform well according to the major publication metrics. Introduction. Mol Ecol 2014; 23:1-15. [PMID: 24372750 DOI: 10.1111/mec.12586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/06/2013] [Indexed: 11/28/2022]
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Kingston SE, Navarro-Sigüenza AG, García-Trejo EA, Vázquez-Miranda H, Fagan WF, Braun MJ. Genetic differentiation and habitat connectivity across towhee hybrid zones in Mexico. Evol Ecol 2013. [DOI: 10.1007/s10682-013-9673-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Hamilton JA, Aitken SN. Genetic and morphological structure of a spruce hybrid (Picea sitchensis x P. glauca) zone along a climatic gradient. AMERICAN JOURNAL OF BOTANY 2013; 100:1651-1662. [PMID: 23935108 DOI: 10.3732/ajb.1200654] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Historic colonization and contemporary evolutionary processes contribute to patterns of genetic variation and differentiation among populations. However, separating the respective influences of these processes remains a challenge, particularly for natural hybrid zones, where standing genetic variation may result from evolutionary processes both preceding and following contact, influencing the evolutionary trajectory of hybrid populations. Where adaptation to novel environments may be facilitated by interspecific hybridization, teasing apart these processes will have practical implications for forest management in changing environments. METHODS We evaluated the neutral genetic architecture of the Picea sitchensis (Sitka spruce) × P. glauca (white spruce) hybrid zone along the Nass and Skeena river valleys in northwestern British Columbia using chloroplast, mitochondrial, and nuclear microsatellite markers, in combination with cone morphological traits. KEY RESULTS Sitka spruce mitotype "capture", evidenced by this species dominating the maternal lineage, is consistent with earlier colonization of the region by Sitka spruce. This "capture" differs from the spatial distribution of chloroplast haplotypes, indicating pollen dispersal and its contribution to geographic structure. Genetic ancestry, based on nuclear markers, was strongly influenced by climate and geography. Highly parallel results for replicate transects along environmental gradients provide support for the bounded hybrid superiority model of hybrid zone maintenance. • CONCLUSIONS This broad-scale analysis of neutral genetic structure indicates the importance of historic and contemporary gene flow, environmental selection, and their interaction in shaping neutral genetic variation within this hybrid zone, informative to seed transfer development and reforestation for future climates.
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Affiliation(s)
- Jill A Hamilton
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia.
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Delmore KE, Brenneman RA, Lei R, Bailey CA, Brelsford A, Louis EE, Johnson SE. Clinal variation in a brown lemur (Eulemur
spp.) hybrid zone: Combining morphological, genetic and climatic data to examine stability. J Evol Biol 2013; 26:1677-90. [DOI: 10.1111/jeb.12178] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 02/15/2013] [Accepted: 03/26/2013] [Indexed: 11/27/2022]
Affiliation(s)
- K. E. Delmore
- Department of Anthropology; University of Calgary; Calgary AB Canada
| | - R. A. Brenneman
- Center for Conservation and Research; Omaha's Henry Doorly Zoo; Omaha NE USA
| | - R. Lei
- Center for Conservation and Research; Omaha's Henry Doorly Zoo; Omaha NE USA
| | - C. A. Bailey
- Center for Conservation and Research; Omaha's Henry Doorly Zoo; Omaha NE USA
| | - A. Brelsford
- Department of Ecology and Evolution; University of Lausanne; Lausanne Switzerland
| | - E. E. Louis
- Center for Conservation and Research; Omaha's Henry Doorly Zoo; Omaha NE USA
| | - S. E. Johnson
- Department of Anthropology; University of Calgary; Calgary AB Canada
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Affiliation(s)
- Luisa Orsini
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Leuven, Belgium.
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Hamilton JA, Lexer C, Aitken SN. Differential introgression reveals candidate genes for selection across a spruce (Picea sitchensis × P. glauca) hybrid zone. THE NEW PHYTOLOGIST 2013; 197:927-938. [PMID: 23228022 DOI: 10.1111/nph.12055] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 10/18/2012] [Indexed: 06/01/2023]
Abstract
Differential patterns of introgression between species across ecological gradients provide a fine-scale depiction of extrinsic and intrinsic factors that contribute to the maintenance of species barriers and adaptation across heterogeneous environments. Introgression was examined for 721 individuals collected from the ecological transition zone spanning maritime to continental climates within the Picea sitchensis-Picea glauca contact zone using a panel of 268 candidate gene single nucleotide polymorphisms. Geographic clines showed a strong spatial relationship between allele frequencies and both distance from the ocean along major rivers and mean annual precipitation, indicating a strong role for environmental selection. Interspecific patterns of differentiation using outlier tests revealed three candidate genes that may be targets of long-term divergent selection between the parental species, although contemporary genomic clines within the hybrid zone suggested neutral patterns of introgression for these genes. This study provides a fine-scale analysis of locus-specific introgression, identifying a suite of candidate loci that may be targets of extrinsic or intrinsic selection, with broad application in understanding local adaptation to climate.
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Affiliation(s)
- Jill A Hamilton
- Centre for Forest Conservation Genetics and Department of Forest Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Christian Lexer
- Department of Biology, Unit of Ecology and Evolution, University of Fribourg, Fribourg, Switzerland
| | - Sally N Aitken
- Centre for Forest Conservation Genetics and Department of Forest Sciences, University of British Columbia, Vancouver, BC, Canada
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