1
|
Zhou Q, Karunarathne P, Andersson-Li L, Chen C, Opgenoorth L, Heer K, Piotti A, Vendramin GG, Nakvasina E, Lascoux M, Milesi P. Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles. Mol Ecol 2024:e17495. [PMID: 39148357 DOI: 10.1111/mec.17495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 07/15/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024]
Abstract
Most tree species underwent cycles of contraction and expansion during the Quaternary. These cycles led to an ancient and complex genetic structure that has since been affected by extensive gene flow and by strong local adaptation. The extent to which hybridization played a role in this multi-layered genetic structure is important to be investigated. To study the effect of hybridization on the joint population genetic structure of two dominant species of the Eurasian boreal forest, Picea abies and P. obovata, we used targeted resequencing and obtained around 480 K nuclear SNPs and 87 chloroplast SNPs in 542 individuals sampled across most of their distribution ranges. Despite extensive gene flow and a clear pattern of Isolation-by-Distance, distinct genetic clusters emerged, indicating the presence of barriers and corridors to migration. Two cryptic refugia located in the large hybrid zone between the two species played a critical role in shaping their current distributions. The two species repeatedly hybridized during the Pleistocene and the direction of introgression depended on latitude. Our study suggests that hybridization helped both species to overcome main shifts in their distribution ranges during glacial cycles and highlights the importance of considering whole species complex instead of separate entities to retrieve complex demographic histories.
Collapse
Affiliation(s)
- Qiujie Zhou
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
| | - Piyal Karunarathne
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
- Institute of Population Genetics, Heinrich-Heine University, Düsseldorf, Universitäts Straße 1, Düsseldorf, Germany
| | - Lili Andersson-Li
- Department of Microbiology, Tumor and Cell Biology, Karolinska L2:02, Solna, Sweden
| | - Chen Chen
- Plant Pathology Group, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Lars Opgenoorth
- Department of Biology, Plant Ecology and Geobotany, Philipps-Universität Marburg, Marburg, Germany
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Katrin Heer
- Faculty of Environment and Natural Resources, Eva Mayr-Stihl Professorship for Forest Genetics, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
| | - Andrea Piotti
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | | | - Elena Nakvasina
- Department of Forestry and Forest Management, Northern (Arctic) Federal University Named after M.V. Lomonosov, Arkhangelsk, Russian Federation
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
| |
Collapse
|
2
|
Ma XG, Ren YB, Sun H. Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China. Cladistics 2024; 40:357-373. [PMID: 38197450 DOI: 10.1111/cla.12570] [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: 04/17/2023] [Revised: 11/27/2023] [Accepted: 12/09/2023] [Indexed: 01/11/2024] Open
Abstract
Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex evolutionary relationships in closely related species and to observe variations in species relationships across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution in southwest China and probably constitute a syngameon. In this study, we mapped resequencing data from different species in this group to the Quercus aquifolioides reference genome to obtain a high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. We reconstructed their phylogenetic relationships, explored the level and pattern of introgression among these species and investigated gene tree variation in the genomes of these species using sliding windows. The same or closely related plastomes were found to be shared extensively among different species within a specific geographical area. Phylogenomic analyses of genome-wide SNP data found that most oaks in the Himalayan-Hengduan subalpine clade showed genetic coherence, but several species were found to be connected by introgression. The gene trees obtained using sliding windows showed that the phylogenetic relationships in the genomes of oaks are highly heterogeneous and therefore highly obscured. Our study found that all the oaks of the Himalayan-Hengduan subalpine clade from southwest China form a syngameon. The obscured phylogenetic relationships observed empirically across the genome are best explained by interspecific gene flow in conjunction with incomplete lineage sorting.
Collapse
Affiliation(s)
- Xiang-Guang Ma
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yue-Bo Ren
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| |
Collapse
|
3
|
Modica A, Lalagüe H, Muratorio S, Scotti I. Rolling down that mountain: microgeographical adaptive divergence during a fast population expansion along a steep environmental gradient in European beech. Heredity (Edinb) 2024; 133:99-112. [PMID: 38890557 PMCID: PMC11286953 DOI: 10.1038/s41437-024-00696-z] [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: 02/07/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
Forest tree populations harbour high genetic diversity thanks to large effective population sizes and strong gene flow, allowing them to diversify through adaptation to local environmental pressures within dispersal distance. Many tree populations also experienced historical demographic fluctuations, including spatial population contraction or expansions at various temporal scales, which may constrain their ability to adapt to environmental variations. Our aim is to investigate how recent contraction and expansion events interfere with local adaptation, by studying patterns of adaptive divergence between closely related stands undergoing environmentally contrasted conditions, and having or not recently expanded. To investigate genome-wide signatures of local adaptation while accounting for demography, we analysed divergence in a European beech population by testing pairwise differentiation among four tree stands at ~35k Single Nucleotide Polymorphisms from ~9k genomic regions. We applied three divergence outlier search methods resting on different assumptions and targeting either single SNPs or contiguous genomic regions, while accounting for the effect of population size variations on genetic divergence. We found 27 signals of selective signatures in 19 target regions. Putatively adaptive divergence involved all stand pairs. We retrieved signals both when comparing old-growth stands and recently colonised areas and when comparing stands within the old-growth area. Therefore, adaptive divergence processes have taken place both over short time spans, under strong environmental contrasts, and over short ecological gradients, in populations that have been stable in the long term. This suggests that standing genetic variation supports local, microgeographic divergence processes, which can maintain genetic diversity at the landscape level.
Collapse
Affiliation(s)
- Andrea Modica
- INRAE, URFM, 228, Route de l'Aérodrome, 84914, Avignon, France
| | - Hadrien Lalagüe
- INRAE, EcoFoG, Campus agronomique, 97310, Kourou, French Guiana
| | - Sylvie Muratorio
- INRAE, EcoBioP, 173, Route de Saint-Jean-de-Luz RD 918, 64310, Saint-Pée-sur-Nivelle, France
| | - Ivan Scotti
- INRAE, URFM, 228, Route de l'Aérodrome, 84914, Avignon, France.
| |
Collapse
|
4
|
Gómez Quijano MJ, Gross BL, Etterson JR. Genetic differentiation across a steep and narrow environmental gradient: Quantitative genetic and genomic insights into Lake Superior populations of Quercus rubra. Mol Ecol 2024:e17483. [PMID: 39056407 DOI: 10.1111/mec.17483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/05/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
Adaptive differentiation of traits and underlying loci can occur at a small geographical scale if natural selection is stronger than countervailing gene flow and drift. We investigated this hypothesis using coupled quantitative genetic and genomic approaches for a wind-pollinated tree species, Quercus rubra, along the steep, narrow gradient of the Lake Superior coast that encompasses four USDA Hardiness Zones within 100 km. For the quantitative genetic component of this study, we examined phenotypic differentiation among eight populations in a common garden, measuring seed mass, germination, height, stem diameter, leaf number, specific leaf area and survival. For the genomic component, we quantified genetic differentiation for 26 populations from the same region using RAD-seq. Because hybridisation with Quercus ellipsoidalis occurs in other parts of the species' range, we included two populations of this congener for comparison. In the common garden study, we found a strong signal of population differentiation that was significantly associated with at least one climate factor for nine of 10 measured traits. In contrast, we found no evidence of genomic differentiation among populations based on FST or any other measures. However, both distance-based and genotype-environment association analyses identified loci showing the signature of selection, with one locus in common across five analyses. This locus was associated with the minimum temperature of the coldest month, a factor that defines the climate zones and was also significant in the common garden analyses. In addition, we documented introgression from Q. ellipsoidalis into Q. rubra, with rates of introgression correlated with the climate gradient. In sum, this study reveals signatures of selection at the quantitative trait and genomic level consistent with climate adaptation, a pattern that is more often documented at a much broader geographical scale, especially in long-lived wind-pollinated species.
Collapse
Affiliation(s)
- María José Gómez Quijano
- Department of Biology, Queen's University, Kingston, Ontario, Canada
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Briana L Gross
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Julie R Etterson
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Zhang F, Long R, Ma Z, Xiao H, Xu X, Liu Z, Wei C, Wang Y, Peng Y, Yang X, Shi X, Cao S, Li M, Xu M, He F, Jiang X, Zhang T, Wang Z, Li X, Yu LX, Kang J, Zhang Z, Zhou Y, Yang Q. Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa. MOLECULAR PLANT 2024; 17:867-883. [PMID: 38678365 DOI: 10.1016/j.molp.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Given the escalating impact of climate change on agriculture and food security, gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation can empower the breeding of climate-resilient crops to face future climate change. Alfalfa (Medicago sativa subsp. sativa), the queen of forages, shows remarkable adaptability across diverse global environments, making it an excellent model for investigating species responses to climate change. In this study, we performed population genomic analyses using genome resequencing data from 702 accessions of 24 Medicago species to unravel alfalfa's climatic adaptation and genetic susceptibility to future climate change. We found that interspecific genetic exchange has contributed to the gene pool of alfalfa, particularly enriching defense and stress-response genes. Intersubspecific introgression between M. sativa subsp. falcata (subsp. falcata) and alfalfa not only aids alfalfa's climatic adaptation but also introduces genetic burden. A total of 1671 genes were associated with climatic adaptation, and 5.7% of them were introgressions from subsp. falcata. By integrating climate-associated variants and climate data, we identified populations that are vulnerable to future climate change, particularly in higher latitudes of the Northern Hemisphere. These findings serve as a clarion call for targeted conservation initiatives and breeding efforts. We also identified pre-adaptive populations that demonstrate heightened resilience to climate fluctuations, illuminating a pathway for future breeding strategies. Collectively, this study enhances our understanding about the local adaptation mechanisms of alfalfa and facilitates the breeding of climate-resilient alfalfa cultivars, contributing to effective agricultural strategies for facing future climate change.
Collapse
Affiliation(s)
- Fan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhiyao Ma
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xiaodong Xu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Chunxue Wei
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yiwen Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xuanwen Yang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xiaoya Shi
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Mingna Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ming Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xueqian Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tiejun Zhang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Zhen Wang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Xianran Li
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Long-Xi Yu
- U.S. Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| |
Collapse
|
7
|
Xu WQ, Ren CQ, Zhang XY, Comes HP, Liu XH, Li YG, Kettle CJ, Jalonen R, Gaisberger H, Ma YZ, Qiu YX. Genome sequences and population genomics reveal climatic adaptation and genomic divergence between two closely related sweetgum species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1372-1387. [PMID: 38343032 DOI: 10.1111/tpj.16675] [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: 10/24/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 05/31/2024]
Abstract
Understanding the genetic basis of population divergence and adaptation is an important goal in population genetics and evolutionary biology. However, the relative roles of demographic history, gene flow, and/or selective regime in driving genomic divergence, climatic adaptation, and speciation in non-model tree species are not yet fully understood. To address this issue, we generated whole-genome resequencing data of Liquidambar formosana and L. acalycina, which are broadly sympatric but altitudinally segregated in the Tertiary relict forests of subtropical China. We integrated genomic and environmental data to investigate the demographic history, genomic divergence, and climatic adaptation of these two sister species. We inferred a scenario of allopatric species divergence during the late Miocene, followed by secondary contact during the Holocene. We identified multiple genomic islands of elevated divergence that mainly evolved through divergence hitchhiking and recombination rate variation, likely fostered by long-term refugial isolation and recent differential introgression in low-recombination genomic regions. We also found some candidate genes with divergent selection signatures potentially involved in climatic adaptation and reproductive isolation. Our results contribute to a better understanding of how late Tertiary/Quaternary climatic change influenced speciation, genomic divergence, climatic adaptation, and introgressive hybridization in East Asia's Tertiary relict flora. In addition, they should facilitate future evolutionary, conservation genomics, and molecular breeding studies in Liquidambar, a genus of important medicinal and ornamental values.
Collapse
Affiliation(s)
- Wu-Qin Xu
- Systematic & Evolutionary Botany and Biodiversity Group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Lab, Hangzhou, Zhejiang, China
| | - Chao-Qian Ren
- Systematic & Evolutionary Botany and Biodiversity Group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Xin-Yi Zhang
- Systematic & Evolutionary Botany and Biodiversity Group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Hans-Peter Comes
- Department of Environment & Biodiversity, Salzburg University, Salzburg, Austria
| | - Xin-Hong Liu
- Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Yin-Gang Li
- Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | | | - Riina Jalonen
- Bioversity International, Regional Office for Asia, Penang, Malaysia
| | | | - Ya-Zhen Ma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Ying-Xiong Qiu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| |
Collapse
|
8
|
Pernicová N, Urban O, Čáslavský J, Kolář T, Rybníček M, Sochová I, Peñuelas J, Bošeľa M, Trnka M. Impacts of elevated CO 2 levels and temperature on photosynthesis and stomatal closure along an altitudinal gradient are counteracted by the rising atmospheric vapor pressure deficit. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171173. [PMID: 38401718 DOI: 10.1016/j.scitotenv.2024.171173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/09/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
The efficiency of water use in plants, a critical ecophysiological parameter closely related to water and carbon cycles, is essential for understanding the interactions between plants and their environment. This study investigates the effects of ongoing climate change and increasing atmospheric CO2 concentration on intrinsic (stomata-based; iWUE) and evaporative (transpiration-based; eWUE) water use efficiency in oak trees along a naturally small altitudinal gradient (130-630 m a.s.l.) of Vihorlat Mountains (eastern Slovakia, Central Europe). To assess changes in iWUE and eWUE values over the past 60 years (1961-2020), stable carbon isotope ratios in latewood cellulose (δ13Ccell) of annually resolved tree rings were analyzed. Such an approach was sensitive enough to distinguish tree responses to growth environments at different altitudes. Our findings revealed a rising trend in iWUE, particularly in oak trees at low and middle altitudes. However, this increase was negligible at high altitudes. Warmer and drier conditions at lower altitudes likely led to significant stomatal closure and enhanced efficiency in photosynthetic CO2 uptake due to rising CO2 concentration. Conversely, the increasing intracellular-to-ambient CO2 ratio (Ci/Ca) at higher altitudes indicated lower efficiency in photosynthetic CO2 uptake. In contrast to iWUE, eWUE showed no increasing trends over the last 60 years. This suggests that the positive impacts of elevated CO2 concentrations and temperature on photosynthesis and stomatal closure are counteracted by the rising atmospheric vapor pressure deficit (VPD). These differences underscore the importance of the correct interpretation of stomata-based and transpiration-based WUEs and highlight the necessity of atmospheric VPD correction when applying tree-ring δ13C-derived WUE at ecosystem and global levels.
Collapse
Affiliation(s)
- Natálie Pernicová
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, CZ-603 00 Brno, Czech Republic; Mendel University in Brno, Department of Agrosystems and Bioclimatology, Faculty of AgriSciences, Zemědělská 1, CZ-613 00 Brno, Czech Republic
| | - Otmar Urban
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, CZ-603 00 Brno, Czech Republic.
| | - Josef Čáslavský
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, CZ-603 00 Brno, Czech Republic
| | - Tomáš Kolář
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, CZ-603 00 Brno, Czech Republic; Mendel University in Brno, Department of Wood Science and Technology, Faculty of Forestry and Wood Technology, Zemědělská 1, CZ-613 00 Brno, Czech Republic
| | - Michal Rybníček
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, CZ-603 00 Brno, Czech Republic; Mendel University in Brno, Department of Wood Science and Technology, Faculty of Forestry and Wood Technology, Zemědělská 1, CZ-613 00 Brno, Czech Republic
| | - Irena Sochová
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, CZ-603 00 Brno, Czech Republic; Mendel University in Brno, Department of Wood Science and Technology, Faculty of Forestry and Wood Technology, Zemědělská 1, CZ-613 00 Brno, Czech Republic
| | - Josep Peñuelas
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, CZ-603 00 Brno, Czech Republic; CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra 08193, Catalonia, Spain; CREAF, Cerdanyola del Vallès 08193, Catalonia, Spain
| | - Michal Bošeľa
- Faculty of Forestry, Technical University in Zvolen, T. G. Masaryka 24, SK-960 01 Zvolen, Slovakia
| | - Miroslav Trnka
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, CZ-603 00 Brno, Czech Republic; Mendel University in Brno, Department of Agrosystems and Bioclimatology, Faculty of AgriSciences, Zemědělská 1, CZ-613 00 Brno, Czech Republic
| |
Collapse
|
9
|
Luo CS, Li TT, Jiang XL, Song Y, Fan TT, Shen XB, Yi R, Ao XP, Xu GB, Deng M. High-quality haplotype-resolved genome assembly for ring-cup oak (Quercus glauca) provides insight into oaks demographic dynamics. Mol Ecol Resour 2024; 24:e13914. [PMID: 38108568 DOI: 10.1111/1755-0998.13914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/15/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
Quercus section Cyclobalanopsis represents a dominant woody lineage in East Asian evergreen broadleaved forests. Regardless of its ecological and economic importance, little is known about the genomes of species in this unique oak lineage. Quercus glauca is one of the most widespread tree species in the section Cyclobalanopsis. In this study, a high-quality haplotype-resolved reference genome was assembled for Q. glauca from PacBio HiFi and Hi-C reads. The genome size, contig N50, and scaffold N50 measured 902.88, 7.60, and 69.28 Mb, respectively, for haplotype1, and 913.28, 7.20, and 71.53 Mb, respectively, for haplotype2. A total of 37,457 and 38,311 protein-coding genes were predicted in haplotype1 and haplotype2, respectively. Homologous chromosomes in the Q. glauca genome had excellent gene pair collinearity. The number of R-genes in Q. glauca was similar to most East Asian oaks but less than oak species from Europe and America. Abundant structural variation in the Q. glauca genome could contribute to environmental stress tolerance in Q. glauca. Sections Cyclobalanopsis and Cerris diverged in the Oligocene, in agreement with fossil records for section Cyclobalanopsis, which document its presence in East Asia since the early Miocene. The demographic dynamics of closely related oak species were largely similar. The high-quality reference genome provided here for the most widespread species in section Cyclobalanopsis will serve as an essential genomic resource for evolutionary studies of key oak lineages while also supporting studies of interspecific introgression, local adaptation, and speciation in oaks.
Collapse
Affiliation(s)
- Chang-Sha Luo
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Tian-Tian Li
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Xiao-Long Jiang
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Ying Song
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Ting-Ting Fan
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Xiang-Bao Shen
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Rong Yi
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Xiao-Ping Ao
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Gang-Biao Xu
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Min Deng
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, Yunnan University, Kunming, Yunnan, China
| |
Collapse
|
10
|
Dai X, Xiang S, Zhang Y, Yang S, Hu Q, Wu Z, Zhou T, Xiang J, Chen G, Tan X, Wang J, Ding J. Genomic evidence for evolutionary history and local adaptation of two endemic apricots: Prunus hongpingensis and P. zhengheensis. HORTICULTURE RESEARCH 2024; 11:uhad215. [PMID: 38689695 PMCID: PMC11059793 DOI: 10.1093/hr/uhad215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 10/16/2023] [Indexed: 05/02/2024]
Abstract
Apricot, belonging to the Armeniaca section of Rosaceae, is one of the economically important crop fruits that has been extensively cultivated. The natural wild apricots offer valuable genetic resources for crop improvement. However, some of them are endemic, with small populations, and are even at risk of extinction. In this study we unveil chromosome-level genome assemblies for two southern China endemic apricots, Prunus hongpingensis (PHP) and P. zhengheensis (PZH). We also characterize their evolutionary history and the genomic basis of their local adaptation using whole-genome resequencing data. Our findings reveal that PHP and PZH are closely related to Prunus armeniaca and form a distinct lineage. Both species experienced a decline in effective population size following the Last Glacial Maximum (LGM), which likely contributed to their current small population sizes. Despite the observed decrease in genetic diversity and heterozygosity, we do not observe an increased accumulation of deleterious mutations in these two endemic apricots. This is likely due to the combined effects of a low inbreeding coefficient and strong purifying selection. Furthermore, we identify a set of genes that have undergone positive selection and are associated with local environmental adaptation in PHP and PZH, respectively. These candidate genes can serve as valuable genetic resources for targeted breeding and improvement of cultivated apricots. Overall, our study not only enriches our comprehension of the evolutionary history of apricot species but also offers crucial insights for the conservation and future breeding of other endemic species amidst rapid climate changes.
Collapse
Affiliation(s)
- Xiaokang Dai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Songzhu Xiang
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Yulin Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, China
| | - Siting Yang
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Qianqian Hu
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Zhihao Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Tingting Zhou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Jingsong Xiang
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Gongyou Chen
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Xiaohua Tan
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, China
| | - Jihua Ding
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| |
Collapse
|
11
|
Ravikanthachari N, Steward RA, Boggs CL. Patterns of genetic variation and local adaptation of a native herbivore to a lethal invasive plant. Mol Ecol 2024:e17326. [PMID: 38515231 DOI: 10.1111/mec.17326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/03/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024]
Abstract
Understanding the evolutionary processes that influence fitness is critical to predicting species' responses to selection. Interactions among evolutionary processes including gene flow, drift and the strength of selection can lead to either local adaptation or maladaptation, especially in heterogenous landscapes. Populations experiencing novel environments or resources are ideal for understanding the mechanisms underlying adaptation or maladaptation, specifically in locally co-evolved interactions. We used the interaction between a native herbivore that oviposits on a patchily distributed introduced plant that in turn causes significant mortality to the larvae to test for signatures of local adaptation in areas where the two co-occurred. We used whole-genome sequencing to explore population structure, patterns of gene flow and signatures of local adaptation. We found signatures of local adaptation in response to the introduced plant in the absence of strong population structure with no genetic differentiation and low genetic variation. Additionally, we found localized allele frequency differences within a single population between habitats with and without the lethal plant, highlighting the effects of strong selection. Finally, we identified that selection was acting on larval ability to feed on the plant rather than on females' ability to avoid oviposition, thus uncovering the specific ontogenetic target of selection. Our work highlights the potential for adaptation to occur in a fine-grained landscape in the presence of gene flow and low genetic variation.
Collapse
Affiliation(s)
- Nitin Ravikanthachari
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
| | - Rachel A Steward
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
- Department of Biology, Lund University, Lund, Sweden
| | - Carol L Boggs
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
- School of Earth, Ocean & Environment, University of South Carolina, Columbia, South Carolina, USA
| |
Collapse
|
12
|
Song Y, Xu GB, Long KX, Wang CC, Chen R, Li H, Jiang XL, Deng M. Ensemble species distribution modeling and multilocus phylogeography provide insight into the spatial genetic patterns and distribution dynamics of a keystone forest species, Quercus glauca. BMC PLANT BIOLOGY 2024; 24:168. [PMID: 38438905 PMCID: PMC10910841 DOI: 10.1186/s12870-024-04830-1] [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: 12/13/2023] [Accepted: 02/16/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Forests are essential for maintaining species diversity, stabilizing local and global climate, and providing ecosystem services. Exploring the impact of paleogeographic events and climate change on the genetic structure and distribution dynamics of forest keystone species could help predict responses to future climate change. In this study, we combined an ensemble species distribution model (eSDM) and multilocus phylogeography to investigate the spatial genetic patterns and distribution change of Quercus glauca Thunb, a keystone of East Asian subtropical evergreen broad-leaved forest. RESULTS A total of 781 samples were collected from 77 populations, largely covering the natural distribution of Q. glauca. The eSDM showed that the suitable habitat experienced a significant expansion after the last glacial maximum (LGM) but will recede in the future under a general climate warming scenario. The distribution centroid will migrate toward the northeast as the climate warms. Using nuclear SSR data, two distinct lineages split between east and west were detected. Within-group genetic differentiation was higher in the West than in the East. Based on the identified 58 haplotypes, no clear phylogeographic structure was found. Populations in the Nanling Mountains, Wuyi Mountains, and the southwest region were found to have high genetic diversity. CONCLUSIONS A significant negative correlation between habitat stability and heterozygosity might be explained by the mixing of different lineages in the expansion region after LGM and/or hybridization between Q. glauca and closely related species. The Nanling Mountains may be important for organisms as a dispersal corridor in the west-east direction and as a refugium during the glacial period. This study provided new insights into spatial genetic patterns and distribution dynamics of Q. glauca.
Collapse
Affiliation(s)
- Ying Song
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Gang-Biao Xu
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Ke-Xin Long
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Chun-Cheng Wang
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Ran Chen
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - He Li
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Xiao-Long Jiang
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China.
| | - Min Deng
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, 650500, China.
| |
Collapse
|
13
|
Sinaga P, Klichowska E, Nowak A, Nobis M. Hybridization and introgression events in cooccurring populations of closely related grasses (Poaceae: Stipa) in high mountain steppes of Central Asia. PLoS One 2024; 19:e0298760. [PMID: 38412151 PMCID: PMC10898772 DOI: 10.1371/journal.pone.0298760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024] Open
Abstract
Stipa is a genus comprising ca. 150 species found in warm temperate regions of the Old World and around 30% of its representatives are of hybrid origin. In this study, using integrative taxonomy approach, we tested the hypothesis that hybridization and introgression are the explanations of the morphological intermediacy in species belonging to Stipa sect. Smirnovia, one of the species-rich sections in the mountains of Central Asia. Two novel nothospecies, S. magnifica × S. caucasica subsp. nikolai and S. lingua × S. caucasica subsp. nikolai, were identified based on a combination of morphological characters and SNPs markers. SNPs marker revealed that all S. lingua × S. caucasica samples were F1 hybrids, whereas most of S. magnifica × S. caucasica samples were backcross hybrids. Furthermore, the above mentioned hybrids exhibit transgressive morphological characters to each of their parental species. These findings have implications for understanding the process of hybridization in the genus Stipa, particularly in the sect. Smirnovia. As a taxonomic conclusion, we describe the two new nothospecies S. × muksuensis (from Tajikistan) and S. × ochyrae (from Kyrgyzstan) and present an identification key to species morphologically similar to the taxa mentioned above.
Collapse
Affiliation(s)
- Patar Sinaga
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden – Center for Biological Diversity Conservation in Powsin, Warszawa, Poland
- Botanical Garden of the Wrocław University, Wrocław, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| |
Collapse
|
14
|
Wang LL, Li Y, Zheng SS, Kozlowski G, Xu J, Song YG. Complete Chloroplast Genomes of Four Oaks from the Section Cyclobalanopsis Improve the Phylogenetic Analysis and Understanding of Evolutionary Processes in the Genus Quercus. Genes (Basel) 2024; 15:230. [PMID: 38397219 PMCID: PMC10888318 DOI: 10.3390/genes15020230] [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: 01/05/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Quercus is a valuable genus ecologically, economically, and culturally. They are keystone species in many ecosystems. Species delimitation and phylogenetic studies of this genus are difficult owing to frequent hybridization. With an increasing number of genetic resources, we will gain a deeper understanding of this genus. In the present study, we collected four Quercus section Cyclobalanopsis species (Q. poilanei, Q. helferiana, Q. camusiae, and Q. semiserrata) distributed in Southeast Asia and sequenced their complete genomes. Following analysis, we compared the results with those of other species in the genus Quercus. These four chloroplast genomes ranged from 160,784 bp (Q. poilanei) to 161,632 bp (Q. camusiae) in length, with an overall guanine and cytosine (GC) content of 36.9%. Their chloroplast genomic organization and order, as well as their GC content, were similar to those of other Quercus species. We identified seven regions with relatively high variability (rps16, ndhk, accD, ycf1, psbZ-trnG-GCC, rbcL-accD, and rpl32-trnL-UAG) which could potentially serve as plastid markers for further taxonomic and phylogenetic studies within Quercus. Our phylogenetic tree supported the idea that the genus Quercus forms two well-differentiated lineages (corresponding to the subgenera Quercus and Cerris). Of the three sections in the subgenus Cerris, the section Ilex was split into two clusters, each nested in the other two sections. Moreover, Q. camusiae and Q. semiserrata detected in this study diverged first in the section Cyclobalanopsis and mixed with Q. engleriana in the section Ilex. In particular, 11 protein coding genes (atpF, ndhA, ndhD, ndhF, ndhK, petB, petD, rbcL, rpl22, ycf1, and ycf3) were subjected to positive selection pressure. Overall, this study enriches the chloroplast genome resources of Quercus, which will facilitate further analyses of phylogenetic relationships in this ecologically important tree genus.
Collapse
Affiliation(s)
- Ling-Ling Wang
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai 201418, China;
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
| | - Yu Li
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
| | - Si-Si Zheng
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
| | - Gregor Kozlowski
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
- Department of Biology and Botanic Garden, University of Fribourg, 1700 Fribourg, Switzerland
- Natural History Museum Fribourg, 1700 Fribourg, Switzerland
| | - Jin Xu
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai 201418, China;
| | - Yi-Gang Song
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
| |
Collapse
|
15
|
Hipp AL, Lazic D. Ancient tree genomes for old questions. Mol Ecol 2024; 33:e17259. [PMID: 38179684 DOI: 10.1111/mec.17259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/19/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024]
Abstract
Most foundational work on the evolution and migration of plant species relies on genomic data from contemporary samples. Ancient plant samples can give us access to allele sequences and distributions on the landscape dating back to the mid Holocene or earlier (Gugerli et al., 2005). Nuclear DNA from ancient wood, however, has been mostly inaccessible until now. In a From the Cover article in this issue of Molecular Ecology, Wagner et al. (2023) present the first resequenced nuclear genomes from ancient oak wood, including two samples dated to the 15th century and one that dates to more than 3500 years ago. These ancient tree genomes open the possibility for investigating species adaptation, migration, divergence, and hybridisation in the deep past. They pave the way for what we hope will be a new era in the use of paleogenomics to study Holocene tree histories.
Collapse
Affiliation(s)
- Andrew L Hipp
- Herbarium and Center for Tree Science, The Morton Arboretum, Lisle, Illinois, USA
- Botany Department, The Field Museum, Chicago, Illinois, USA
| | - Desanka Lazic
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| |
Collapse
|
16
|
Wagner S, Seguin-Orlando A, Leplé JC, Leroy T, Lalanne C, Labadie K, Aury JM, Poirier S, Wincker P, Plomion C, Kremer A, Orlando L. Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood. Mol Ecol 2024; 33:e16859. [PMID: 36748324 PMCID: PMC7615563 DOI: 10.1111/mec.16859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 12/08/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023]
Abstract
Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.
Collapse
Affiliation(s)
- Stefanie Wagner
- Plant Genomic Resources Center (CNRGV), INRAE, Castanet-Tolosan, France
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| | - Andaine Seguin-Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| | | | - Thibault Leroy
- IRHS UMR1345, Université d’Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | | | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Patrick Wincker
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | | | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| |
Collapse
|
17
|
Sanderson BJ, Gambhir D, Feng G, Hu N, Cronk QC, Percy DM, Freaner FM, Johnson MG, Smart LB, Keefover-Ring K, Yin T, Ma T, DiFazio SP, Liu J, Olson MS. Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives. Syst Biol 2023; 72:1220-1232. [PMID: 37449764 DOI: 10.1093/sysbio/syad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 06/02/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023] Open
Abstract
Despite the economic, ecological, and scientific importance of the genera Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a "spectacular failure" due to a speculated radiation of the subgenera Vetrix and Chamaetia. Here, we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed the polyphyly of others. Using an fbranch analysis, we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the Vetrix-Chamaetia clade in Salix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both Salix and Populus have played important roles in the diversification and diversity in these two genera.
Collapse
Affiliation(s)
- Brian J Sanderson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
- Department of Biology, West Virginia University, Morgantown, WV 26506,USA
| | - Diksha Gambhir
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Guanqiao Feng
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Nan Hu
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Quentin C Cronk
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Diana M Percy
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, New York 14456, USA
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tongming Yin
- Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506,USA
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| |
Collapse
|
18
|
Ramírez-Sánchez D, Gibelin-Viala C, Roux F, Vailleau F. Genetic architecture of the response of Arabidopsis thaliana to a native plant-growth-promoting bacterial strain. FRONTIERS IN PLANT SCIENCE 2023; 14:1266032. [PMID: 38023938 PMCID: PMC10665851 DOI: 10.3389/fpls.2023.1266032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
By improving plant nutrition and alleviating abiotic and biotic stresses, plant growth-promoting bacteria (PGPB) can help to develop eco-friendly and sustainable agricultural practices. Besides climatic conditions, soil conditions, and microbe-microbe interactions, the host genotype influences the effectiveness of PGPB. Yet, most GWAS conducted to characterize the genetic architecture of response to PGPB are based on non-native interactions between a host plant and PGPB strains isolated from the belowground compartment of other plants. In this study, a GWAS was set up under in vitro conditions to describe the genetic architecture of the response of Arabidopsis thaliana to the PGPB Pseudomonas siliginis, by inoculating seeds of 162 natural accessions from the southwest of France with one strain isolated from the leaf compartment in the same geographical region. Strong genetic variation of plant growth response to this native PGPB was observed at a regional scale, with the strain having a positive effect on the vegetative growth of small plants and a negative effect on the vegetative growth of large plants. The polygenic genetic architecture underlying this negative trade-off showed suggestive signatures of local adaptation. The main eco-evolutionary relevant candidate genes are involved in seed and root development.
Collapse
|
19
|
Villa-Machío I, Heuertz M, Álvarez I, Nieto Feliner G. Demography-driven and adaptive introgression in a hybrid zone of the Armeria syngameon. Mol Ecol 2023. [PMID: 37837272 DOI: 10.1111/mec.17167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023]
Abstract
Syngameons represent networks of otherwise distinct species connected by limited gene exchange. Although most studies have focused on how species maintain their cohesiveness despite gene flow, there are additional relevant questions regarding the evolutionary dynamics of syngameons and their drivers, as well as the success of their members and the network as a whole. Using a ddRADseq approach, we analysed the genetic structure, genomic clines and demographic history of a coastal hybrid zone involving two species of the Armeria (Plumbaginaceae) syngameon in southern Spain. We inferred that a peripheral population of the sand dune-adapted A. pungens diverged from the rest of the conspecific populations and subsequently hybridized with a locally more abundant pinewood congener, A. macrophylla. Both species display extensive plastid DNA haplotype sharing. Genomic cline analysis identified bidirectional introgression, but more outlier loci with excess A. pungens than A. macrophylla ancestry, suggesting the possibility of selection for A. pungens alleles. This is consistent with the finding that the A. pungens phenotype is selected for in open habitats, and with the strong correlation found between ancestry and phenotype. Taken together, our analyses suggest an intriguing scenario in which bidirectional introgression may, on the one hand, help to avoid reduced levels of genetic diversity due to the small size and isolated location of the A. pungens range-edge population, thereby minimizing demographic risks of stochastic extinction. On the other hand, the data also suggest that introgression into A. macrophylla may allow individuals to grow in open, highly irradiated, deep sandy, salt-exposed habitats.
Collapse
Affiliation(s)
- Irene Villa-Machío
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | | | - Inés Álvarez
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | - Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| |
Collapse
|
20
|
Bock DG, Cai Z, Elphinstone C, González-Segovia E, Hirabayashi K, Huang K, Keais GL, Kim A, Owens GL, Rieseberg LH. Genomics of plant speciation. PLANT COMMUNICATIONS 2023; 4:100599. [PMID: 37050879 PMCID: PMC10504567 DOI: 10.1016/j.xplc.2023.100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can form. Now, the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation research. Here, we review these recent genome-enabled developments in plant speciation. We discuss complications related to identification of reproductive isolation (RI) loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation, as increasingly revealed by new sequencing technologies. Further, we review how genomics has advanced what we know of some routes to new species formation, like hybridization or whole-genome duplication, while casting doubt on others, like population bottlenecks and genetic drift. While genomics can fast-track identification of genes and mutations that confer RI, we emphasize that follow-up molecular and field experiments remain critical. Nonetheless, genomics has clarified the outsized role of ancient variants rather than new mutations, particularly early during speciation. We conclude by highlighting promising avenues of future study. These include expanding what we know so far about the role of epigenetic and structural changes during speciation, broadening the scope and taxonomic breadth of plant speciation genomics studies, and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.
Collapse
Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Zhe Cai
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Cassandra Elphinstone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Eric González-Segovia
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Graeme L Keais
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Amy Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
21
|
Tóth EG, Cseke K, Benke A, Lados BB, Tomov VT, Zhelev P, Kámpel JD, Borovics A, Köbölkuti ZA. Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data. Heredity (Edinb) 2023:10.1038/s41437-023-00629-2. [PMID: 37316726 PMCID: PMC10382515 DOI: 10.1038/s41437-023-00629-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023] Open
Abstract
Knowledge on the genetic composition of Quercus petraea in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-seq loci to the Quercus robur reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of Q. petraea were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north-southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4-16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined Q. petraea populations.
Collapse
Affiliation(s)
- Endre Gy Tóth
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary.
| | - Klára Cseke
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Attila Benke
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Botond B Lados
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Vladimir T Tomov
- Department of Landscape Architecture, Faculty of Ecology and Landscape Architecture, University of Forestry (UF), Kliment Ohridsky 10, Sofia, 1797, Bulgaria
| | - Petar Zhelev
- Department of Dendrology, Faculty of Forestry, University of Forestry (UF), Kliment Ohridsky 10, Sofia, 1797, Bulgaria
| | - József D Kámpel
- Ottó Herman Environmental and Agricultural Technical School, Vocational School and College (Agricultural Vocational Centre of the Kisalföld Region), Ernuszt Kelemen 1, Szombathely, 9700, Hungary
| | - Attila Borovics
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Zoltán A Köbölkuti
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
- Departement of Applied Forest Genetics Research, Bavarian Office for Forest Genetics (AWG), Forstamtsplatz 1, Teisendorf, 83317, Germany
| |
Collapse
|
22
|
Stull GW, Pham KK, Soltis PS, Soltis DE. Deep reticulation: the long legacy of hybridization in vascular plant evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:743-766. [PMID: 36775995 DOI: 10.1111/tpj.16142] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 05/27/2023]
Abstract
Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well-documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community.
Collapse
Affiliation(s)
- Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Kasey K Pham
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| |
Collapse
|
23
|
Huang WC, Liao B, Liu H, Liang YY, Chen XY, Wang B, Xia H. A chromosome-scale genome assembly of Castanopsis hystrix provides new insights into the evolution and adaptation of Fagaceae species. FRONTIERS IN PLANT SCIENCE 2023; 14:1174972. [PMID: 37215286 PMCID: PMC10197965 DOI: 10.3389/fpls.2023.1174972] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/22/2023] [Indexed: 05/24/2023]
Abstract
Fagaceae species dominate forests and shrublands throughout the Northern Hemisphere, and have been used as models to investigate the processes and mechanisms of adaptation and speciation. Compared with the well-studied genus Quercus, genomic data is limited for the tropical-subtropical genus Castanopsis. Castanopsis hystrix is an ecologically and economically valuable species with a wide distribution in the evergreen broad-leaved forests of tropical-subtropical Asia. Here, we present a high-quality chromosome-scale reference genome of C. hystrix, obtained using a combination of Illumina and PacBio HiFi reads with Hi-C technology. The assembled genome size is 882.6 Mb with a contig N50 of 40.9 Mb and a BUSCO estimate of 99.5%, which are higher than those of recently published Fagaceae species. Genome annotation identified 37,750 protein-coding genes, of which 97.91% were functionally annotated. Repeat sequences constituted 50.95% of the genome and LTRs were the most abundant repetitive elements. Comparative genomic analysis revealed high genome synteny between C. hystrix and other Fagaceae species, despite the long divergence time between them. Considerable gene family expansion and contraction were detected in Castanopsis species. These expanded genes were involved in multiple important biological processes and molecular functions, which may have contributed to the adaptation of the genus to a tropical-subtropical climate. In summary, the genome assembly of C. hystrix provides important genomic resources for Fagaceae genomic research communities, and improves understanding of the adaptation and evolution of forest trees.
Collapse
Affiliation(s)
- Wei-Cheng Huang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Borong Liao
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Hui Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Hanhan Xia
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| |
Collapse
|
24
|
Whittemore AT, Miller RE. Dynamic properties of the pinyon pine syngameon. THE NEW PHYTOLOGIST 2023; 237:1943-1945. [PMID: 36652627 DOI: 10.1111/nph.18707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Alan T Whittemore
- Herbarium, Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
| | - Richard E Miller
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
- Flower Diversity Institute, Arvada, CO, 80003, USA
| |
Collapse
|
25
|
Le Provost G, Lalanne C, Lesur I, Louvet JM, Delzon S, Kremer A, Labadie K, Aury JM, Da Silva C, Moritz T, Plomion C. Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology. BMC PLANT BIOLOGY 2023; 23:108. [PMID: 36814198 PMCID: PMC9948485 DOI: 10.1186/s12870-023-04069-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Global warming raises serious concerns about the persistence of species and populations locally adapted to their environment, simply because of the shift it produces in their adaptive landscape. For instance, the phenological cycle of tree species may be strongly affected by higher winter temperatures and late frost in spring. Given the variety of ecosystem services they provide, the question of forest tree adaptation has received increasing attention in the scientific community and catalyzed research efforts in ecology, evolutionary biology and functional genomics to study their adaptive capacity to respond to such perturbations. RESULTS In the present study, we used an elevation gradient in the Pyrenees Mountains to explore the gene expression network underlying dormancy regulation in natural populations of sessile oak stands sampled along an elevation cline and potentially adapted to different climatic conditions mainly driven by temperature. By performing analyses of gene expression in terminal buds we identified genes displaying significant dormancy, elevation or dormancy-by-elevation interaction effects. Our Results highlighted that low- and high-altitude populations have evolved different molecular strategies for minimizing late frost damage and maximizing the growth period, thereby increasing potentially their respective fitness in these contrasting environmental conditions. More particularly, population from high elevation overexpressed genes involved in the inhibition of cell elongation and delaying flowering time while genes involved in cell division and flowering, enabling buds to flush earlier were identified in population from low elevation. CONCLUSION Our study made it possible to identify key dormancy-by-elevation responsive genes revealing that the stands analyzed in this study have evolved distinct molecular strategies to adapt their bud phenology in response to temperature.
Collapse
Affiliation(s)
| | | | - Isabelle Lesur
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
- Helix Venture, F-33700, Mérignac, France
| | | | | | | | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 87, Umeå, Sweden
| | | |
Collapse
|
26
|
Rougemont Q, Xuereb A, Dallaire X, Moore JS, Normandeau E, Perreault-Payette A, Bougas B, Rondeau EB, Withler RE, Van Doornik DM, Crane PA, Naish KA, Garza JC, Beacham TD, Koop BF, Bernatchez L. Long-distance migration is a major factor driving local adaptation at continental scale in Coho salmon. Mol Ecol 2023; 32:542-559. [PMID: 35000273 DOI: 10.1111/mec.16339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/19/2021] [Accepted: 12/23/2021] [Indexed: 01/25/2023]
Abstract
Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behaviour may promote the establishment of local adaptation. We genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. The results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidate single nucleotide polymorphisms associated with long-distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.
Collapse
Affiliation(s)
- Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,CEFE, Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier, Montpellier, France
| | - Amanda Xuereb
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Xavier Dallaire
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Jean-Sébastien Moore
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Alysse Perreault-Payette
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Bérénice Bougas
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric B Rondeau
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada.,Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Ruth E Withler
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Donald M Van Doornik
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Manchester Research Station, Port Orchard, Washington, USA
| | - Penelope A Crane
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, Anchorage, Alaska, USA
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - John Carlos Garza
- Department of Ocean Sciences and Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, California, USA
| | - Terry D Beacham
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| |
Collapse
|
27
|
Gaczorek TS, Marszałek M, Dudek K, Arntzen JW, Wielstra B, Babik W. Interspecific introgression of MHC genes in Triturus newts: Evidence from multiple contact zones. Mol Ecol 2023; 32:867-880. [PMID: 36458894 PMCID: PMC10108261 DOI: 10.1111/mec.16804] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 11/03/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022]
Abstract
The major histocompatibility complex (MHC) genes are central to the adaptive immune response in vertebrates. Selection generally maintains high MHC variation because the spectrum of recognized pathogens depends on MHC polymorphism. Novel alleles favoured by selection originate by interallelic recombination or de novo mutations but may also be acquired by introgression from related species. However, the extent and prevalence of MHC introgression remain an open question. In this study, we tested for MHC introgression in six hybrid zones formed by six Triturus newt species. We sequenced and genotyped the polymorphic second exons of the MHC class I and II genes and compared their interspecific similarity at various distances from the centre of the hybrid zone. We found evidence for introgression of both MHC classes in the majority of examined hybrid zones, with support for a more substantial class I introgression. Furthermore, the overall MHC allele sharing outside of hybrid zones was elevated between pairs of Triturus species with abutting ranges, regardless of the phylogenetic distance between them. No effect of past hybrid zone movement on MHC allele sharing was found. Finally, using previously published genome-wide data, we demonstrated that MHC introgression was more extensive than genome-wide introgression, supporting its adaptive potential. Our study thus provides evidence for the prevalence of MHC introgression across multiple Triturus hybrid zones, indicating that MHC introgression between divergent hybridizing species may be widespread and adaptive.
Collapse
Affiliation(s)
- Tomasz S Gaczorek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Marzena Marszałek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| |
Collapse
|
28
|
Compton S, Stackpole C, Dixit A, Sekhwal MK, Kolb T, De la Torre AR. Differences in heat tolerance, water use efficiency and growth among Douglas-fir families and varieties evidenced by GWAS and common garden studies. AOB PLANTS 2023; 15:plad008. [PMID: 37007611 PMCID: PMC10052383 DOI: 10.1093/aobpla/plad008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Severe and frequent heat and drought events challenge the survival and development of long-generation trees. In this study, we investigated the genomic basis of heat tolerance, water use efficiency and growth by performing genome-wide association studies in coastal Douglas-fir (Pseudotsuga menziesii) and intervarietal (menziesii × glauca) hybrid seedlings. GWAS results identified 32 candidate genes involved in primary and secondary metabolism, abiotic stress and signaling, among other functions. Water use efficiency (inferred from carbon isotope discrimination), photosynthetic capacity (inferred from %N), height and heat tolerance (inferred from electrolyte leakage in a heat stress experiment) were significantly different among Douglas-fir families and varieties. High-elevation seed sources had increased water use efficiency, which could be a result of higher photosynthetic capacity. Similarly, families with greater heat tolerance also had higher water use efficiency and slower growth, suggesting a conservative growth strategy. Intervarietal hybrids showed increased heat tolerance (lower electrolyte leakage at 50 and 55 °C) and higher water use efficiency compared with coastal families, suggesting that hybridization might be a source of pre-adapted alleles to warming climates and should be considered for large-scale reforestation projects under increasingly arid conditions.
Collapse
Affiliation(s)
| | | | - Aalap Dixit
- Department of Forestry, New Mexico Highlands University, Las Vegas, NM 87701, USA
| | - Manoj K Sekhwal
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, AZ 86011, USA
| | - Thomas Kolb
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, AZ 86011, USA
| | | |
Collapse
|
29
|
Schroeder H, Kersten B. A Small Set of Nuclear Markers for Reliable Differentiation of the Two Closely Related Oak Species Quercus Robur and Q. Petraea. PLANTS (BASEL, SWITZERLAND) 2023; 12:566. [PMID: 36771649 PMCID: PMC9919172 DOI: 10.3390/plants12030566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Quercus robur and Q. petraea are, in addition to Fagus sylvatica, the main economically used deciduous tree species in Europe. Identification of these two species is crucial because they differ in their ecological demands. Because of a changing climate, foresters must know more than ever which species will perform better under given environmental conditions. The search for differentiating molecular markers between these two species has already lasted for decades. Until now, differentiation has only been possible in approaches with a combination of several molecular markers and a subsequent statistical analysis to calculate the probability of being one or the other species. Here, we used MiSeq Illumina data from pools of Q. robur and Q. petraea specimens and identified nuclear SNPs and small InDels versus the Q. robur reference genome. Selected sequence variants with 100% allele frequency difference between the two pools were further validated in an extended set of Q. robur and Q. petraea specimens, and then the number of markers was deliberately reduced to the smallest possible set for species differentiation. A combination of six markers from four nuclear regions is enough to identify Q. robur, Q. petraea or hybrids between these two species quite well and represents a marker set that is cost-efficient and useable in every laboratory.
Collapse
|
30
|
Satler JD, Herre EA, Heath TA, Machado CA, Gómez Zúñiga A, Jandér KC, Eaton DAR, Nason JD. Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps. Ecol Evol 2023; 13:e9673. [PMID: 36699574 PMCID: PMC9848820 DOI: 10.1002/ece3.9673] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/20/2022] [Accepted: 12/02/2022] [Indexed: 01/20/2023] Open
Abstract
Obligate pollination mutualisms, in which plant and pollinator lineages depend on each other for reproduction, often exhibit high levels of species specificity. However, cases in which two or more pollinator species share a single host species (host sharing), or two or more host species share a single pollinator species (pollinator sharing), are known to occur in current ecological time. Further, evidence for host switching in evolutionary time is increasingly being recognized in these systems. The degree to which departures from strict specificity differentially affect the potential for hybridization and introgression in the associated host or pollinator is unclear. We addressed this question using genome-wide sequence data from five sympatric Panamanian free-standing fig species (Ficus subgenus Pharmacosycea, section Pharmacosycea) and their six associated fig-pollinator wasp species (Tetrapus). Two of the five fig species, F. glabrata and F. maxima, were found to regularly share pollinators. In these species, ongoing hybridization was demonstrated by the detection of several first-generation (F1) hybrid individuals, and historical introgression was indicated by phylogenetic network analysis. By contrast, although two of the pollinator species regularly share hosts, all six species were genetically distinct and deeply divergent, with no evidence for either hybridization or introgression. This pattern is consistent with results from other obligate pollination mutualisms, suggesting that, in contrast to their host plants, pollinators appear to be reproductively isolated, even when different species of pollinators mate in shared hosts.
Collapse
Affiliation(s)
- Jordan D. Satler
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| | | | - Tracy A. Heath
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| | | | | | - K. Charlotte Jandér
- Department of Ecology and Genetics, Plant Ecology and EvolutionUppsala UniversityUppsalaSweden
| | - Deren A. R. Eaton
- Department of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNew YorkUSA
| | - John D. Nason
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| |
Collapse
|
31
|
Yuan S, Shi Y, Zhou BF, Liang YY, Chen XY, An QQ, Fan YR, Shen Z, Ingvarsson PK, Wang B. Genomic vulnerability to climate change in Quercus acutissima, a dominant tree species in East Asian deciduous forests. Mol Ecol 2023; 32:1639-1655. [PMID: 36626136 DOI: 10.1111/mec.16843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Understanding the evolutionary processes that shape the landscape of genetic variation and influence the response of species to future climate change is critical for biodiversity conservation. Here, we sampled 27 populations across the distribution range of a dominant forest tree, Quercus acutissima, in East Asia, and applied genome-wide analyses to track the evolutionary history and predict the fate of populations under future climate. We found two genetic groups (East and West) in Q. acutissima that diverged during Pliocene. We also found a heterogeneous landscape of genomic variation in this species, which may have been shaped by population demography and linked selections. Using genotype-environment association analyses, we identified climate-associated SNPs in a diverse set of genes and functional categories, indicating a model of polygenic adaptation in Q. acutissima. We further estimated three genetic offset metrics to quantify genomic vulnerability of this species to climate change due to the complex interplay between local adaptation and migration. We found that marginal populations are under higher risk of local extinction because of future climate change, and may not be able to track suitable habitats to maintain the gene-environment relationships observed under the current climate. We also detected higher reverse genetic offsets in northern China, indicating that genetic variation currently present in the whole range of Q. acutissima may not adapt to future climate conditions in this area. Overall, this study illustrates how evolutionary processes have shaped the landscape of genomic variation, and provides a comprehensive genome-wide view of climate maladaptation in Q. acutissima.
Collapse
Affiliation(s)
- Shuai Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Qing-Qing An
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Yan-Ru Fan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Zhao Shen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| |
Collapse
|
32
|
Noguerales V, Ortego J. Genomic evidence of speciation by fusion in a recent radiation of grasshoppers. Evolution 2022; 76:2618-2633. [PMID: 35695020 PMCID: PMC9796961 DOI: 10.1111/evo.14508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/22/2022] [Accepted: 04/02/2022] [Indexed: 01/22/2023]
Abstract
Postdivergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). Although neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (based on both scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between the sister taxa C. binotatus (that exclusively feeds on scrub legumes) and C. saulcyi (that only feeds on gramineous herbs). Genetic clustering analyses and inferences from coalescent-based demographic simulations confirm that C. s. algoaldensis represents an independently evolving lineage and support the ancient hybrid origin of this taxon (about 1.4 Ma), which sheds light on its uncertain phylogenetic position and might explain its broader trophic niche. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate their long-term persistence through geographic isolation from parental forms in topographically complex landscapes.
Collapse
Affiliation(s)
- Víctor Noguerales
- Department of Biological SciencesUniversity of CyprusNicosia1678Cyprus,Island Ecology and Evolution GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de La Laguna38206Spain
| | - Joaquín Ortego
- Department of Integrative EcologyEstación Biológica de Doñana (EBD‐CSIC)Sevilla41092Spain
| |
Collapse
|
33
|
Dimitrova A, Csilléry K, Klisz M, Lévesque M, Heinrichs S, Cailleret M, Andivia E, Madsen P, Böhenius H, Cvjetkovic B, De Cuyper B, de Dato G, Ferus P, Heinze B, Ivetić V, Köbölkuti Z, Lazarević J, Lazdina D, Maaten T, Makovskis K, Milovanović J, Monteiro AT, Nonić M, Place S, Puchalka R, Montagnoli A. Risks, benefits, and knowledge gaps of non-native tree species in Europe. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.908464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Changing ecosystem conditions and diverse socio-economical events have contributed to an ingrained presence of non-native tree species (NNTs) in the natural and cultural European landscapes. Recent research endeavors have focused on different aspects of NNTs such as legislation, benefits, and risks for forestry, emphasizing that large knowledge gaps remain. As an attempt to fulfill part of these gaps, within the PEN-CAFoRR COST Action (CA19128) network, we established an open-access questionnaire that allows both academic experts and practitioners to provide information regarding NNTs from 20 European countries. Then, we integrated the data originating from the questionnaire, related to the country-based assessment of both peer-reviewed and grey literature, with information from available datasets (EUFORGEN and EU-Forest), which gave the main structure to the study and led to a mixed approach review. Finally, our study provided important insights into the current state of knowledge regarding NNTs. In particular, we highlighted NNTs that have shown to be less commonly addressed in research, raising caution about those characterized by an invasive behavior and used for specific purposes (e.g., wood production, soil recultivation, afforestation, and reforestation). NNTs were especially explored in the context of resilient and adaptive forest management. Moreover, we emphasized the assisted and natural northward migration of NNTs as another underscored pressing issue, which needs to be addressed by joint efforts, especially in the context of the hybridization potential. This study represents an additional effort toward the knowledge enhancement of the NNTs situation in Europe, aiming for a continuously active common source deriving from interprofessional collaboration.
Collapse
|
34
|
Van Daele F, Honnay O, De Kort H. Genomic analyses point to a low evolutionary potential of prospective source populations for assisted migration in a forest herb. Evol Appl 2022; 15:1859-1874. [DOI: 10.1111/eva.13485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/13/2022] [Accepted: 09/17/2022] [Indexed: 11/26/2022] Open
Affiliation(s)
- Frederik Van Daele
- Department of Biology, Plant Conservation and Population Biology KU Leuven Leuven Belgium
| | - Olivier Honnay
- Department of Biology, Plant Conservation and Population Biology KU Leuven Leuven Belgium
| | - Hanne De Kort
- Department of Biology, Plant Conservation and Population Biology KU Leuven Leuven Belgium
| |
Collapse
|
35
|
Burbrink FT, Crother BI, Murray CM, Smith BT, Ruane S, Myers EA, Pyron RA. Empirical and philosophical problems with the subspecies rank. Ecol Evol 2022; 12:e9069. [PMID: 35845367 PMCID: PMC9271888 DOI: 10.1002/ece3.9069] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 11/12/2022] Open
Abstract
Species‐level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species “concepts.” These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what “kind” of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology. This lack of coherence is in part responsible for the persistence of the subspecies rank, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse of incipient species. Thus, prospective events like lineages merging or diverging require information from unknowable future information. This is also conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies can seem attractive given that many lineages do not exhibit intrinsic reproductive isolation. We argue that using subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatiotemporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from evolutionary ontology and do not consider genealogy. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.
Collapse
Affiliation(s)
- Frank T Burbrink
- Department of Herpetology American Museum of Natural History New York New York USA
| | - Brian I Crother
- Department of Biological Sciences Southeastern Louisiana University Hammond Louisiana USA
| | - Christopher M Murray
- Department of Biological Sciences Southeastern Louisiana University Hammond Louisiana USA
| | - Brian Tilston Smith
- Department of Ornithology American Museum of Natural History New York New York USA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center Field Museum of Natural History Chicago Illinois USA
| | - Edward A Myers
- Department of Herpetology American Museum of Natural History New York New York USA.,Department of Biological Sciences Clemson University Clemson South Carolina USA.,Department of Vertebrate Zoology Smithsonian Institution, National Museum of Natural History Washington District of Columbia USA
| | - Robert Alexander Pyron
- Department of Vertebrate Zoology Smithsonian Institution, National Museum of Natural History Washington District of Columbia USA.,Department of Biological Sciences The George Washington University Washington District of Columbia USA
| |
Collapse
|
36
|
Genome-wide analyses of introgression between two sympatric Asian oak species. Nat Ecol Evol 2022; 6:924-935. [PMID: 35513577 DOI: 10.1038/s41559-022-01754-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/29/2022] [Indexed: 12/13/2022]
Abstract
Introgression can be an important source of new alleles for adaption under rapidly changing environments, perhaps even more important than standing variation. Though introgression has been extensively studied in many plants and animals, key questions on the underlying mechanisms of introgression still remain unanswered. In particular, we are yet to determine the genomic distribution of introgressed regions along the genome; whether the extent and patterns of introgression are influenced by ecological factors; and when and how introgression contributes to adaptation. Here, we generated high-quality genomic resources for two sympatric widespread Asian oak species, Quercus acutissima and Q. variabilis, sampled in multiple forests to study introgression between them. We show that introgressed regions are broadly distributed across the genome. Introgression was affected by genetic divergence between pairs of populations and by the similarity of the environments in which they live-populations occupying similar ecological sites tended to share the same introgressed regions. Introgressed genomic footprints of adaptation were preferentially located in regions with suppressed recombination rate. Introgression probably confers adaptation in these oak populations by introducing allelic variation in cis-regulatory elements, in particular through transposable element insertions, thereby altering the regulation of genes related to stress. Our results provide new avenues of research for uncovering mechanisms of adaptation due to hybridization in sympatric species.
Collapse
|
37
|
Archambeau J, Garzón MB, Barraquand F, Miguel MD, Plomion C, González-Martínez SC. Combining climatic and genomic data improves range-wide tree height growth prediction in a forest tree. Am Nat 2022; 200:E141-E159. [DOI: 10.1086/720619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
38
|
Liang YY, Chen XY, Zhou BF, Mitchell-Olds T, Wang B. Globally Relaxed Selection and Local Adaptation in Boechera stricta. Genome Biol Evol 2022; 14:evac043. [PMID: 35349686 PMCID: PMC9011030 DOI: 10.1093/gbe/evac043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 11/25/2022] Open
Abstract
The strength of selection varies among populations and across the genome, but the determinants of efficacy of selection remain unclear. In this study, we used whole-genome sequencing data from 467 Boechera stricta accessions to quantify the strength of selection and characterize the pattern of local adaptation. We found low genetic diversity on 0-fold degenerate sites and conserved non-coding sites, indicating functional constraints on these regions. The estimated distribution of fitness effects and the proportion of fixed substitutions suggest relaxed negative and positive selection in B. stricta. Among the four population groups, the NOR and WES groups have smaller effective population size (Ne), higher proportions of effectively neutral sites, and lower rates of adaptive evolution compared with UTA and COL groups, reflecting the effect of Ne on the efficacy of natural selection. We also found weaker selection on GC-biased sites compared with GC-conservative (unbiased) sites, suggested that GC-biased gene conversion has affected the strength of selection in B. stricta. We found mixed evidence for the role of the recombination rate on the efficacy of selection. The positive and negative selection was stronger in high-recombination regions compared with low-recombination regions in COL but not in other groups. By scanning the genome, we found different subsets of selected genes suggesting differential adaptation among B. stricta groups. These results show that differences in effective population size, nucleotide composition, and recombination rate are important determinants of the efficacy of selection. This study enriches our understanding of the roles of natural selection and local adaptation in shaping genomic variation.
Collapse
Affiliation(s)
- Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences,
Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences,
Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences,
Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | | | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences,
Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
39
|
Zhou BF, Yuan S, Crowl AA, Liang YY, Shi Y, Chen XY, An QQ, Kang M, Manos PS, Wang B. Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere. Nat Commun 2022; 13:1320. [PMID: 35288565 PMCID: PMC8921187 DOI: 10.1038/s41467-022-28917-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/16/2022] [Indexed: 12/12/2022] Open
Abstract
Northern Hemisphere forests changed drastically in the early Eocene with the diversification of the oak family (Fagaceae). Cooling climates over the next 20 million years fostered the spread of temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we use phylogenomic analyses of nuclear and plastid genomes to investigate the timing and pattern of major macroevolutionary events and ancient genome-wide signatures of hybridization across Fagaceae. Innovation related to seed dispersal is implicated in triggering waves of continental radiations beginning with the rapid diversification of major lineages and resulting in unparalleled transformation of forest dynamics within 15 million years following the K-Pg extinction. We detect introgression at multiple time scales, including ancient events predating the origination of genus-level diversity. As oak lineages moved into newly available temperate habitats in the early Miocene, secondary contact between previously isolated species occurred. This resulted in adaptive introgression, which may have further amplified the diversification of white oaks across Eurasia. Fagaceae are diverse family including trees of ecological and economic importance. This phylogenomic analysis of nuclear and plastid genomes reconstructs evolutionary history and finds evidence of multiple adaptive introgression events in this important plant family.
Collapse
|
40
|
Hu Y, Feng C, Yang L, Edger PP, Kang M. Genomic population structure and local adaptation of the wild strawberry Fragaria nilgerrensis. HORTICULTURE RESEARCH 2022; 9:uhab059. [PMID: 35043184 PMCID: PMC8993681 DOI: 10.1093/hr/uhab059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/15/2021] [Indexed: 06/14/2023]
Abstract
The crop wild relative, Fragaria nilgerrensis, is adapted to a variety of diverse habitats across its native range in China. Thus, discoveries made in this species could serve useful to guide the development of new superior strawberry cultivars that are resilient to new or variable environments. However, the genetic diversity and genetic architecture of traits in this species underlying important adaptive traits remain poorly understood. Here, we used whole-genome resequencing data from 193 F. nilgerrensis individuals spanning the distribution range in China to investigate the genetic diversity, population structure and the genomic basis of local adaptation. We identified four genetic groups, with the western group located in Hengduan Mountains exhibited the highest genetic diversity. Redundancy analysis suggests that both environment and geographic variables shaped a significant proportion of genomic variation. Our analyses revealed that the environmental difference explains more of the observed genetic variation than geographic distance. This suggests that adaptation to distinct habitats, unique combination of abiotic factors, likely drove genetic differentiation. Lastly, by implementing selective sweeps scans and genome-environment association analysis throughout the genome, we identified the genetic variation associated with local adaptation and investigated the functions of putative candidate genes in F. nilgerrensis.
Collapse
Affiliation(s)
- Yuxi Hu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| |
Collapse
|
41
|
Liu S, Zhang L, Sang Y, Lai Q, Zhang X, Jia C, Long Z, Wu J, Ma T, Mao K, Street NR, Ingvarsson PK, Liu J, Wang J. Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome. Mol Biol Evol 2022; 39:6505222. [PMID: 35022759 PMCID: PMC8826634 DOI: 10.1093/molbev/msac008] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.
Collapse
Affiliation(s)
- Shuyu Liu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Lei Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Yupeng Sang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Qiang Lai
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Xinxin Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Changfu Jia
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Zhiqin Long
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Jiali Wu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Tao Ma
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Kangshan Mao
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Nathaniel R Street
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Pär K Ingvarsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jianquan Liu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| |
Collapse
|
42
|
Saleh D, Chen J, Leplé J, Leroy T, Truffaut L, Dencausse B, Lalanne C, Labadie K, Lesur I, Bert D, Lagane F, Morneau F, Aury J, Plomion C, Lascoux M, Kremer A. Genome-wide evolutionary response of European oaks during the Anthropocene. Evol Lett 2022; 6:4-20. [PMID: 35127134 PMCID: PMC8802238 DOI: 10.1002/evl3.269] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 12/23/2022] Open
Abstract
The pace of tree microevolution during Anthropocene warming is largely unknown. We used a retrospective approach to monitor genomic changes in oak trees since the Little Ice Age (LIA). Allelic frequency changes were assessed from whole-genome pooled sequences for four age-structured cohorts of sessile oak (Quercus petraea) dating back to 1680, in each of three different oak forests in France. The genetic covariances of allelic frequency changes increased between successive time periods, highlighting genome-wide effects of linked selection. We found imprints of parallel linked selection in the three forests during the late LIA, and a shift of selection during more recent time periods of the Anthropocene. The changes in allelic covariances within and between forests mirrored the documented changes in the occurrence of extreme events (droughts and frosts) over the last 300 years. The genomic regions with the highest covariances were enriched in genes involved in plant responses to pathogens and abiotic stresses (temperature and drought). These responses are consistent with the reported sequence of frost (or drought) and disease damage ultimately leading to the oak dieback after extreme events. They provide support for adaptive evolution of long-lived species during recent climatic changes. Although we acknowledge that other sources (e.g., gene flow, generation overlap) may have contributed to temporal covariances of allelic frequency changes, the consistent and correlated response across the three forests lends support to the existence of a systematic driving force such as natural selection.
Collapse
Affiliation(s)
- Dounia Saleh
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| | - Jun Chen
- College of Life SciencesZhejiang UniversityHangzhou310058China
| | | | - Thibault Leroy
- Department of Botany and Biodiversity ResearchUniversity of ViennaVienna1010Austria
| | - Laura Truffaut
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| | | | - Céline Lalanne
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| | - Karine Labadie
- Genoscope, Institut de Biologie François Jacob, Commissariat à l’énergie atomique (CEA)Université de Paris‐SaclayEvry91057France
| | | | - Didier Bert
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| | | | - François Morneau
- Département Recherche Développement InnovationOffice National des ForêtsBoigny‐Sur‐Bionne45760France,Current Address: Service de l'Information Statistique Forestière et EnvironnementaleInstitut National de l'Information géographique et ForestièreNogent‐sur‐Vernisson45290France
| | - Jean‐Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRSUniv Evry, Université Paris‐SaclayEvry91057France
| | | | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSE‐75236Sweden
| | - Antoine Kremer
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| |
Collapse
|
43
|
Liang YY, Shi Y, Yuan S, Zhou BF, Chen XY, An QQ, Ingvarsson PK, Plomion C, Wang B. Linked selection shapes the landscape of genomic variation in three oak species. THE NEW PHYTOLOGIST 2022; 233:555-568. [PMID: 34637540 DOI: 10.1111/nph.17793] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Natural selection shapes genome-wide patterns of diversity within species and divergence between species. However, quantifying the efficacy of selection and elucidating the relative importance of different types of selection in shaping genomic variation remain challenging. We sequenced whole genomes of 101 individuals of three closely related oak species to track the divergence history, and to dissect the impacts of selective sweeps and background selection on patterns of genomic variation. We estimated that the three species diverged around the late Neogene and experienced a bottleneck during the Pleistocene. We detected genomic regions with elevated relative differentiation ('FST -islands'). Population genetic inferences from the site frequency spectrum and ancestral recombination graph indicated that FST -islands were formed by selective sweeps. We also found extensive positive selection; the fixation of adaptive mutations and reduction neutral diversity around substitutions generated a signature of selective sweeps. Prevalent negative selection and background selection have reduced genetic diversity in both genic and intergenic regions, and contributed substantially to the baseline variation in genetic diversity. Our results demonstrate the importance of linked selection in shaping genomic variation, and illustrate how the extent and strength of different selection models vary across the genome.
Collapse
Affiliation(s)
- Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Shuai Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Qing-Qing An
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | | | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| |
Collapse
|
44
|
Larson DA, Vargas OM, Vicentini A, Dick CW. Admixture may be extensive among hyperdominant Amazon rainforest tree species. THE NEW PHYTOLOGIST 2021; 232:2520-2534. [PMID: 34389989 PMCID: PMC9292926 DOI: 10.1111/nph.17675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/04/2021] [Indexed: 05/25/2023]
Abstract
Admixture is a mechanism by which species of long-lived plants may acquire novel alleles. However, the potential role of admixture in the origin and maintenance of tropical plant diversity is unclear. We ask whether admixture occurs in an ecologically important clade of Eschweilera (Parvifolia clade, Lecythidaceae), which includes some of the most widespread and abundant tree species in Amazonian forests. Using target capture sequencing, we conducted a detailed phylogenomic investigation of 33 species in the Parvifolia clade and investigated specific hypotheses of admixture within a robust phylogenetic framework. We found strong evidence of admixture among three ecologically dominant species, E. coriacea, E. wachenheimii and E. parviflora, but a lack of evidence for admixture among other lineages. Accepted species were largely distinguishable from one another, as was geographic structure within species. We show that hybridization may play a role in the evolution of the most widespread and ecologically variable Amazonian tree species. While admixture occurs among some species of Eschweilera, it has not led to widespread erosion of most species' genetic or morphological identities. Therefore, current morphological based species circumscriptions appear to provide a useful characterization of the clade's lineage diversity.
Collapse
Affiliation(s)
- Drew A. Larson
- Department of Ecology & Evolutionary BiologyUniversity of MichiganAnn ArborMI48109USA
| | - Oscar M. Vargas
- Department of Biological SciencesHumboldt State UniversityArcataCA95521USA
| | - Alberto Vicentini
- Instituto Nacional de Pesquisas da Amazônia (INPA)ManausAMCEP 69067‐375Brazil
| | - Christopher W. Dick
- Department of Ecology & Evolutionary BiologyUniversity of MichiganAnn ArborMI48109USA
- Smithsonian Tropical Research InstitutePanama CityRepublic of Panama
| |
Collapse
|
45
|
Zheng W, Yan LJ, Burgess KS, Luo YH, Zou JY, Qin HT, Wang JH, Gao LM. Natural hybridization among three Rhododendron species (Ericaceae) revealed by morphological and genomic evidence. BMC PLANT BIOLOGY 2021; 21:529. [PMID: 34763662 PMCID: PMC8582147 DOI: 10.1186/s12870-021-03312-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 11/02/2021] [Indexed: 06/08/2023]
Abstract
BACKGROUND Natural hybridization can influence the adaptive response to selection and accelerate species diversification. Understanding the composition and structure of hybrid zones may elucidate patterns of hybridization processes that are important to the formation and maintenance of species, especially for taxa that have experienced rapidly adaptive radiation. Here, we used morphological traits, ddRAD-seq and plastid DNA sequence data to investigate the structure of a Rhododendron hybrid zone and uncover the hybridization patterns among three sympatric and closely related species. RESULTS Our results show that the hybrid zone is complex, where bi-directional hybridization takes place among the three sympatric parental species: R. spinuliferum, R. scabrifolium, and R. spiciferum. Hybrids between R. spinuliferum and R. spiciferum (R. ×duclouxii) comprise multiple hybrid classes and a high proportion of F1 generation hybrids, while a novel hybrid taxon between R. spinuliferum and R. scabrifolium dominated the F2 generation, but no backcross individuals were detected. The hybrid zone showed basically coincident patterns of population structure between genomic and morphological data. CONCLUSIONS Natural hybridization exists among the three Rhododendron species in the hybrid zone, although patterns of hybrid formation vary between hybrid taxa, which may result in different evolutionary outcomes. This study represents a unique opportunity to dissect the ecological and evolutionary mechanisms associated with adaptive radiation of Rhododendron species in a biodiversity hotspot.
Collapse
Affiliation(s)
- Wei Zheng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Li-Jun Yan
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
- College of Vocational and Technical Education, Yunnan Normal University, 650092, Kunming, Yunnan, China
| | - Kevin S Burgess
- Department of Biology, Columbus State University, University System of Georgia, 31907-5645, Columbus, GA, USA
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Jia-Yun Zou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Han-Tao Qin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Ji-Hua Wang
- The Flower Research Institute, Yunnan Academy of Agricultural Sciences, 650205, Kunming, China.
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China.
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, 674100, Lijiang, Yunnan, China.
| |
Collapse
|
46
|
Sun Y, Guo J, Zeng X, Chen R, Feng Y, Chen S, Yang K. Chromosome-scale genome assembly of Castanopsis tibetana provides a powerful comparative framework to study the evolution and adaptation of Fagaceae trees. Mol Ecol Resour 2021; 22:1178-1189. [PMID: 34689424 DOI: 10.1111/1755-0998.13539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/27/2022]
Abstract
Fagaceae species are increasingly used as models to elucidate the process and mechanism of adaptation and speciation by integrating ecology, evolution and genomics. The genus Castanopsis belongs to the family Fagaceae and is mainly distributed across subtropical and tropical Asia. In the present study, we reported the first chromosome-scale genome assembly of Castanopsis tibetana, a common species of evergreen broadleaved forests in subtropical China. The combination of Nanopore sequencing and Hi-C technologies enabled a high-quality genome assembly. The final assembled genome size of C. tibetana was 878.6 Mb (97.6% of the estimated genome size), consisting of 477 contigs with an N50 length of 3.3 Mb. The benchmarking universal single-copy orthologue (BUSCO) assessment indicated a completeness of 93.0%. Hi-C scaffolding generated 12 pseudochromosomes, representing 98.7% of the assembled genome. Subsequently, 40,937 protein-coding genes were predicted and 90.04% of them were functionally annotated. More than 476.9 Mb of repetitive sequences (54.3% of the genome) were identified, and the percentage of the genome covered by TE elements was 39.98%. Comparative genomics analysis revealed that C. tibetana was most closely related to Castanea mollissima and diverged at 18.48 Ma, and that C. tibetana has undergone considerable gene family expansion and contraction. Evidence of positive selection was detected in 53 genes, which showed different arrangement pattern compared to Quercus robur. The chromosome-scale genome assembly of C. tibetana will expand Fagaceae genome resources across the family and provide a powerful comparative framework to study the adaptation and evolution of Fagaceae trees.
Collapse
Affiliation(s)
- Ye Sun
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Jianling Guo
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xiaorong Zeng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Risheng Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yi Feng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Shuang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Kai Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| |
Collapse
|
47
|
Impact of Gene Flow and Introgression on the Range Wide Genetic Structure of Quercus robur (L.) in Europe. FORESTS 2021. [DOI: 10.3390/f12101425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As for most other temperate broadleaved tree species, large-scale genetic inventories of pedunculate oak (Quercus robur L.) have focused on the plastidial genome, which showed the impact of post-glacial recolonization and manmade seed transfer. However, how have pollen mediated gene flow and introgression impacted the large-scale genetic structure? To answer these questions, we did a genetic inventory on 1970 pedunculate oak trees from 197 locations in 13 European countries. All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs, and 5 mitochondrial SNPs). In a former analysis with additional 1763 putative Quercus petraea trees screened for the same gene markers we obtained estimates on the species admixture of all pedunculate oak trees. We identified 13 plastidial haplotypes, which showed a strong spatial pattern with a highly significant autocorrelation up to a range of 1250 km. Significant spatial genetic structure up to 1250 km was also observed at the nuclear loci. However, the differentiation at the nuclear gene markers was much lower compared to the organelle gene markers. The matrix of genetic distances among locations was partially correlated between nuclear and organelle genomes. Bayesian clustering analysis revealed the best fit to the data for a sub-division into two gene pools. One gene pool is dominating the west and the other is the most abundant in the east. The western gene pool was significantly influenced by introgression from Quercus petraea in the past. In Germany, we identified a contact zone of pedunculate oaks with different introgression intensity, likely resulting from different historical levels of introgression in glacial refugia or during postglacial recolonization. The main directions of postglacial recolonization were south to north and south to northwest in West and Central Europe, and for the eastern haplotypes also east to west in Central Europe. By contrast, the pollen mediated gene flow and introgression from Q. petraea modified the large-scale structure at the nuclear gene markers with significant west–east direction.
Collapse
|
48
|
Morales-Cruz A, Aguirre-Liguori JA, Zhou Y, Minio A, Riaz S, Walker AM, Cantu D, Gaut BS. Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation. Genome Biol 2021; 22:254. [PMID: 34479604 PMCID: PMC8414701 DOI: 10.1186/s13059-021-02467-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/12/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgression, we investigate six wild Vitis species that are native to the Southwestern United States and useful for breeding grapevine (V. vinifera) rootstocks. RESULTS By creating a reference genome assembly from one wild species, V. arizonica, and by resequencing 130 accessions, we focus on identifying putatively introgressed regions (pIRs) between species. We find six species pairs with signals of introgression between them, comprising up to ~ 8% of the extant genome for some pairs. The pIRs tend to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explore SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierce's disease (Xylella fastidiosa). pIRs are enriched for SNPs associated with both climate and bacterial levels, suggesting that introgression is driven by adaptation to biotic and abiotic stressors. CONCLUSIONS Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the evolutionary history of economically important wild relatives of a critical crop.
Collapse
Affiliation(s)
- Abraham Morales-Cruz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
| | | | - Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Andrew M. Walker
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
| |
Collapse
|
49
|
Pazhenkova EA, Lukhtanov VA. Genomic introgression from a distant congener in the Levant fritillary butterfly, Melitaea acentria. Mol Ecol 2021; 30:4819-4832. [PMID: 34288183 DOI: 10.1111/mec.16085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
Abstract
Introgressive hybridization is more common in nature than previously thought, and its role and creative power in evolution is hotly discussed but not completely understood. Introgression occurs more frequently in sympatry between recently diverged taxa, or when the speciation process has not yet been completed. However, there are relatively few documented cases of hybridization that erodes reproductive barriers between distantly related species. Here, we use whole genome and mitochondrial data to examine how introgression from a distant congener affects pattern of genetic differentiation in the Levant fritillary butterfly Melitaea acentria. We show that this local taxon has evolved as a peripatric geographic isolate of the widespread Melitaea persea, and that there has been significant unidirectional gene flow from the sympatric, nonclosely related Melitaea didyma to M. acentria. We found direct evidence of ongoing sporadic hybridization between M. didyma and M. acentria, which are separated by at least 5 million years of independent evolution. Elevated differentiation and lower level of introgression on the sex Z chromosome compared to autosomes suggest that the Z chromosome has accumulated loci acting as intrinsic postzygotic barriers. Our results show that introgression from M. didyma has been an additional source of nucleotide diversity in the M. acentria population, providing material for drift and selection.
Collapse
Affiliation(s)
- Elena A Pazhenkova
- Department of Entomology, St. Petersburg State University, St. Petersburg, Russia.,Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
| |
Collapse
|
50
|
Ahmad M, Leroy T, Krigas N, Temsch EM, Weiss-Schneeweiss H, Lexer C, Sehr EM, Paun O. Spatial and Ecological Drivers of Genetic Structure in Greek Populations of Alkanna tinctoria (Boraginaceae), a Polyploid Medicinal Herb. FRONTIERS IN PLANT SCIENCE 2021; 12:706574. [PMID: 34335669 PMCID: PMC8317432 DOI: 10.3389/fpls.2021.706574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/16/2021] [Indexed: 06/08/2023]
Abstract
Background and Aims: Quantifying genetic variation is fundamental to understand a species' demographic trajectory and its ability to adapt to future changes. In comparison with diploids, however, genetic variation and factors fostering genetic divergence remain poorly studied in polyploids due to analytical challenges. Here, by employing a ploidy-aware framework, we investigated the genetic structure and its determinants in polyploid Alkanna tinctoria (Boraginaceae), an ancient medicinal herb that is the source of bioactive compounds known as alkannin and shikonin (A/S). From a practical perspective, such investigation can inform biodiversity management strategies. Methods: We collected 14 populations of A. tinctoria within its main distribution range in Greece and genotyped them using restriction site-associated DNA sequencing. In addition, we included two populations of A. sieberi. By using a ploidy-aware genotype calling based on likelihoods, we generated a dataset of 16,107 high-quality SNPs. Classical and model-based analysis was done to characterize the genetic structure within and between the sampled populations, complemented by genome size measurements and chromosomal counts. Finally, to reveal the drivers of genetic structure, we searched for associations between allele frequencies and spatial and climatic variables. Key Results: We found support for a marked regional structure in A. tinctoria along a latitudinal gradient in line with phytogeographic divisions. Several analyses identified interspecific admixture affecting both mainland and island populations. Modeling of spatial and climatic variables further demonstrated a larger contribution of neutral processes and a lesser albeit significant role of selection in shaping the observed genetic structure in A. tinctoria. Conclusion: Current findings provide evidence of strong genetic structure in A. tinctoria mainly driven by neutral processes. The revealed natural genomic variation in Greek Alkanna can be used to further predict variation in A/S production, whereas our bioinformatics approach should prove useful for the study of other non-model polyploid species.
Collapse
Affiliation(s)
- Muhammad Ahmad
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Thibault Leroy
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Nikos Krigas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, Thessaloniki, Greece
| | - Eva M. Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Eva Maria Sehr
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| |
Collapse
|