1
|
Woźniak NJ, Sartori K, Kappel C, Tran TC, Zhao L, Erban A, Gallinger J, Fehrle I, Jantzen F, Orsucci M, Ninkovic V, Rosa S, Lenhard M, Kopka J, Sicard A. Convergence and molecular evolution of floral fragrance after independent transitions to self-fertilization. Curr Biol 2024; 34:2702-2711.e6. [PMID: 38776901 DOI: 10.1016/j.cub.2024.04.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/26/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Studying the independent evolution of similar traits provides valuable insights into the ecological and genetic factors driving phenotypic evolution.1 The transition from outcrossing to self-fertilization is common in plant evolution2 and is often associated with a reduction in floral attractive features such as display size, chemical signals, and pollinator rewards.3 These changes are believed to result from the reallocation of the resources used for building attractive flowers, as the need to attract pollinators decreases.2,3 We investigated the similarities in the evolution of flower fragrance following independent transitions to self-fertilization in Capsella.4,5,6,7,8,9 We identified several compounds that exhibited similar changes in different selfer lineages, such that the flower scent composition reflects mating systems rather than evolutionary history within this genus. We further demonstrate that the repeated loss of β-ocimene emission, one of the compounds most strongly affected by these transitions, was caused by mutations in different genes. In one of the Capsella selfing lineages, the loss of its emission was associated with a mutation altering subcellular localization of the ortholog of TERPENE SYNTHASE 2. This mutation appears to have been fixed early after the transition to selfing through the capture of variants segregating in the ancestral outcrossing population. The large extent of convergence in the independent evolution of flower scent, together with the evolutionary history and molecular consequences of a causal mutation, suggests that the emission of specific volatiles evolved as a response to changes in ecological pressures rather than resource limitation.
Collapse
Affiliation(s)
- Natalia Joanna Woźniak
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Kevin Sartori
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, 75007 Uppsala, Sweden
| | - Christian Kappel
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Thi Chi Tran
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Lihua Zhao
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, 75007 Uppsala, Sweden
| | - Alexander Erban
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Jannicke Gallinger
- Department of Ecology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Ines Fehrle
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Friederike Jantzen
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Marion Orsucci
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, 75007 Uppsala, Sweden
| | - Velemir Ninkovic
- Department of Ecology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Stefanie Rosa
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, 75007 Uppsala, Sweden
| | - Michael Lenhard
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Joachim Kopka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Adrien Sicard
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, 75007 Uppsala, Sweden.
| |
Collapse
|
2
|
Liu B, Li M, Qiu J, Xue J, Liu W, Cheng Q, Zhao H, Xue Y, Nasrallah ME, Nasrallah JB, Liu P. A pollen selection system links self and interspecific incompatibility in the Brassicaceae. Nat Ecol Evol 2024; 8:1129-1139. [PMID: 38637692 DOI: 10.1038/s41559-024-02399-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 03/19/2024] [Indexed: 04/20/2024]
Abstract
Self-incompatibility and recurrent transitions to self-compatibility have shaped the extant mating systems underlying the nonrandom mating critical for speciation in angiosperms. Linkage between self-incompatibility and speciation is illustrated by the shared pollen rejection pathway between self-incompatibility and interspecific unilateral incompatibility (UI) in the Brassicaceae. However, the pollen discrimination system that activates this shared pathway for heterospecific pollen rejection remains unknown. Here we show that Stigma UI3.1, the genetically identified stigma determinant of UI in Arabidopsis lyrata × Arabidopsis arenosa crosses, encodes the S-locus-related glycoprotein 1 (SLR1). Heterologous expression of A. lyrata or Capsella grandiflora SLR1 confers on some Arabidopsis thaliana accessions the ability to discriminate against heterospecific pollen. Acquisition of this ability also requires a functional S-locus receptor kinase (SRK), whose ligand-induced dimerization activates the self-pollen rejection pathway in the stigma. SLR1 interacts with SRK and interferes with SRK homomer formation. We propose a pollen discrimination system based on competition between basal or ligand-induced SLR1-SRK and SRK-SRK complex formation. The resulting SRK homomer levels would be sensed by the common pollen rejection pathway, allowing discrimination among conspecific self- and cross-pollen as well as heterospecific pollen. Our results establish a mechanistic link at the pollen recognition phase between self-incompatibility and interspecific incompatibility.
Collapse
Affiliation(s)
- Bo Liu
- State Key Laboratory of Nutrient Use and Management, Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Mengya Li
- State Key Laboratory of Nutrient Use and Management, Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Jianfang Qiu
- State Key Laboratory of Nutrient Use and Management, Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Jing Xue
- State Key Laboratory of Nutrient Use and Management, Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Wenhong Liu
- State Key Laboratory of Nutrient Use and Management, Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Qingqing Cheng
- State Key Laboratory of Nutrient Use and Management, Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Hainan Zhao
- State Key Laboratory of Nutrient Use and Management, Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Yongbiao Xue
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mikhail E Nasrallah
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - June B Nasrallah
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Pei Liu
- State Key Laboratory of Nutrient Use and Management, Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.
| |
Collapse
|
3
|
Zeng ZH, Zhong L, Sun HY, Wu ZK, Wang X, Wang H, Li DZ, Barrett SCH, Zhou W. Parallel evolution of morphological and genomic selfing syndromes accompany the breakdown of heterostyly. THE NEW PHYTOLOGIST 2024; 242:302-316. [PMID: 38214455 DOI: 10.1111/nph.19522] [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: 11/07/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024]
Abstract
Evolutionary transitions from outcrossing to selfing in flowering plants have convergent morphological and genomic signatures and can involve parallel evolution within related lineages. Adaptive evolution of morphological traits is often assumed to evolve faster than nonadaptive features of the genomic selfing syndrome. We investigated phenotypic and genomic changes associated with transitions from distyly to homostyly in the Primula oreodoxa complex. We determined whether the transition to selfing occurred more than once and investigated stages in the evolution of morphological and genomic selfing syndromes using 22 floral traits and both nuclear and plastid genomic data from 25 populations. Two independent transitions were detected representing an earlier and a more recently derived selfing lineage. The older lineage exhibited classic features of the morphological and genomic selfing syndrome. Although features of both selfing syndromes were less developed in the younger selfing lineage, they exhibited parallel development with the older selfing lineage. This finding contrasts with the prediction that some genomic changes should lag behind adaptive changes to morphological traits. Our findings highlight the value of comparative studies on the timing and extent of transitions from outcrossing to selfing between related lineages for investigating the tempo of morphological and molecular evolution.
Collapse
Affiliation(s)
- Zhi-Hua Zeng
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhong
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hua-Ying Sun
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, China
| | - Zhi-Kun Wu
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550002, China
| | - Xin Wang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Wei Zhou
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, 674100, China
| |
Collapse
|
4
|
Dew-Budd KJ, Chow HT, Kendall T, David BC, Rozelle JA, Mosher RA, Beilstein MA. Mating system is associated with seed phenotypes upon loss of RNA-directed DNA methylation in Brassicaceae. PLANT PHYSIOLOGY 2024; 194:2136-2148. [PMID: 37987565 DOI: 10.1093/plphys/kiad622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/03/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023]
Abstract
In plants, de novo DNA methylation is guided by 24-nt short interfering (si)RNAs in a process called RNA-directed DNA methylation (RdDM). Primarily targeted at transposons, RdDM causes transcriptional silencing and can indirectly influence expression of neighboring genes. During reproduction, a small number of siRNA loci are dramatically upregulated in the maternally derived seed coat, suggesting that RdDM might have a special function during reproduction. However, the developmental consequence of RdDM has been difficult to dissect because disruption of RdDM does not result in overt phenotypes in Arabidopsis (Arabidopsis thaliana), where the pathway has been most thoroughly studied. In contrast, Brassica rapa mutants lacking RdDM have a severe seed production defect, which is determined by the maternal sporophytic genotype. To explore the factors that underlie the different phenotypes of these species, we produced RdDM mutations in 3 additional members of the Brassicaceae family: Camelina sativa, Capsella rubella, and Capsella grandiflora. Among these 3 species, only mutations in the obligate outcrosser, C. grandiflora, displayed a seed production defect similar to Brassica rapa mutants, suggesting that mating system is a key determinant for reproductive phenotypes in RdDM mutants.
Collapse
Affiliation(s)
- Kelly J Dew-Budd
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Hiu Tung Chow
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Timmy Kendall
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Brandon C David
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - James A Rozelle
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Rebecca A Mosher
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Mark A Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| |
Collapse
|
5
|
Jiang J, Xu YC, Zhang ZQ, Chen JF, Niu XM, Hou XH, Li XT, Wang L, Zhang YE, Ge S, Guo YL. Forces driving transposable element load variation during Arabidopsis range expansion. THE PLANT CELL 2024; 36:840-862. [PMID: 38036296 PMCID: PMC10980350 DOI: 10.1093/plcell/koad296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/25/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Genetic load refers to the accumulated and potentially life-threatening deleterious mutations in populations. Understanding the mechanisms underlying genetic load variation of transposable element (TE) insertion, a major large-effect mutation, during range expansion is an intriguing question in biology. Here, we used 1,115 global natural accessions of Arabidopsis (Arabidopsis thaliana) to study the driving forces of TE load variation during its range expansion. TE load increased with range expansion, especially in the recently established Yangtze River basin population. Effective population size, which explains 62.0% of the variance in TE load, high transposition rate, and selective sweeps contributed to TE accumulation in the expanded populations. We genetically mapped and identified multiple candidate causal genes and TEs, and revealed the genetic architecture of TE load variation. Overall, this study reveals the variation in TE genetic load during Arabidopsis expansion and highlights the causes of TE load variation from the perspectives of both population genetics and quantitative genetics.
Collapse
Affiliation(s)
- Juan Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Zhi-Qin Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Fu Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Min Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xing-Hui Hou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xin-Tong Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wang
- Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yong E Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
6
|
Wang X, Ingvarsson PK. Quantifying adaptive evolution and the effects of natural selection across the Norway spruce genome. Mol Ecol 2023; 32:5288-5304. [PMID: 37622583 DOI: 10.1111/mec.17106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Detecting natural selection is one of the major goals of evolutionary genomics. Here, we sequenced the whole genome of 25 Picea abies individuals and quantified the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we showed that both negative selection and the rate of positively selected substitutions are very limited in coding regions. We found a positive correlation between the rate of adaptive substitutions and recombination rate and a negative correlation between the rate of adaptive substitutions and gene density, suggesting a widespread influence from Hill-Robertson interference on the efficiency of protein adaptation in P. abies. Finally, the distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicated the impact of natural selection on the genomic architecture of Norway spruce. Further gene ontology enrichment analysis for genes located in regions identified as undergoing either positive or long-term balancing selection also highlighted the specific molecular functions and biological processes that appear to be targets of selection in Norway spruce.
Collapse
Affiliation(s)
- Xi Wang
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
7
|
Nasrallah JB. Stop and go signals at the stigma-pollen interface of the Brassicaceae. PLANT PHYSIOLOGY 2023; 193:927-948. [PMID: 37423711 PMCID: PMC10517188 DOI: 10.1093/plphys/kiad301] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/16/2023] [Indexed: 07/11/2023]
Affiliation(s)
- June B Nasrallah
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
8
|
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
|
9
|
Zhang W, Hu Y, Zhang S, Shao J. Integrative taxonomy in a rapid speciation group associated with mating system transition: A case study in the Primula cicutariifolia complex. Mol Phylogenet Evol 2023:107840. [PMID: 37279815 DOI: 10.1016/j.ympev.2023.107840] [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: 02/17/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/08/2023]
Abstract
Accurate species delimitation is the key to biodiversity conservation and is fundamental to most branches of biology. However, species delimitation remains challenging in those evolutionary radiations associated with mating system transition from outcrossing to self-fertilization, which have frequently occurred in angiosperms and are usually accompanied by rapid speciation. Here, using the Primula cicutariifolia complex as a case, we integrated molecular, morphological and reproductive isolation evidence to test and verify whether its outcrossing (distylous) and selfing (homostylous) populations have developed into independent evolutionary lineages. Phylogenetic trees based on whole plastomes and SNPs of the nuclear genome both indicated that the distylous and homostylous populations grouped into two different clades. Multispecies coalescent, gene flow and genetic structure analyses all supported such two clades as two different genetic entities. In morphology, as expected changes in selfing syndrome, homostylous populations have significantly fewer umbel layers and smaller flower and leaf sizes compared to distylous populations, and the variation range of some floral traits, such as corolla diameter and umbel layers, show obvious discontinuity. Furthermore, hand-pollinated hybridization between the two clades produced almost no seeds, indicating that well post-pollination reproductive isolation has been established between them. Therefore, the distylous and homostylous populations in this studied complex are two independent evolutionary lineages, and thus these distylous populations should be treated as a distinct species, here named Primula qiandaoensis W. Zhang & J.W. Shao sp. nov.. Our empirical study of the P. cicutariifolia complex highlights the importance of applying multiple lines of evidence, in particular genomic data, to delimit species in pervasive evolutionary plant radiations associated with mating system transition.
Collapse
Affiliation(s)
- Wei Zhang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China; College of Life Sciences, Anqing Normal University, Anqing 246011, Anhui, China
| | - Yingfeng Hu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Siyu Zhang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Jianwen Shao
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China; Provincial Key Laboratory of Conservation and Utilization of Biological Resources, Wuhu 241000, Anhui, China.
| |
Collapse
|
10
|
Zhang X, Comes HP, Qiu Y. Did Late Quaternary climate change trigger shifts in mating system in temperate plant species of the Sino-Japanese Floristic Region? A commentary on 'Genetic and demographic signatures accompanying the evolution of the selfing syndrome in Daphne kiusiana, an evergreen shrub'. ANNALS OF BOTANY 2023; 131:iii-v. [PMID: 36869730 PMCID: PMC10184437 DOI: 10.1093/aob/mcad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
This article comments on:
Eun-Kyeong Han, Ichiro Tamaki, Sang-Hun Oh, Jong-Soo Park, Won-Bum Cho, Dong-Pil Jin, Bo-Yun Kim, Sungyu Yang, Dong Chan Son, Hyeok-Jae Choi, Amarsanaa Gantsetseg, Yuji Isagi, and Jung-Hyun Lee. Genetic and demographic signatures accompanying the evolution of the selfing syndrome in Daphne kiusiana, an evergreen shrub, Annals of Botany, Volume 131, Issue 5, 11 April 2023, Pages 751–767, https://doi.org/10.1093/aob/mcac142
Collapse
Affiliation(s)
- Xinyi Zhang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Systematic & Evolutionary Botany and Biodiversity Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hans Peter Comes
- Department of Environment & Biodiversity, Salzburg University, Salzburg, Austria
| | - Yingxiong Qiu
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| |
Collapse
|
11
|
Han EK, Tamaki I, Oh SH, Park JS, Cho WB, Jin DP, Kim BY, Yang S, Son DC, Choi HJ, Gantsetseg A, Isagi Y, Lee JH. Genetic and demographic signatures accompanying the evolution of the selfing syndrome in Daphne kiusiana, an evergreen shrub. ANNALS OF BOTANY 2023; 131:751-767. [PMID: 36469429 PMCID: PMC10184445 DOI: 10.1093/aob/mcac142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/23/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS The evolution of mating systems from outcrossing to self-fertilization is a common transition in flowering plants. This shift is often associated with the 'selfing syndrome', which is characterized by less visible flowers with functional changes to control outcrossing. In most cases, the evolutionary history and demographic dynamics underlying the evolution of the selfing syndrome remain poorly understood. METHODS Here, we characterize differences in the demographic genetic consequences and associated floral-specific traits between two distinct geographical groups of a wild shrub, Daphne kiusiana, endemic to East Asia; plants in the eastern region (southeastern Korea and Kyushu, Japan) exhibit smaller and fewer flowers compared to those of plants in the western region (southwestern Korea). Genetic analyses were conducted using nuclear microsatellites and chloroplast DNA (multiplexed phylogenetic marker sequencing) datasets. KEY RESULTS A high selfing rate with significantly increased homozygosity characterized the eastern lineage, associated with lower levels of visibility and herkogamy in the floral traits. The two lineages harboured independent phylogeographical histories. In contrast to the western lineage, the eastern lineage showed a gradual reduction in the effective population size with no signs of a severe bottleneck despite its extreme range contraction during the last glacial period. CONCLUSIONS Our results suggest that the selfing-associated morphological changes in D. kiusiana are of relatively old origin (at least 100 000 years ago) and were driven by directional selection for efficient self-pollination. We provide evidence that the evolution of the selfing syndrome in D. kiusiana is not strongly associated with a severe population bottleneck.
Collapse
Affiliation(s)
- Eun-Kyeong Han
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu 501-3714, Japan
| | - Sang-Hun Oh
- Department of Biology, Daejeon University, Daejeon 34520, Republic of Korea
| | - Jong-Soo Park
- Department of Botany, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea
| | - Won-Bum Cho
- Department of Plant Variety Protection, National Forest Seed and Variety Center, Chungju 27495, Republic of Korea
| | - Dong-Pil Jin
- Urban Biodiversity Research Division, Sejong National Arboretum, Sejong 30106, Republic of Korea
| | - Bo-Yun Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Sungyu Yang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon 11186, Republic of Korea
| | - Hyeok-Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Republic of Korea
| | - Amarsanaa Gantsetseg
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yuji Isagi
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Jung-Hyun Lee
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
| |
Collapse
|
12
|
Farhat P, Mandáková T, Divíšek J, Kudoh H, German DA, Lysak MA. The evolution of the hypotetraploid Catolobus pendulus genome - the poorly known sister species of Capsella. FRONTIERS IN PLANT SCIENCE 2023; 14:1165140. [PMID: 37223809 PMCID: PMC10200890 DOI: 10.3389/fpls.2023.1165140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/04/2023] [Indexed: 05/25/2023]
Abstract
The establishment of Arabidopsis as the most important plant model has also brought other crucifer species into the spotlight of comparative research. While the genus Capsella has become a prominent crucifer model system, its closest relative has been overlooked. The unispecific genus Catolobus is native to temperate Eurasian woodlands, from eastern Europe to the Russian Far East. Here, we analyzed chromosome number, genome structure, intraspecific genetic variation, and habitat suitability of Catolobus pendulus throughout its range. Unexpectedly, all analyzed populations were hypotetraploid (2n = 30, ~330 Mb). Comparative cytogenomic analysis revealed that the Catolobus genome arose by a whole-genome duplication in a diploid genome resembling Ancestral Crucifer Karyotype (ACK, n = 8). In contrast to the much younger Capsella allotetraploid genomes, the presumably autotetraploid Catolobus genome (2n = 32) arose early after the Catolobus/Capsella divergence. Since its origin, the tetraploid Catolobus genome has undergone chromosomal rediploidization, including a reduction in chromosome number from 2n = 32 to 2n = 30. Diploidization occurred through end-to-end chromosome fusion and other chromosomal rearrangements affecting a total of six of 16 ancestral chromosomes. The hypotetraploid Catolobus cytotype expanded toward its present range, accompanied by some longitudinal genetic differentiation. The sister relationship between Catolobus and Capsella allows comparative studies of tetraploid genomes of contrasting ages and different degrees of genome diploidization.
Collapse
Affiliation(s)
- Perla Farhat
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Divíšek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Dmitry A. German
- South-Siberian Botanical Garden, Altai State University, Barnaul, Russia
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czechia
| |
Collapse
|
13
|
Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales). Int J Mol Sci 2023; 24:ijms24021451. [PMID: 36674965 PMCID: PMC9866071 DOI: 10.3390/ijms24021451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Asexual lineages are perceived to be short-lived on evolutionary timescales. Hence, reports for exceptional cases of putative 'ancient asexuals' usually raise questions about the persistence of such species. So far, there have been few studies to solve the mystery in plants. The monotypic Kingdonia dating to the early Eocene, contains only K. uniflora that has no known definitive evidence for sexual reproduction nor records for having congeneric sexual species, raising the possibility that the species has persisted under strict asexuality for a long period of time. Here, we analyze whole genome polymorphism and divergence in K. uniflora. Our results show that K. uniflora is characterized by high allelic heterozygosity and elevated πN/πS ratio, in line with theoretical expectations under asexual evolution. Allele frequency spectrum analysis reveals the origin of asexuality in K. uniflora occurred prior to lineage differentiation of the species. Although divergence within K. uniflora individuals exceeds that between populations, the topologies of the two haplotype trees, however, fail to match each other, indicating long-term asexuality is unlikely to account for the high allele divergence and K. uniflora may have a recent hybrid origin. Phi-test shows a statistical probability of recombination for the conflicting phylogenetic signals revealed by the split network, suggesting K. uniflora engages in undetected sexual reproduction. Detection of elevated genetic differentiation and premature stop codons (in some populations) in genes regulating seed development indicates mutational degradation of sexuality-specific genes in K. uniflora. This study unfolds the origin and persistence mechanism of a plant lineage that has been known to reproduce asexually and presents the genomic consequences of lack of sexuality.
Collapse
|
14
|
Suetsugu K, Fukushima K, Makino T, Ikematsu S, Sakamoto T, Kimura S. Transcriptomic heterochrony and completely cleistogamous flower development in the mycoheterotrophic orchid Gastrodia. THE NEW PHYTOLOGIST 2023; 237:323-338. [PMID: 36110047 DOI: 10.1111/nph.18495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
Cleistogamy, in which plants can reproduce via self-fertilization within permanently closed flowers, has evolved in > 30 angiosperm lineages; however, consistent with Darwin's doubts about its existence, complete cleistogamy - the production of only cleistogamous flowers - has rarely been recognized. Thus far, the achlorophyllous orchid genus, Gastrodia, is the only known genus with several plausible completely cleistogamous species. Here, we analyzed the floral developmental transcriptomes of two recently evolved, completely cleistogamous Gastrodia species and their chasmogamous sister species to elucidate the possible changes involved in producing common cleistogamous traits. The ABBA-BABA test did not support introgression and protein sequence convergence as evolutionary mechanisms leading to cleistogamy, leaving convergence in gene expression as a plausible mechanism. Regarding transcriptomic differentiation, the two cleistogamous species had common modifications in the expression of developmental regulators, exhibiting a gene family-wide signature of convergent expression changes in MADS-box genes. Our transcriptomic pseudotime analysis revealed a prolonged juvenile state and eventual maturation, a heterochronic pattern consistent with partial neoteny, in cleistogamous flower development. These findings indicate that transcriptomic partial neoteny, arising from changes in the expression of conserved developmental regulators, might have contributed to the rapid and repeated evolution of cleistogamous flowers in Gastrodia.
Collapse
Affiliation(s)
- Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, 97082, Würzburg, Germany
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, 6-3, Aramaki Aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Shuka Ikematsu
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Tomoaki Sakamoto
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| |
Collapse
|
15
|
Yi H, Wang J, Wang J, Rausher M, Kang M. Genomic insights into inter- and intraspecific mating system shifts in Primulina. Mol Ecol 2022; 31:5699-5713. [PMID: 36178058 DOI: 10.1111/mec.16706] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 08/17/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
The mating system shift from outcrossing to selfing is one of the most frequent evolutionary trends in flowering plants. However, the genomic consequences of this shift remain poorly understood. Specifically, the relative importance of the demographic and genetic processes causing changes in genetic variation and selection efficacy associated with the evolution of selfing is unclear. Here we sequenced the genomes of two Primulina species with contrasting mating systems: P. eburnea (outcrossing) versus P. tabacum (outcrossing, mixed-mating and selfing populations). Whole-genome resequencing data were used to investigate the genomic consequences of mating system shifts within and between species. We found that highly selfing populations of P. tabacum display loss of genetic diversity, increased deleterious mutations, higher genomic burden and fewer adaptive substitutions. However, compared with outcrossing populations, mixed-mating populations did not display loss of genetic diversity and accumulation of genetic load. We find no evidence of population bottlenecks associated with the shift to selfing, which suggests that the genetic effects of selfing on Ne and possibly linked selection, rather than demographic history, are the primary drivers of diversity reduction in highly selfing populations. Our results highlight the importance of distinguishing the relative contribution of mating system and demography on the genomic consequences associated with mating system evolution in plants.
Collapse
Affiliation(s)
- Huiqin Yi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jieyu Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Mark Rausher
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Ming Kang
- 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
|
16
|
Sardos J, Breton C, Perrier X, Van den Houwe I, Carpentier S, Paofa J, Rouard M, Roux N. Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas. FRONTIERS IN PLANT SCIENCE 2022; 13:969220. [PMID: 36275535 PMCID: PMC9586208 DOI: 10.3389/fpls.2022.969220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/05/2022] [Indexed: 06/08/2023]
Abstract
Hybridization and introgressions are important evolutionary forces in plants. They contribute to the domestication of many species, including understudied clonal crops. Here, we examine their role in the domestication of a clonal crop of outmost importance, banana (Musa ssp.). We used genome-wide SNPs generated for 154 diploid banana cultivars and 68 samples of the wild M. acuminata to estimate and geo-localize the contribution of the different subspecies of M. acuminata to cultivated banana. We further investigated the wild to domesticate transition in New Guinea, an important domestication center. We found high levels of admixture in many cultivars and confirmed the existence of unknown wild ancestors with unequal contributions to cultivated diploid. In New Guinea, cultivated accessions exhibited higher diversity than their direct wild ancestor, the latter recovering from a bottleneck. Introgressions, balancing selection and positive selection were identified as important mechanisms for banana domestication. Our results shed new lights on the radiation of M. acuminata subspecies and on how they shaped banana domestication. They point candidate regions of origin for two unknown ancestors and suggest another contributor in New Guinea. This work feed research on the evolution of clonal crops and has direct implications for conservation, collection, and breeding.
Collapse
Affiliation(s)
- Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Catherine Breton
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Xavier Perrier
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Janet Paofa
- Papua New Guinea (PNG) National Agricultural Research Institute, Southern Regional Centre, Laloki, Port Moresby, Papua New Guinea
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| |
Collapse
|
17
|
Almeida SC, Neiva J, Sousa F, Martins N, Cox CJ, Melo-Ferreira J, Guiry MD, Serrão EA, Pearson GA. A low-latitude species pump: Peripheral isolation, parapatric speciation and mating-system evolution converge in a marine radiation. Mol Ecol 2022; 31:4797-4817. [PMID: 35869812 DOI: 10.1111/mec.16623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 11/27/2022]
Abstract
Geologically recent radiations can shed light on speciation processes, but incomplete lineage sorting and introgressive gene flow render accurate evolutionary reconstruction and interpretation challenging. Independently evolving metapopulations of low dispersal taxa may provide an additional level of phylogeographic information, given sufficiently broad sampling and genome-wide sequencing. Evolution in the marine brown algal genus Fucus in the south-eastern North Atlantic was shaped by Quaternary climate-driven range shifts. Over this timescale, divergence and speciation occurred against a background of expansion-contraction cycles from multiple refugia, together with mating-system shifts from outcrossing (dioecy) to selfing hermaphroditism. We tested the hypothesis that peripheral isolation of range edge (dioecious) F. vesiculosus led to parapatric speciation and radiation of hermaphrodite lineages. Species tree methods using 876 single-copy nuclear genes and extensive geographic coverage produced conflicting topologies with respect to geographic clades of F. vesiculosus. All methods, however, revealed a new and early diverging hermaphrodite species, Fucus macroguiryi sp. nov. Both the multispecies coalescent and polymorphism-aware models (in contrast to concatenation) support sequential paraphyly in F. vesiculosus resulting from distinct evolutionary processes. Our results support (1) peripheral isolation of the southern F. vesiculosus clade prior to parapatric speciation and radiation of hermaphrodite lineages-a "low-latitude species pump". (2) Directional introgressive gene flow into F. vesiculosus around the present-day secondary contact zone (sympatric-allopatric boundary) between dioecious/hermaphrodite lineages as hermaphrodites expanded northwards, supported by concordance analysis and statistical tests of introgression. (3) Species boundaries in the extensive sympatric range are probably maintained by reproductive system (selfing in hermaphrodites) and reinforcement.
Collapse
Affiliation(s)
- Susana C Almeida
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - João Neiva
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Filipe Sousa
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Neusa Martins
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Cymon J Cox
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - José Melo-Ferreira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, R. Padre Armando Quintas, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Michael D Guiry
- AlgaeBase, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Ester A Serrão
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Gareth A Pearson
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| |
Collapse
|
18
|
Tsuchimatsu T, Fujii S. The selfing syndrome and beyond: diverse evolutionary consequences of mating system transitions in plants. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200510. [PMID: 35634918 PMCID: PMC9149797 DOI: 10.1098/rstb.2020.0510] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/04/2021] [Indexed: 07/20/2023] Open
Abstract
The shift from outcrossing to self-fertilization (selfing) is considered one of the most prevalent evolutionary transitions in flowering plants. Selfing species tend to share similar reproductive traits in morphology and function, and such a set of traits is called the 'selfing syndrome'. Although the genetic basis of the selfing syndrome has been of great interest to evolutionary biologists, knowledge of the causative genes or mutations was limited until recently. Thanks to advances in population genomic methodologies combined with high-throughput sequencing technologies, several studies have successfully unravelled the molecular and genetic basis for evolution of the selfing syndrome in Capsella, Arabidopsis, Solanum and other genera. Here we first introduce recent research examples that have explored the loci, genes and mutations responsible for the selfing syndrome traits, such as reductions in petal size or in pollen production, that are mainly relevant to pre-pollination processes. Second, we review the relationship between the evolution of selfing and interspecific pollen transfer, highlighting the findings of post-pollination reproductive barriers at the molecular level. We then discuss the emerging view of patterns in evolution of the selfing syndrome, such as the pervasive involvement of loss-of-function mutations and the relative importance of selection versus neutral degradation. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.
Collapse
Affiliation(s)
- Takashi Tsuchimatsu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 113-0033, Japan
| | - Sota Fujii
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku 113-8657, Japan
- Suntory Rising Stars Encouragement Program in Life Sciences (SunRiSE) Fellow, Bunkyo, Japan
| |
Collapse
|
19
|
Orsucci M, Yang X, Vanikiotis T, Guerrina M, Duan T, Lascoux M, Glémin S. Competitive ability depends on mating system and ploidy level across Capsella species. ANNALS OF BOTANY 2022; 129:697-708. [PMID: 35325927 PMCID: PMC9113120 DOI: 10.1093/aob/mcac044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 10/14/2021] [Accepted: 03/23/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Self-fertilization is often associated with ecological traits corresponding to the ruderal strategy, and selfers are expected to be less competitive than outcrossers, either because of a colonization/competition trade-off or because of the deleterious genetic effects of selfing. Range expansion could reduce further competitive ability while polyploidy could mitigate the effects of selfing. If pollinators are not limited, individual fitness is thus expected to be higher in outcrossers than in selfers and, within selfers, in polyploids than in diploids. Although often proposed in the botanical literature and also suggested by meta-analyses, these predictions have not been directly tested yet. METHODS In order to compare fitness and the competitive ability of four Capsella species with a different mating system and ploidy level, we combined two complementary experiments. First, we carried out an experiment outdoors in north-west Greece, i.e. within the range of the obligate outcrossing species, C. grandiflora, where several life history traits were measured under two different disturbance treatments, weeded plots vs. unweeded plots. To better control competition and to remove potential effects of local adaptation of the outcrosser, we also performed a similar competition experiment but under growth chamber conditions. KEY RESULTS In the outdoor experiment, disturbance of the environment did not affect the phenotype in any of the four species. For most traits, the obligate outcrossing species performed better than all selfing species. In contrast, polyploids did not survive or reproduce better than diploids. Under controlled conditions, as in the field experiment, the outcrosser had a higher fitness than selfing species and was less affected by competition. Finally, contrary to the outdoor experiment where the two behaved identically, polyploid selfers were less affected by competition than diploid selfes. CONCLUSIONS In the Capsella genus, selfing induces lower fitness than outcrossing and can also reduce competitive ability. The effect of polyploidy is, however, unclear. These results highlight the possible roles of ecological context in the evolution of selfing species.
Collapse
Affiliation(s)
- Marion Orsucci
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Xuyue Yang
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Theofilos Vanikiotis
- Department of Biological Applications & Technology, University of Ioannina, Leof. S. Niarchou GR-451 10, Ioannina, Greece
| | - Maria Guerrina
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Tianlin Duan
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
- UMR CNRS 6553 ECOBIO, Campus Beaulieu, bât 14a, CS 74205, 35042 Rennes, France
| |
Collapse
|
20
|
Xu K. The genetic basis of selfing rate evolution. Evolution 2022; 76:883-898. [PMID: 35395695 DOI: 10.1111/evo.14480] [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: 05/18/2021] [Revised: 02/02/2022] [Accepted: 02/28/2022] [Indexed: 01/21/2023]
Abstract
Evolution of selfing is common in plant populations, but the genetic basis of selfing rate evolution remains unclear. Although the effects of genetic properties on fixation for mating-unrelated alleles have been investigated, loci that modify the selfing rate (selfing modifiers) differ from mating-unrelated loci in several aspects. Using population genetic models, I investigate the genetic basis of selfing rate evolution. For mating-unrelated alleles, selfing promotes fixation only for recessive mutations, but for selfing modifiers, because the selection coefficient depends on the background selfing rate, selfing can promote fixation even for dominant modifiers. For mating-unrelated alleles, the fixation probability from standing variation is independent of dominance and decreases with an increased background selfing rate. However, for selfing modifiers, the fixation probability peaks at an intermediate selfing rate and when alleles are recessive, because a change of its selection coefficient necessarily involves a change of the inbreeding coefficient, because both depend on the level of inbreeding depression. Furthermore, evolution of selfing involving multiple modifier loci is more likely when selfing is controlled by few large-effect rather than many slight-effect modifiers. I discuss how these characteristics of selfing modifiers have implications for the unidirectional transition from outcrossing to selfing and other empirical patterns.
Collapse
Affiliation(s)
- Kuangyi Xu
- Department of Biology, University of North Carolina at Chapel Hill, Coker Hall, 120 South Road, Chapel Hill, North Carolina, 27599, United States
| |
Collapse
|
21
|
McElderry RM, Spigler RB, Vogler DW, Kalisz S. How early does the selfing syndrome arise? Associations between selfing ability and flower size within populations of the mixed-mater Collinsia verna. AMERICAN JOURNAL OF BOTANY 2022; 109:333-344. [PMID: 34778956 PMCID: PMC9305746 DOI: 10.1002/ajb2.1804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Widespread associations between selfing rate and floral size within and among taxa suggest that these traits may evolve in concert. Does this association develop immediately because of shared genetic and/or developmental control, or stepwise with selection shaping the evolution of one trait following the other? If the former, then association ought to appear within and across selfing populations. We explore this fundamental question in three populations of the mixed-mater Collinsia verna where autonomous selfing (AS) ability has been shown to be under selection by the pollination environment. METHODS We grew clonal replicates of C. verna in a controlled environment to characterize broad-sense genetic correlations among traits within populations and to assess whether divergence in mating system and floral traits among these populations is consistent with their previously observed selection pressures. RESULTS As predicted by their respective pollination environments, we demonstrate significant genetic divergence among populations in AS ability. However, patterns of divergence in floral traits (petal, stamen, and style size, stigmatic receptivity, and stigma-anther distance) were not as expected. Within populations, genetic variation in AS appeared largely independent from floral traits, except for a single weak negative association in one population between flower size and AS rate. CONCLUSIONS Together, these results suggest that associations between selfing rate and floral traits across Collinsia species are not reflected at microevolutionary scales. If C. verna were to continue evolving toward the selfing syndrome, floral trait evolution would likely follow stepwise from mating system evolution.
Collapse
Affiliation(s)
- Robert M. McElderry
- Department of Ecology and Evolutionary BiologyUniversity of Tennessee KnoxvilleKnoxvilleTennesseeUSA
| | | | | | - Susan Kalisz
- Department of Ecology and Evolutionary BiologyUniversity of Tennessee KnoxvilleKnoxvilleTennesseeUSA
| |
Collapse
|
22
|
Horvath R, Josephs EB, Pesquet E, Stinchcombe JR, Wright SI, Scofield D, Slotte T. Selection on Accessible Chromatin Regions in Capsella grandiflora. Mol Biol Evol 2021; 38:5563-5575. [PMID: 34498072 PMCID: PMC8662636 DOI: 10.1093/molbev/msab270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Accurate estimates of genome-wide rates and fitness effects of new mutations are essential for an improved understanding of molecular evolutionary processes. Although eukaryotic genomes generally contain a large noncoding fraction, functional noncoding regions and fitness effects of mutations in such regions are still incompletely characterized. A promising approach to characterize functional noncoding regions relies on identifying accessible chromatin regions (ACRs) tightly associated with regulatory DNA. Here, we applied this approach to identify and estimate selection on ACRs in Capsella grandiflora, a crucifer species ideal for population genomic quantification of selection due to its favorable population demography. We describe a population-wide ACR distribution based on ATAC-seq data for leaf samples of 16 individuals from a natural population. We use population genomic methods to estimate fitness effects and proportions of positively selected fixations (α) in ACRs and find that intergenic ACRs harbor a considerable fraction of weakly deleterious new mutations, as well as a significantly higher proportion of strongly deleterious mutations than comparable inaccessible intergenic regions. ACRs are enriched for expression quantitative trait loci (eQTL) and depleted of transposable element insertions, as expected if intergenic ACRs are under selection because they harbor regulatory regions. By integrating empirical identification of intergenic ACRs with analyses of eQTL and population genomic analyses of selection, we demonstrate that intergenic regulatory regions are an important source of nearly neutral mutations. These results improve our understanding of selection on noncoding regions and the role of nearly neutral mutations for evolutionary processes in outcrossing Brassicaceae species.
Collapse
Affiliation(s)
- Robert Horvath
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, Lansing, MI, USA
| | - Edouard Pesquet
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Douglas Scofield
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| |
Collapse
|
23
|
Gorman CE, Li Y, Dorken ME, Stift M. No evidence for incipient speciation by selfing in North American Arabidopsis lyrata. J Evol Biol 2021; 34:1397-1405. [PMID: 34228843 DOI: 10.1111/jeb.13901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/01/2021] [Accepted: 07/03/2021] [Indexed: 01/01/2023]
Abstract
Self-fertilization inherently restricts gene flow by reducing the fraction of offspring that can be produced by inter-population matings. Therefore, mating system transitions from outcrossing to selfing could result in reproductive isolation between selfing and outcrossing lineages and provide a starting point for speciation. In newly diverged lineages, for example after a transition to selfing, further reproductive isolation can be caused by a variety of prezygotic and post-zygotic mechanisms that operate before, during and after pollination. In animals, prezygotic barriers tend to evolve faster than post-zygotic ones. This is not necessarily the case for plants, for which the relative importance of post-mating, post-fertilization and early-acting post-zygotic barriers has been investigated far less. To test whether post-pollination isolation exists between populations of North American Arabidopsis lyrata that differ in breeding (self-incompatible versus self-compatible) and mating system (outcrossing versus selfing), we compared patterns of seed set after crosses made within populations, between populations of the same mating system and between populations with different mating systems. We found no evidence for post-pollination isolation between plants from selfing populations (self-compatible, low outcrossing rates) and outcrossing populations (self-incompatible, high outcrossing rates) via either prezygotic or early-acting post-zygotic mechanisms. Together with the results of other studies indicating the absence of reproductive barriers acting before and during pollination, we conclude that the transition to selfing in this study system has not led to the formation of reproductive barriers between selfing and outcrossing populations of North American A. lyrata.
Collapse
Affiliation(s)
| | - Yan Li
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Marcel E Dorken
- Department of Biology, Trent University, Peterborough, ON, Canada
| | - Marc Stift
- Department of Biology, University of Konstanz, Konstanz, Germany
| |
Collapse
|
24
|
Petrén H, Toräng P, Ågren J, Friberg M. Evolution of floral scent in relation to self-incompatibility and capacity for autonomous self-pollination in the perennial herb Arabis alpina. ANNALS OF BOTANY 2021; 127:737-747. [PMID: 33555338 PMCID: PMC8103803 DOI: 10.1093/aob/mcab007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS The transition from outcrossing to selfing is a frequent evolutionary shift in flowering plants and is predicted to result in reduced allocation to pollinator attraction if plants can self-pollinate autonomously. The evolution of selfing is associated with reduced visual floral signalling in many systems, but effects on floral scent have received less attention. We compared multiple populations of the arctic-alpine herb Arabis alpina (Brassicaceae), and asked whether the transition from self-incompatibility to self-compatibility has been associated with reduced visual and chemical floral signalling. We further examined whether floral signalling differ between self-compatible populations with low and high capacity for autonomous self-pollination, as would be expected if benefits of signalling decrease with reduced dependence on pollinators for pollen transfer. METHODS In a common garden we documented flower size and floral scent emission rate and composition in eight self-compatible and nine self-incompatible A. alpina populations. These included self-compatible Scandinavian populations with high capacity for autonomous self-pollination, self-compatible populations with low capacity for autonomous self-pollination from France and Spain, and self-incompatible populations from Italy and Greece. KEY RESULTS The self-compatible populations produced smaller and less scented flowers than the self-incompatible populations. However, flower size and scent emission rate did not differ between self-compatible populations with high and low capacity for autonomous self-pollination. Floral scent composition differed between self-compatible and self-incompatible populations, but also varied substantially among populations within the two categories. CONCLUSIONS Our study demonstrates extensive variation in floral scent among populations of a geographically widespread species. Contrary to expectation, floral signalling did not differ between self-compatible populations with high and low capacity for autonomous self-pollination, indicating that dependence on pollinator attraction can only partly explain variation in floral signalling. Additional variation may reflect adaptation to other aspects of local environments, genetic drift, or a combination of these processes.
Collapse
Affiliation(s)
- Hampus Petrén
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Per Toräng
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
- SLU Swedish Species Information Centre, Box 7007, SE-750 07 Uppsala, Sweden
| | - Jon Ågren
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Magne Friberg
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| |
Collapse
|
25
|
Jones MR, Winkler DE, Massatti R. The demographic and ecological factors shaping diversification among rare
Astragalus
species. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Matthew R. Jones
- Southwest Biological Science Center U.S. Geological Survey Flagstaff AZ USA
| | - Daniel E. Winkler
- Southwest Biological Science Center U.S. Geological Survey Moab UT USA
| | - Rob Massatti
- Southwest Biological Science Center U.S. Geological Survey Flagstaff AZ USA
| |
Collapse
|
26
|
Jiménez-Lobato V, Núñez-Farfán J. Mating system of Datura inoxia: association between selfing rates and herkogamy within populations. PeerJ 2021; 9:e10698. [PMID: 33777507 PMCID: PMC7983856 DOI: 10.7717/peerj.10698] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/13/2020] [Indexed: 11/20/2022] Open
Abstract
Plant mating system determines, to a great extent, the demographic and genetic properties of populations, hence their potential for adaptive evolution. Variation in plant mating system has been documented between phylogenetically related species as well between populations of a species. A common evolutionary transition, from outcrossing to selfing, is likely to occur under environmental spatial variation in the service of pollinators. Here, we studied two phenotypically (in floral traits) and genetically (in neutral molecular markers) differentiated populations of the annual, insect-pollinated, plant Datura inoxia in Mexico, that differ in the service of pollinators (Mapimí and Cañada Moreno). First, we determined the populations’ parameters of phenotypic in herkogamy, outcrossing and selfing rates with microsatellite loci, and assessed between generation (adults and seedlings) inbreeding, and inbreeding depression. Second, we compared the relationships between parameters in each population. Results point strong differences between populations: plants in Mapimí have, on average, approach herkogamy, higher outcrossing rate (tm = 0.68), lower primary selfing rate (r = 0.35), and lower inbreeding at equilibrium (Fe = 0.24) and higher inbreeding depression (δ = 0.25), than the populations of Cañada. Outcrossing seems to be favored in Mapimí while selfing in Cañada. The relationship between r and Fe were negatively associated with herkogamy in Mapimí; here, progenies derived from plants with no herkogamy or reverse herkogamy had higher selfing rate and inbreeding coefficient than plants with approach herkogamy. The difference Fe–F is positively related to primary selfing rate (r) only in Cañada Moreno which suggests inbreeding depression in selfing individuals and then genetic purging. In conclusion, mating system evolution may occur differentially among maternal lineages within populations of Datura inoxia, in which approach herkogamy favors higher outcrossing rates and low levels of inbreeding and inbreeding depression, while no herkogamy or reverse herkogamy lead to the evolution of the “selfing syndrome” following the purge of deleterious alleles despite high inbreeding among individuals.
Collapse
Affiliation(s)
- Vania Jiménez-Lobato
- Escuela Superior de Desarrollo Sustentable, Universidad Autónoma de Guerrero, Cátedras CONACYT, México.,Laboratorio de Genética Ecológica y Evolución, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Distrito Federal, Mexico
| | - Juan Núñez-Farfán
- Laboratorio de Genética Ecológica y Evolución, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Distrito Federal, Mexico
| |
Collapse
|
27
|
Lucek K, Willi Y. Drivers of linkage disequilibrium across a species' geographic range. PLoS Genet 2021; 17:e1009477. [PMID: 33770075 PMCID: PMC8026057 DOI: 10.1371/journal.pgen.1009477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/07/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022] Open
Abstract
While linkage disequilibrium (LD) is an important parameter in genetics and evolutionary biology, the drivers of LD remain elusive. Using whole-genome sequences from across a species’ range, we assessed the impact of demographic history and mating system on LD. Both range expansion and a shift from outcrossing to selfing in North American Arabidopsis lyrata were associated with increased average genome-wide LD. Our results indicate that range expansion increases short-distance LD at the farthest range edges by about the same amount as a shift to selfing. However, the extent over which LD in genic regions unfolds was shorter for range expansion compared to selfing. Linkage among putatively neutral variants and between neutral and deleterious variants increased to a similar degree with range expansion, providing support that genome-wide LD was positively associated with mutational load. As a consequence, LD combined with mutational load may decelerate range expansions and set range limits. Finally, a small number of genes were identified as LD outliers, suggesting that they experience selection by either of the two demographic processes. These included genes involved in flowering and photoperiod for range expansion, and the self-incompatibility locus for mating system. Nearby genomic variants are often co-inherited because of limited recombination. The extent of non-random association of alleles at different loci is called linkage disequilibrium (LD) and is commonly used in genomic analyses, for example to detect regions under selection or to determine effective population size. Here we reversed testing and addressed how demographic history may affect LD within a species. Using genomic data from more than a thousand individuals of North American Arabidopsis lyrata from across the entire species’ range, we quantified the effect of postglacial range expansion and a shift in mating system from outcrossing to selfing on LD. We show that both factors lead to increased LD, and that the maximal effect of range expansion is comparable with a shift in mating system to selfing. Heightened LD involves deleterious mutations, and therefore, LD can also serve as an indicator of mutation accumulation. Furthermore, we provide evidence that some genes experienced stronger increases in LD possibly due to selection associated with the two demographic changes. Our results provide a novel and broad view on the evolutionary factors shaping LD that may also apply to the very many species that underwent postglacial range expansion.
Collapse
Affiliation(s)
- Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
- * E-mail:
| | - Yvonne Willi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| |
Collapse
|
28
|
Dziasek K, Simon L, Lafon-Placette C, Laenen B, Wärdig C, Santos-González J, Slotte T, Köhler C. Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm. PLoS Genet 2021; 17:e1009370. [PMID: 33571184 PMCID: PMC7904229 DOI: 10.1371/journal.pgen.1009370] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 02/24/2021] [Accepted: 01/15/2021] [Indexed: 11/18/2022] Open
Abstract
Hybridization of closely related plant species is frequently connected to endosperm arrest and seed failure, for reasons that remain to be identified. In this study, we investigated the molecular events accompanying seed failure in hybrids of the closely related species pair Capsella rubella and C. grandiflora. Mapping of QTL for the underlying cause of hybrid incompatibility in Capsella identified three QTL that were close to pericentromeric regions. We investigated whether there are specific changes in heterochromatin associated with interspecific hybridizations and found a strong reduction of chromatin condensation in the endosperm, connected with a strong loss of CHG and CHH methylation and random loss of a single chromosome. Consistent with reduced DNA methylation in the hybrid endosperm, we found a disproportionate deregulation of genes located close to pericentromeric regions, suggesting that reduced DNA methylation allows access of transcription factors to targets located in heterochromatic regions. Since the identified QTL were also associated with pericentromeric regions, we propose that relaxation of heterochromatin in response to interspecies hybridization exposes and activates loci leading to hybrid seed failure.
Collapse
Affiliation(s)
- Katarzyna Dziasek
- Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala, Sweden
| | - Lauriane Simon
- Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala, Sweden
| | - Clément Lafon-Placette
- Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala, Sweden
- Present address: Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Benjamin Laenen
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Cecilia Wärdig
- Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala, Sweden
- * E-mail:
| |
Collapse
|
29
|
Imai R, Tsuda Y, Ebihara A, Matsumoto S, Tezuka A, Nagano AJ, Ootsuki R, Watano Y. Mating system evolution and genetic structure of diploid sexual populations of Cyrtomium falcatum in Japan. Sci Rep 2021; 11:3124. [PMID: 33542454 PMCID: PMC7862634 DOI: 10.1038/s41598-021-82731-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 01/12/2021] [Indexed: 11/09/2022] Open
Abstract
Evolution of mating systems has become one of the most important research areas in evolutionary biology. Cyrtomium falcatum is a homosporous fern species native to eastern Asia. Two subspecies belonging to a sexual diploid race of C. falcatum are recognized: subsp. littorale and subsp. australe. Subspecies littorale shows intermediate selfing rates, while subsp. australe is an obligate outcrosser. We aimed to evaluate the process of mating system evolution and divergence for the two subspecies using restriction site associated DNA sequencing (RAD-seq). The results showed that subsp. littorale had lower genetic diversity and stronger genetic drift than subsp. australe. Fluctuations in the effective population size over time were evaluated by extended Bayesian skyline plot and Stairway plot analyses, both of which revealed a severe population bottleneck about 20,000 years ago in subsp. littorale. This bottleneck and the subsequent range expansion after the LGM appear to have played an important role in the divergence of the two subspecies and the evolution of selfing in subsp. littorale. These results shed new light on the relationship between mating system evolution and past demographic change in fern species.
Collapse
Affiliation(s)
- Ryosuke Imai
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda , Nagano, 386-2204, Japan.
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda , Nagano, 386-2204, Japan
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Sadamu Matsumoto
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Ayumi Tezuka
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Ryo Ootsuki
- Department of Natural Sciences, Faculty of Arts and Sciences, Komazawa University, 1-23-1 Komazawa, Setagaya-ku, Tokyo, 154-8525, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Inage, Chiba, Chiba, 263-8522, Japan
| |
Collapse
|
30
|
Florez-Rueda AM, Scharmann M, Roth M, Städler T. Population Genomics of the "Arcanum" Species Group in Wild Tomatoes: Evidence for Separate Origins of Two Self-Compatible Lineages. FRONTIERS IN PLANT SCIENCE 2021; 12:624442. [PMID: 33815438 PMCID: PMC8018279 DOI: 10.3389/fpls.2021.624442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/24/2021] [Indexed: 05/07/2023]
Abstract
Given their diverse mating systems and recent divergence, wild tomatoes (Solanum section Lycopersicon) have become an attractive model system to study ecological divergence, the build-up of reproductive barriers, and the causes and consequences of the breakdown of self-incompatibility. Here we report on a lesser-studied group of species known as the "Arcanum" group, comprising the nominal species Solanum arcanum, Solanum chmielewskii, and Solanum neorickii. The latter two taxa are self-compatible but are thought to self-fertilize at different rates, given their distinct manifestations of the morphological "selfing syndrome." Based on experimental crossings and transcriptome sequencing of a total of 39 different genotypes from as many accessions representing each species' geographic range, we provide compelling evidence for deep genealogical divisions within S. arcanum; only the self-incompatible lineage known as "var. marañón" has close genealogical ties to the two self-compatible species. Moreover, there is evidence under multiple inference schemes for different geographic subsets of S. arcanum var. marañón being closest to S. chmielewskii and S. neorickii, respectively. To broadly characterize the population-genomic consequences of these recent mating-system transitions and their associated speciation events, we fit demographic models indicating strong reductions in effective population size, congruent with reduced nucleotide and S-locus diversity in the two independently derived self-compatible species.
Collapse
|
31
|
Wang Z, Butel N, Santos-González J, Borges F, Yi J, Martienssen RA, Martinez G, Köhler C. Polymerase IV Plays a Crucial Role in Pollen Development in Capsella. THE PLANT CELL 2020; 32:950-966. [PMID: 31988265 PMCID: PMC7145478 DOI: 10.1105/tpc.19.00938] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 05/04/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), DNA-dependent RNA polymerase IV (Pol IV) is required for the formation of transposable element (TE)-derived small RNA transcripts. These transcripts are processed by DICER-LIKE3 into 24-nucleotide small interfering RNAs (siRNAs) that guide RNA-directed DNA methylation. In the pollen grain, Pol IV is also required for the accumulation of 21/22-nucleotide epigenetically activated siRNAs, which likely silence TEs via post-transcriptional mechanisms. Despite this proposed role of Pol IV, its loss of function in Arabidopsis does not cause a discernible pollen defect. Here, we show that the knockout of NRPD1, encoding the largest subunit of Pol IV, in the Brassicaceae species Capsella (Capsella rubella), caused postmeiotic arrest of pollen development at the microspore stage. As in Arabidopsis, all TE-derived siRNAs were depleted in Capsella nrpd1 microspores. In the wild-type background, the same TEs produced 21/22-nucleotide and 24-nucleotide siRNAs; these processes required Pol IV activity. Arrest of Capsella nrpd1 microspores was accompanied by the deregulation of genes targeted by Pol IV-dependent siRNAs. TEs were much closer to genes in Capsella compared with Arabidopsis, perhaps explaining the essential role of Pol IV in pollen development in Capsella. Our discovery that Pol IV is functionally required in Capsella microspores emphasizes the relevance of investigating different plant models.
Collapse
Affiliation(s)
- Zhenxing Wang
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Nicolas Butel
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Filipe Borges
- Howard Hughes Medical Institute and Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Jun Yi
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Robert A Martienssen
- Howard Hughes Medical Institute and Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - German Martinez
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| |
Collapse
|
32
|
Woźniak NJ, Kappel C, Marona C, Altschmied L, Neuffer B, Sicard A. A Similar Genetic Architecture Underlies the Convergent Evolution of the Selfing Syndrome in Capsella. THE PLANT CELL 2020; 32:935-949. [PMID: 31964802 PMCID: PMC7145481 DOI: 10.1105/tpc.19.00551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 11/19/2019] [Accepted: 01/13/2020] [Indexed: 05/11/2023]
Abstract
Whether, and to what extent, phenotypic evolution follows predictable genetic paths remains an important question in evolutionary biology. Convergent evolution of similar characters provides a unique opportunity to address this question. The transition to selfing and the associated changes in flower morphology are among the most prominent examples of repeated evolution in plants. In this study, we take advantage of the independent transitions to self-fertilization in the genus Capsella to compare the similarities between parallel modifications of floral traits and test for genetic and developmental constraints imposed on flower evolution in the context of the selfing syndrome. Capsella rubella and Capsella orientalis emerged independently but evolved almost identical flower characters. Not only is the evolutionary outcome identical but the same developmental strategies underlie the convergent reduction of flower size. This has been associated with convergent evolution of gene expression changes. The transcriptomic changes common to both selfing lineages are enriched in genes with low network connectivity and with organ-specific expression patterns. Comparative genetic mapping also suggests that, at least in the case of petal size evolution, these similarities have a similar genetic basis. Based on these results, we hypothesize that the limited availability of low-pleiotropy paths predetermines closely related species to similar evolutionary outcomes.
Collapse
Affiliation(s)
| | - Christian Kappel
- Institut für Biochemie und Biologie, Universität Potsdam, 14476 Potsdam-Golm, Germany
| | - Cindy Marona
- Institut für Biochemie und Biologie, Universität Potsdam, 14476 Potsdam-Golm, Germany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Barbara Neuffer
- Department of Botany, University of Osnabrück, 49076 Osnabrück, Germany
| | - Adrien Sicard
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter and Linnean Centre for Plant Biology, 75007 Uppsala, Sweden
| |
Collapse
|
33
|
Akiyama R, Milosavljevic S, Leutenegger M, Shimizu-Inatsugi R. Trait-dependent resemblance of the flowering phenology and floral morphology of the allopolyploid Cardamine flexuosa to those of the parental diploids in natural habitats. JOURNAL OF PLANT RESEARCH 2020; 133:147-155. [PMID: 31925575 PMCID: PMC7026219 DOI: 10.1007/s10265-019-01164-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 12/08/2019] [Indexed: 05/24/2023]
Abstract
Allopolyploids possess complete sets of genomes derived from different parental species and exhibit a range of variation in various traits. Reproductive traits may play a key role in the reproductive isolation between allopolyploids and their parental species, thus affecting the thriving of allopolyploids. However, empirical data, especially in natural habitats, comparing reproductive trait variation between allopolyploids and their parental species remain rare. Here, we documented the flowering phenology and floral morphology of the allopolyploid wild plant Cardamine flexuosa and its diploid parents C. amara and C. hirsuta in their native range in Switzerland. The flowering of C. flexuosa started at an intermediate time compared with those of the parents and the flowering period of C. flexuosa overlapped with those of the parents. Cardamine flexuosa resembled C. hirsuta in the size of flowers and petals and the length/width ratio of petals, while it resembled C. amara in the length/width ratio of flowers. These results provide empirical evidence of the trait-dependent variation of allopolyploid phenotypes in natural habitats at the local scale. They also suggest that the variation in some reproductive traits in C. flexuosa is associated with self-fertilization. Therefore, it is helpful to consider the mating system in furthering the understanding of the processes that may have shaped trait variation in polyploids in nature.
Collapse
Affiliation(s)
- Reiko Akiyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrase 190, 8057, Zurich, Switzerland
| | - Stefan Milosavljevic
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrase 190, 8057, Zurich, Switzerland
| | - Matthias Leutenegger
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrase 190, 8057, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrase 190, 8057, Zurich, Switzerland.
| |
Collapse
|
34
|
Uzunović J, Josephs EB, Stinchcombe JR, Wright SI. Transposable Elements Are Important Contributors to Standing Variation in Gene Expression in Capsella Grandiflora. Mol Biol Evol 2020; 36:1734-1745. [PMID: 31028401 DOI: 10.1093/molbev/msz098] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) make up a significant portion of eukaryotic genomes and are important drivers of genome evolution. However, the extent to which TEs affect gene expression variation on a genome-wide scale in comparison with other types of variants is still unclear. We characterized TE insertion polymorphisms and their association with gene expression in 124 whole-genome sequences from a single population of Capsella grandiflora, and contrasted this with the effects of single nucleotide polymorphisms (SNPs). Population frequency of insertions was negatively correlated with distance to genes, as well as density of conserved noncoding elements, suggesting that the negative effects of TEs on gene regulation are important in limiting their abundance. Rare TE variants strongly influence gene expression variation, predominantly through downregulation. In contrast, rare SNPs contribute equally to up- and down-regulation, but have a weaker individual effect than TEs. An expression quantitative trait loci (eQTL) analysis shows that a greater proportion of common TEs are eQTLs as opposed to common SNPs, and a third of the genes with TE eQTLs do not have SNP eQTLs. In contrast with rare TE insertions, common insertions are more likely to increase expression, consistent with recent models of cis-regulatory evolution favoring enhancer alleles. Taken together, these results imply that TEs are a significant contributor to gene expression variation and are individually more likely than rare SNPs to cause extreme changes in gene expression.
Collapse
Affiliation(s)
- Jasmina Uzunović
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Koffler Scientific Reserve, University of Toronto, Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
35
|
Oleques SS, Radaeski JN, Bauerman S, Chauveau O, de Souza-Chies TT. The specialization–generalization continuum in oil-bee pollination systems: a case study of six Brazilian species of Tigridieae (Iridaceae). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Several South American species of Iridaceae, especially those of Tigridieae, produce floral oils as rewards to oil-bee pollinators. The present study aimed to contribute to a deeper understanding of the reproductive biology, pollination ecology and level of specialization of the interactions of species encompassed in Tigridieae. Data on breeding and pollination systems were acquired from six species native to Southern Brazil. The visitation frequency and pollen load of pollen- and oil-collecting bees were also investigated. The results strongly suggest that the studied species are distributed along a specialization–generalization continuum. Three oil-producing taxa, Cypella herbertii, Cypella pusilla and Cypella amplimaculata, were pollinated effectively by oil-bees, whereas in the other two studied species, Kelissa brasiliensis and Herbertia pulchella, the oil-bees appeared to function as oil thieves, owing to failure to contact the plant reproductive parts during oil-foraging behaviour. New insights into aspects of the specialization–generalization continuum of pollination systems, differences in pollinator behaviour during oil and pollen foraging, and reproductive outputs of the studied species are provided. Taken together, our results provide a significant contribution towards a better understanding of reproductive biology and plant–pollinator interactions between Iridaceae and oil-collecting bees.
Collapse
Affiliation(s)
- Suiane Santos Oleques
- Departamento de Botânica, Programa de Pós-graduação em Botânica, Universidade Federal do Rio Grande do Sul—UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Pesquisa em Interações Ecológicas, Universidade Federal do Pampa - UNIPAMPA, São Gabriel, Rio Grande do Sul, Brazil
| | - Jefferson Nunes Radaeski
- Departamento de Biologia, Universidade Luterana do Brasil – ULBRA, Laboratório de Palinologia, Canoas, Rio Grande do Sul, Brazil
| | - Soraia Bauerman
- Departamento de Biologia, Universidade Luterana do Brasil – ULBRA, Laboratório de Palinologia, Canoas, Rio Grande do Sul, Brazil
| | - Olivier Chauveau
- Departamento de Botânica, Programa de Pós-graduação em Botânica, Universidade Federal do Rio Grande do Sul—UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Pesquisa em Interações Ecológicas, Universidade Federal do Pampa - UNIPAMPA, São Gabriel, Rio Grande do Sul, Brazil
- Université Paris Sud, Agro Paris Tech, —Unité Écologie, Systématique et Évolution, Orsay, France
| | - Tatiana Teixeira de Souza-Chies
- Departamento de Botânica, Programa de Pós-graduação em Botânica, Universidade Federal do Rio Grande do Sul—UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Pesquisa em Interações Ecológicas, Universidade Federal do Pampa - UNIPAMPA, São Gabriel, Rio Grande do Sul, Brazil
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| |
Collapse
|
36
|
Brom T, Castric V, Billiard S. Breakdown of gametophytic self-incompatibility in subdivided populations. Evolution 2020; 74:270-282. [PMID: 31845323 DOI: 10.1111/evo.13897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/04/2019] [Accepted: 11/11/2019] [Indexed: 01/11/2023]
Abstract
In many hermaphroditic flowering plants, self-fertilization is prevented by self-incompatibility (SI), often controlled by a single locus, the S-locus. In single isolated populations, the maintenance of SI depends chiefly on inbreeding depression and the number of SI alleles at the S-locus. In subdivided populations, however, population subdivision has complicated effects on both the number of SI alleles and the level of inbreeding depression, rendering the maintenance of SI difficult to predict. Here, we explore the conditions for the invasion of a self-compatible mutant in a structured population. We find that the maintenance of SI is strongly compromised when a population becomes subdivided. We show that this effect is mainly caused by the decrease in the local diversity of SI alleles rather than by a change in the dynamics of inbreeding depression. Strikingly, we also find that the diversity of SI alleles at the whole population level is a poor predictor of the maintenance of SI. We discuss the implications of our results for the interpretation of empirical data on the loss of SI in natural populations.
Collapse
Affiliation(s)
- Thomas Brom
- University Lille, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France.,CNRS, UMR 8198, F-59000, Lille, France
| | - Vincent Castric
- University Lille, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France.,CNRS, UMR 8198, F-59000, Lille, France
| | - Sylvain Billiard
- University Lille, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France.,CNRS, UMR 8198, F-59000, Lille, France
| |
Collapse
|
37
|
Mattila TM, Laenen B, Slotte T. Population Genomics of Transitions to Selfing in Brassicaceae Model Systems. Methods Mol Biol 2020; 2090:269-287. [PMID: 31975171 DOI: 10.1007/978-1-0716-0199-0_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Many plants harbor complex mechanisms that promote outcrossing and efficient pollen transfer. These include floral adaptations as well as genetic mechanisms, such as molecular self-incompatibility (SI) systems. The maintenance of such systems over long evolutionary timescales suggests that outcrossing is favorable over a broad range of conditions. Conversely, SI has repeatedly been lost, often in association with transitions to self-fertilization (selfing). This transition is favored when the short-term advantages of selfing outweigh the costs, primarily inbreeding depression. The transition to selfing is expected to have major effects on population genetic variation and adaptive potential, as well as on genome evolution. In the Brassicaceae, many studies on the population genetic, gene regulatory, and genomic effects of selfing have centered on the model plant Arabidopsis thaliana and the crucifer genus Capsella. The accumulation of population genomics datasets have allowed detailed investigation of where, when and how the transition to selfing occurred. Future studies will take advantage of the development of population genetics theory on the impact of selfing, especially regarding positive selection. Furthermore, investigation of systems including recent transitions to selfing, mixed mating populations and/or multiple independent replicates of the same transition will facilitate dissecting the effects of mating system variation from processes driven by demography.
Collapse
Affiliation(s)
- Tiina M Mattila
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Benjamin Laenen
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
| |
Collapse
|
38
|
Lucek K, Hohmann N, Willi Y. Postglacial ecotype formation under outcrossing and self-fertilization in Arabidopsis lyrata. Mol Ecol 2019; 28:1043-1055. [PMID: 30719799 DOI: 10.1111/mec.15035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/18/2019] [Accepted: 01/28/2019] [Indexed: 12/01/2022]
Abstract
The formation of ecotypes has been invoked as an important driver of postglacial biodiversity, because many species colonized heterogeneous habitats and experienced divergent selection. Ecotype formation has been predominantly studied in outcrossing taxa, while far less attention has been paid to the implications of mating system shifts. Here, we addressed whether substrate-related ecotypes exist in selfing and outcrossing populations of Arabidopsis lyrata subsp. lyrata and whether the genomic footprint differs between mating systems. The North American subspecies colonized both rocky and sandy habitats during postglacial range expansion and shifted the mating system from predominantly outcrossing to predominantly selfing in a number of regions. We performed an association study on pooled whole-genome sequence data of 20 selfing or outcrossing populations, which suggested genes involved in adaptation to substrate. Motivated by enriched gene ontology terms, we compared root growth between plants from the two substrates in a common environment and found that plants originating from sand grew roots faster and produced more side roots, independent of mating system. Furthermore, single nucleotide polymorphisms associated with substrate-related ecotypes were more clustered among selfing populations. Our study provides evidence for substrate-related ecotypes in A. lyrata and divergence in the genomic footprint between mating systems. The latter is the likely result of selfing populations having experienced divergent selection on larger genomic regions due to higher genome-wide linkage disequilibrium.
Collapse
Affiliation(s)
- Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Nora Hohmann
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Yvonne Willi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| |
Collapse
|
39
|
Comparative studies on population genetic structure of two closely related selfing and outcrossing Zingiber species in Hainan Island. Sci Rep 2019; 9:17997. [PMID: 31784623 PMCID: PMC6884562 DOI: 10.1038/s41598-019-54526-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 11/15/2019] [Indexed: 02/04/2023] Open
Abstract
How mating system impacts the genetic diversity of plants has long fascinated and puzzled evolutionary biologists. Numerous studies have shown that self-fertilising plants have less genetic diversity at both the population and species levels than outcrossers. However, the phylogenetic relationships between species and correlated ecological traits have not been accounted for in these previous studies. Here, we conduct a comparative population genetic study of two closely related selfing and outcrossing Zingiber species, with sympatric distribution in Hainan Island, and obtain a result contrary to previous studies. The results indicate that selfing Z. corallinum can maintain high genetic diversity through differentiation intensified by local adaptation in populations across the species’ range. In contrast, outcrossing Z. nudicarpum preserves high genetic diversity through gene exchange by frequent export of pollen within or among populations. Contrary to expectations, the major portion of genetic variation of outcrossing Z. nudicarpum may exist among populations, depending on the dispersal ability of pollen and seed. Our results also reveal that the main factor affecting population structure of selfing Z. corallinum is mountain ranges, followed by a moist climate, while that of outcrossing Z. nudicarpum is likely moisture, but not mountain ranges, due to gene flow via pollen.
Collapse
|
40
|
Cutter AD. Reproductive transitions in plants and animals: selfing syndrome, sexual selection and speciation. THE NEW PHYTOLOGIST 2019; 224:1080-1094. [PMID: 31336389 DOI: 10.1111/nph.16075] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/17/2019] [Indexed: 05/23/2023]
Abstract
The evolution of predominant self-fertilisation frequently coincides with the evolution of a collection of phenotypes that comprise the 'selfing syndrome', in both plants and animals. Genomic features also display a selfing syndrome. Selfing syndrome traits often involve changes to male and female reproductive characters that were subject to sexual selection and sexual conflict in the obligatorily outcrossing ancestor, including the gametic phase for both plants and animals. Rapid evolution of reproductive traits, due to both relaxed selection and directional selection under the new status of predominant selfing, lays the genetic groundwork for reproductive isolation. Consequently, shifts in sexual selection pressures coupled to transitions to selfing provide a powerful paradigm for investigating the speciation process. Plant and animal studies, however, emphasise distinct selective forces influencing reproductive-mode transitions: genetic transmission advantage to selfing or reproductive assurance outweighing the costs of inbreeding depression vs the costs of males and meiosis. Here, I synthesise links between sexual selection, evolution of selfing and speciation, with particular focus on identifying commonalities and differences between plant and animal systems and pointing to areas warranting further synergy.
Collapse
Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| |
Collapse
|
41
|
Ho EKH, Bartkowska M, Wright SI, Agrawal AF. Population genomics of the facultatively asexual duckweed Spirodela polyrhiza. THE NEW PHYTOLOGIST 2019; 224:1361-1371. [PMID: 31298732 DOI: 10.1111/nph.16056] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
Clonal propagation allows some plant species to achieve massive population sizes quickly but also reduces the evolutionary independence of different sites in the genome. We examine genome-wide genetic diversity in Spirodela polyrhiza, a duckweed that reproduces primarily asexually. We find that this geographically widespread and numerically abundant species has very low levels of genetic diversity. Diversity at nonsynonymous sites relative to synonymous sites is high, suggesting that purifying selection is weak. A potential explanation for this observation is that a very low frequency of sex renders selection ineffective. However, there is a pronounced decay in linkage disequilibrium over 40 kb, suggesting that though sex may be rare at the individual level it is not too infrequent at the population level. In addition, neutral diversity is affected by the physical proximity of selected sites, which would be unexpected if sex was exceedingly rare at the population level. The amount of genetic mixing as assessed by the decay in linkage disequilibrium is not dissimilar from selfing species such as Arabidopsis thaliana, yet selection appears to be much less effective in duckweed. We discuss alternative explanations for the signature of weak purifying selection.
Collapse
Affiliation(s)
- Eddie K H Ho
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Magdalena Bartkowska
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| |
Collapse
|
42
|
Jantzen F, Lynch JH, Kappel C, Höfflin J, Skaliter O, Wozniak N, Sicard A, Sas C, Adebesin F, Ravid J, Vainstein A, Hilker M, Dudareva N, Lenhard M. Retracing the molecular basis and evolutionary history of the loss of benzaldehyde emission in the genus Capsella. THE NEW PHYTOLOGIST 2019; 224:1349-1360. [PMID: 31400223 DOI: 10.1111/nph.16103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/18/2019] [Indexed: 05/13/2023]
Abstract
The transition from pollinator-mediated outbreeding to selfing has occurred many times in angiosperms. This is generally accompanied by a reduction in traits attracting pollinators, including reduced emission of floral scent. In Capsella, emission of benzaldehyde as a main component of floral scent has been lost in selfing C. rubella by mutation of cinnamate-CoA ligase CNL1. However, the biochemical basis and evolutionary history of this loss remain unknown, as does the reason for the absence of benzaldehyde emission in the independently derived selfer Capsella orientalis. We used plant transformation, in vitro enzyme assays, population genetics and quantitative genetics to address these questions. CNL1 has been inactivated twice independently by point mutations in C. rubella, causing a loss of enzymatic activity. Both inactive haplotypes are found within and outside of Greece, the centre of origin of C. rubella, indicating that they arose before its geographical spread. By contrast, the loss of benzaldehyde emission in C. orientalis is not due to an inactivating mutation in CNL1. CNL1 represents a hotspot for mutations that eliminate benzaldehyde emission, potentially reflecting the limited pleiotropy and large effect of its inactivation. Nevertheless, even closely related species have followed different evolutionary routes in reducing floral scent.
Collapse
Affiliation(s)
- Friederike Jantzen
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, D-14476, Potsdam-Golm, Germany
| | - Joseph H Lynch
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, D-14476, Potsdam-Golm, Germany
| | - Jona Höfflin
- Institute of Biology, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Haderslebener Straße 9, 12163, Berlin, Germany
| | - Oded Skaliter
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, PO Box 12, 76100, Rehovot, Israel
| | - Natalia Wozniak
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, D-14476, Potsdam-Golm, Germany
| | - Adrien Sicard
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, D-14476, Potsdam-Golm, Germany
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Claudia Sas
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, D-14476, Potsdam-Golm, Germany
| | - Funmilayo Adebesin
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Jasmin Ravid
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, PO Box 12, 76100, Rehovot, Israel
| | - Alexander Vainstein
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, PO Box 12, 76100, Rehovot, Israel
| | - Monika Hilker
- Institute of Biology, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Haderslebener Straße 9, 12163, Berlin, Germany
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, D-14476, Potsdam-Golm, Germany
| |
Collapse
|
43
|
Hodgins KA, Yeaman S. Mating system impacts the genetic architecture of adaptation to heterogeneous environments. THE NEW PHYTOLOGIST 2019; 224:1201-1214. [PMID: 31505030 DOI: 10.1111/nph.16186] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Self-fertilisation has consequences for variation across the genome as it reduces effective population size, effect recombination rates and pollen flow, with implications for local adaptation. We conducted simulations of divergent stabilising selection on a quantitative trait with drift, pollen flow, mutation, recombination and different outcrossing rates. We quantified trait divergence and the genetic architecture of adaptation. We conducted an FST outlier analysis to identify candidate loci and quantified the impact of mating system on detectability. Selfing promoted trait divergence mainly through reductions in pollen flow. Moreover, trait architecture became more diffuse with selfing. Average effect size of trait loci was lower, while the number of loci, and their clustering distance increased. The genetic architecture of selfers was also more diffuse than outcrossers for equivalent migration rates. However, when deleterious alleles were included, architectures became more concentrated in selfers, likely to be because of reductions in population size caused by mutational meltdown and impacts of background selection on Ne . Our simulations demonstrate that mating system has important impacts on adaptive divergence of traits and the genetic landscape underlying that divergence. Selfing has a significant effect on detectability of regions of the genome important for adaptation because of neutral divergence and diffuse trait architecture.
Collapse
Affiliation(s)
- Kathryn A Hodgins
- School of Biological Sciences, Monash University - Clayton Campus, Building 17, Wellington Road, Clayton, Victoria, 3800, Australia
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, AB, T2N 4S8, Canada
| |
Collapse
|
44
|
Abstract
Capsella species, including the well-known Shephard's purse, are characterized by small white flowers and heart-shaped fruit. But read on to discover the fascinating insights these diminutive plants have to reveal about the evolution of self-fertilizing plants.
Collapse
Affiliation(s)
- Adrien Sicard
- Swedish University of Agricultural Sciences, Uppsala BioCenter, PO-Box 7080, Almas Allé 5, SE-75007 Uppsala, Sweden
| | - Michael Lenhard
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 25-26, D-14476 Potsdam-Golm, Germany.
| |
Collapse
|
45
|
Bachmann JA, Tedder A, Laenen B, Fracassetti M, Désamoré A, Lafon-Placette C, Steige KA, Callot C, Marande W, Neuffer B, Bergès H, Köhler C, Castric V, Slotte T. Genetic basis and timing of a major mating system shift in Capsella. THE NEW PHYTOLOGIST 2019; 224:505-517. [PMID: 31254395 DOI: 10.1111/nph.16035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 06/20/2019] [Indexed: 05/23/2023]
Abstract
A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male specificity components, encoded by the genes SRK and SCR at the self-incompatibility locus (S-locus). Theory predicts that S-linked mutations, and especially dominant mutations in SCR, are likely to contribute to loss of SI. However, few studies have investigated the contribution of dominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer species Capsella orientalis, by combining genetic mapping, long-read sequencing of complete S-haplotypes, gene expression analyses and controlled crosses. We show that loss of SI in C. orientalis occurred < 2.6 Mya and maps as a dominant trait to the S-locus. We identify a fixed frameshift deletion in the male specificity gene SCR and confirm loss of male SI specificity. We further identify an S-linked small RNA that is predicted to cause dominance of self-compatibility. Our results agree with predictions on the contribution of dominant S-linked mutations to loss of SI, and thus provide new insights into the molecular basis of mating system transitions.
Collapse
Affiliation(s)
- Jörg A Bachmann
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Andrew Tedder
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Benjamin Laenen
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Marco Fracassetti
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Aurélie Désamoré
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Clément Lafon-Placette
- Department of Plant Biology, Swedish University of Agricultural Sciences & Linnean Center for Plant Biology, SE-750 07, Uppsala, Sweden
| | - Kim A Steige
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Caroline Callot
- Institut National de la Recherche Agronomique, UPR 1258, Centre National des Ressources Génomiques Végétales, 31326, Castanet-Tolosan, France
| | - William Marande
- Institut National de la Recherche Agronomique, UPR 1258, Centre National des Ressources Génomiques Végétales, 31326, Castanet-Tolosan, France
| | - Barbara Neuffer
- Department of Botany, University of Osnabruck, 49076, Osnabrück, Germany
| | - Hélène Bergès
- Institut National de la Recherche Agronomique, UPR 1258, Centre National des Ressources Génomiques Végétales, 31326, Castanet-Tolosan, France
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences & Linnean Center for Plant Biology, SE-750 07, Uppsala, Sweden
| | - Vincent Castric
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| |
Collapse
|
46
|
Mattila TM, Laenen B, Horvath R, Hämälä T, Savolainen O, Slotte T. Impact of demography on linked selection in two outcrossing Brassicaceae species. Ecol Evol 2019; 9:9532-9545. [PMID: 31534673 PMCID: PMC6745670 DOI: 10.1002/ece3.5463] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 12/13/2022] Open
Abstract
Genetic diversity is shaped by mutation, genetic drift, gene flow, recombination, and selection. The dynamics and interactions of these forces shape genetic diversity across different parts of the genome, between populations and species. Here, we have studied the effects of linked selection on nucleotide diversity in outcrossing populations of two Brassicaceae species, Arabidopsis lyrata and Capsella grandiflora, with contrasting demographic history. In agreement with previous estimates, we found evidence for a modest population size expansion thousands of generations ago, as well as efficient purifying selection in C. grandiflora. In contrast, the A. lyrata population exhibited evidence for very recent strong population size decline and weaker efficacy of purifying selection. Using multiple regression analyses with recombination rate and other genomic covariates as explanatory variables, we can explain 47% of the variance in neutral diversity in the C. grandiflora population, while in the A. lyrata population, only 11% of the variance was explained by the model. Recombination rate had a significant positive effect on neutral diversity in both species, suggesting that selection at linked sites has an effect on patterns of neutral variation. In line with this finding, we also found reduced neutral diversity in the vicinity of genes in the C. grandiflora population. However, in A. lyrata no such reduction in diversity was evident, a finding that is consistent with expectations of the impact of a recent bottleneck on patterns of neutral diversity near genes. This study thus empirically demonstrates how differences in demographic history modulate the impact of selection at linked sites in natural populations.
Collapse
Affiliation(s)
- Tiina M. Mattila
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Present address:
Department of Organismal BiologyUppsala UniversityUppsalaSweden
| | - Benjamin Laenen
- Science for Life Laboratory, Department of Ecology, Environment, and Plant SciencesStockholm UniversityStockholmSweden
| | - Robert Horvath
- Science for Life Laboratory, Department of Ecology, Environment, and Plant SciencesStockholm UniversityStockholmSweden
| | - Tuomas Hämälä
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
- Present address:
Department of Plant and Microbial BiologyUniversity of Minnesota Twin CitiesSt. PaulMNUSA
| | - Outi Savolainen
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
| | - Tanja Slotte
- Science for Life Laboratory, Department of Ecology, Environment, and Plant SciencesStockholm UniversityStockholmSweden
| |
Collapse
|
47
|
Abstract
The mechanisms underlying rapid adaptation to changing environments in species with reduced genetic variation, referred to as the “genetic paradox of invasion,” are unknown. We report that transposable elements (TEs) are highly enriched in the gene promoter regions of Capsella rubella compared with its outcrossing sister species Capsella grandiflora. We also show that a number of polymorphic TEs in C. rubella are associated with changes in gene expression. Frequent TE insertions at FLOWERING LOCUS C of C. rubella affect flowering-time variation, an important life history trait correlated with fitness. These results indicate that TE insertions drive rapid phenotypic variation, which could potentially help adapting to novel environments in species with limited genetic variation. Rapid phenotypic changes in traits of adaptive significance are crucial for organisms to thrive in changing environments. How such phenotypic variation is achieved rapidly, despite limited genetic variation in species that experience a genetic bottleneck is unknown. Capsella rubella, an annual and inbreeding forb (Brassicaceae), is a great system for studying this basic question. Its distribution is wider than those of its congeneric species, despite an extreme genetic bottleneck event that severely diminished its genetic variation. Here, we demonstrate that transposable elements (TEs) are an important source of genetic variation that could account for its high phenotypic diversity. TEs are (i) highly enriched in C. rubella compared with its outcrossing sister species Capsella grandiflora, and (ii) 4.2% of polymorphic TEs in C. rubella are associated with variation in the expression levels of their adjacent genes. Furthermore, we show that frequent TE insertions at FLOWERING LOCUS C (FLC) in natural populations of C. rubella could explain 12.5% of the natural variation in flowering time, a key life history trait correlated with fitness and adaptation. In particular, we show that a recent TE insertion at the 3′ UTR of FLC affects mRNA stability, which results in reducing its steady-state expression levels, to promote the onset of flowering. Our results highlight that TE insertions can drive rapid phenotypic variation, which could potentially help with adaptation to changing environments in a species with limited standing genetic variation.
Collapse
|
48
|
Koenig D, Hagmann J, Li R, Bemm F, Slotte T, Neuffer B, Wright SI, Weigel D. Long-term balancing selection drives evolution of immunity genes in Capsella. eLife 2019; 8:e43606. [PMID: 30806624 PMCID: PMC6426441 DOI: 10.7554/elife.43606] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/26/2019] [Indexed: 12/14/2022] Open
Abstract
Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. By reconstructing the evolution of the disease-related locus MLO2b, we find that divergence between ancient haplotypes can be obscured by referenced based re-sequencing methods, and that trans-specific alleles can encode substantially diverged protein sequences. Our data point to long-term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.
Collapse
Affiliation(s)
- Daniel Koenig
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - Jörg Hagmann
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - Rachel Li
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - Felix Bemm
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - Tanja Slotte
- Department of Ecology,Environment, and Plant SciencesStockholm UniversityStockholmSweden
| | - Barbara Neuffer
- Department of BiologyUniversity of OsnabrückOsnabrückGermany
| | - Stephen I Wright
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoCanada
| | - Detlef Weigel
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| |
Collapse
|
49
|
Abstract
A major current molecular evolution challenge is to link comparative genomic patterns to species' biology and ecology. Breeding systems are pivotal because they affect many population genetic processes and thus genome evolution. We review theoretical predictions and empirical evidence about molecular evolutionary processes under three distinct breeding systems-outcrossing, selfing, and asexuality. Breeding systems may have a profound impact on genome evolution, including molecular evolutionary rates, base composition, genomic conflict, and possibly genome size. We present and discuss the similarities and differences between the effects of selfing and clonality. In reverse, comparative and population genomic data and approaches help revisiting old questions on the long-term evolution of breeding systems.
Collapse
Affiliation(s)
- Sylvain Glémin
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Clémentine M François
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France.
| |
Collapse
|
50
|
Bamba M, Kawaguchi YW, Tsuchimatsu T. Plant adaptation and speciation studied by population genomic approaches. Dev Growth Differ 2018; 61:12-24. [DOI: 10.1111/dgd.12578] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Masaru Bamba
- Department of Biology (Frontier Science Program); Graduate School of Science and Engineering; Chiba University; Chiba Japan
| | - Yawako W. Kawaguchi
- Department of Biology (Frontier Science Program); Graduate School of Science and Engineering; Chiba University; Chiba Japan
| | - Takashi Tsuchimatsu
- Department of Biology; Graduate School of Science; Chiba University; Chiba Japan
| |
Collapse
|