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Horvath R, Slotte T. The Role of Small RNA-Based Epigenetic Silencing for Purifying Selection on Transposable Elements in Capsella grandiflora. Genome Biol Evol 2018; 9:2911-2920. [PMID: 29036316 PMCID: PMC5737465 DOI: 10.1093/gbe/evx206] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2017] [Indexed: 12/13/2022] Open
Abstract
To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number of mechanisms, including RNA-directed DNA methylation. These epigenetic modifications can extend outside the boundaries of TE insertions and lead to silencing of nearby genes, resulting in a trade-off between TE silencing and interference with nearby gene regulation. Therefore, purifying selection is expected to remove silenced TE insertions near genes more efficiently and prevent their accumulation within a population. To explore how effects of TE silencing on gene regulation shapes purifying selection on TEs, we analyzed whole genome sequencing data from 166 individuals of a large population of the outcrossing species Capsella grandiflora. We found that most TEs are rare, and in chromosome arms, silenced TEs are exposed to stronger purifying selection than those that are not silenced by 24-nucleotide small RNAs, especially with increasing proximity to genes. An age-of-allele test of neutrality on a subset of TEs supports our inference of purifying selection on silenced TEs, suggesting that our results are robust to varying transposition rates. Our results provide new insights into the processes affecting the accumulation of TEs in an outcrossing species and support the view that epigenetic silencing of TEs results in a trade-off between preventing TE proliferation and interference with nearby gene regulation. We also suggest that in the centromeric and pericentromeric regions, the negative aspects of epigenetic TE silencing are missing.
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Affiliation(s)
- Robert Horvath
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
| | - Tanja Slotte
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
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52
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Moyers BT. Is Genetic Evolution Predictable? THE PLANT CELL 2018; 30:1171-1172. [PMID: 29895569 PMCID: PMC6048784 DOI: 10.1105/tpc.18.00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
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53
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Yang L, Wang HN, Hou XH, Zou YP, Han TS, Niu XM, Zhang J, Zhao Z, Todesco M, Balasubramanian S, Guo YL. Parallel Evolution of Common Allelic Variants Confers Flowering Diversity in Capsella rubella. THE PLANT CELL 2018; 30:1322-1336. [PMID: 29764984 PMCID: PMC6048796 DOI: 10.1105/tpc.18.00124] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/13/2018] [Accepted: 05/13/2018] [Indexed: 05/04/2023]
Abstract
Flowering time is an adaptive life history trait. Capsella rubella, a close relative of Arabidopsis thaliana and a young species, displays extensive variation for flowering time but low standing genetic variation due to an extreme bottleneck event, providing an excellent opportunity to understand how phenotypic diversity can occur with a limited initial gene pool. Here, we demonstrate that common allelic variation and parallel evolution at the FLC locus confer variation in flowering time in C. rubella. We show that two overlapping deletions in the 5' untranslated region (UTR) of C. rubella FLC, which are associated with local changes in chromatin conformation and histone modifications, reduce its expression levels and promote flowering. We further show that these two pervasive variants originated independently in natural C. rubella populations after speciation and spread to an intermediate frequency, suggesting a role of this parallel cis-regulatory change in adaptive evolution. Our results provide an example of how parallel mutations in the same 5' UTR region can shape phenotypic evolution in plants.
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Affiliation(s)
- Li Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hui-Na Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xing-Hui Hou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu-Pan Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting-Shen Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- 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
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong Zhao
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Marco Todesco
- Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | | | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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54
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Li L, Liu B, Deng X, Zhao H, Li H, Xing S, Fetzer DD, Li M, Nasrallah ME, Nasrallah JB, Liu P. Evolution of interspecies unilateral incompatibility in the relatives of Arabidopsis thaliana. Mol Ecol 2018; 27:2742-2753. [PMID: 29717521 DOI: 10.1111/mec.14707] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/07/2018] [Accepted: 04/11/2018] [Indexed: 11/26/2022]
Abstract
The evolutionary concurrence of intraspecies self-incompatibility (SI) and explosive angiosperm radiation in the Cretaceous have led to the hypothesis that SI was one of the predominant drivers of rapid speciation in angiosperms. Interspecies unilateral incompatibility (UI) usually occurs when pollen from a self-compatible (SC) species is rejected by the pistils of a SI species, while the reciprocal pollination is compatible (UC). Although this SI × SC type UI is most prevalent and viewed as a prezygotic isolation barrier to promote incipient speciation of angiosperms, comparative evidence to support such a role is lacking. We show that SI × SI type UI in SI species pairs is also common in the well-characterized accessions representing the four major lineages of the Arabidopsis genus and is developmentally regulated. This allowed us to reveal a strong correlation between UI strength and species divergence in these representative accessions. In addition, analyses of a SC accession and the pseudo-self-compatible (psc) spontaneous mutant of Arabidopsis lyrata indicate that UI shares, at least, common pollen rejection pathway with SI. Furthermore, genetic and genomic analyses of SI × SI type UI in A. lyrata × A. arenosa species pair showed that two major-effect quantitative trait loci are the stigma and pollen-side determinant of UI, respectively, which could be involved in heterospecies pollen discrimination. By revealing a close link between UI and SI pathway, particularly between UI and species divergence in these representative accessions, our findings establish a connection between SI and speciation. Thus, the pre-existence of SI system would have facilitated the evolution of UI and accordingly promote speciation.
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Affiliation(s)
- Ling Li
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Bo Liu
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Xiaomei Deng
- Beijing Engineering and Technological Research Center of Plant Tissue Culture, Beijing, China
| | - Hainan Zhao
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Hongyan Li
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Shilai Xing
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Della D Fetzer
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Mengya Li
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Mikhail E Nasrallah
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, New York
| | - June B Nasrallah
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, New York
| | - Pei Liu
- Department of Ecology, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
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55
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Serrato-Capuchina A, Matute DR. The Role of Transposable Elements in Speciation. Genes (Basel) 2018; 9:E254. [PMID: 29762547 PMCID: PMC5977194 DOI: 10.3390/genes9050254] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 01/20/2023] Open
Abstract
Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
| | - Daniel R Matute
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
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56
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Petrone Mendoza S, Lascoux M, Glémin S. Competitive ability of Capsella species with different mating systems and ploidy levels. ANNALS OF BOTANY 2018; 121:1257-1264. [PMID: 29471370 PMCID: PMC5946883 DOI: 10.1093/aob/mcy014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/19/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Capsella is a model genus for studying the transition from outcrossing to selfing, with or without change in ploidy levels. The genomic consequences and changes in reproductive traits (selfing syndrome) associated with these shifts have been studied in depth. However, potential ecological divergence among species of the genus has not been determined. Among ecological traits, competitive ability could be relevant for selfing evolution, as selfing has been shown to be statistically associated with reduced competitiveness in a recent meta-analysis. METHODS We assessed the effect of competition on three Capsella species differing in their mating system and ploidy level. We used an experimental design where fitness related traits were measured in focal individuals with and without competitors. KEY RESULTS The diploid selfer (C. rubella) was most sensitive to competition, whereas the tetraploid selfer (C. bursa-pastoris) performed the best, with the diploid outcrosser (C. grandiflora) being intermediate. CONCLUSIONS These results add to the detailed characterization of Capsella species and highlight the possible roles of ecological context and ploidy in the evolutionary trajectories of selfing species.
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Affiliation(s)
- Sandra Petrone Mendoza
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Institut des Sciences de l’Evolution (ISEM - UMR 5554 Université de Montpellier-CNRS-IRD-EPHE), France
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57
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Touzet P, Villain S, Buret L, Martin H, Holl A, Poux C, Cuguen J. Chloroplastic and nuclear diversity of wild beets at a large geographical scale: Insights into the evolutionary history of the Beta section. Ecol Evol 2018; 8:2890-2900. [PMID: 29531703 PMCID: PMC5838056 DOI: 10.1002/ece3.3774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 12/06/2017] [Accepted: 12/11/2017] [Indexed: 11/09/2022] Open
Abstract
Historical demographic processes and mating systems are believed to be major factors in the shaping of the intraspecies genetic diversity of plants. Among Caryophyllales, the Beta section of the genus Beta, within the Amaranthaceae/Chenopodiaceae alliance, is an interesting study model with species and subspecies (Beta macrocarpa, Beta patula, Beta vulgaris maritima and B.v. adanensis) differing in geographical distribution and mating system. In addition, one of the species, B. macrocarpa, mainly diploid, varies in its level of ploidy with a tetraploid cytotype described in the Canary Islands and in Portugal. In this study, we analyzed the nucleotide diversity of chloroplastic and nuclear sequences on a representative sampling of species and subspecies of the Beta section (except B. patula). Our objectives were (1) to assess their genetic relationships through phylogenetic and multivariate analyses, (2) relate their genetic diversity to their mating system, and (3) reconsider the ploidy status and the origin of the Canarian Beta macrocarpa.
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Affiliation(s)
- Pascal Touzet
- Univ. LilleCNRS, UMR 8198 – Evo‐Eco‐PaleoLilleFrance
| | - Sarah Villain
- Univ. LilleCNRS, UMR 8198 – Evo‐Eco‐PaleoLilleFrance
| | | | - Hélène Martin
- Univ. LilleCNRS, UMR 8198 – Evo‐Eco‐PaleoLilleFrance
| | | | - Céline Poux
- Univ. LilleCNRS, UMR 8198 – Evo‐Eco‐PaleoLilleFrance
| | - Joël Cuguen
- Univ. LilleCNRS, UMR 8198 – Evo‐Eco‐PaleoLilleFrance
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58
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López-Villalobos A, Eckert CG. Consequences of multiple mating-system shifts for population and range-wide genetic structure in a coastal dune plant. Mol Ecol 2018; 27:675-693. [PMID: 29319906 DOI: 10.1111/mec.14484] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 12/17/2017] [Accepted: 12/18/2017] [Indexed: 12/24/2022]
Abstract
Evolutionary transitions from outcrossing to selfing can strongly affect the genetic diversity and structure of species at multiple spatial scales. We investigated the genetic consequences of mating-system shifts in the North American, Pacific coast dune endemic plant Camissoniopsis cheiranthifolia (Onagraceae) by assaying variation at 13 nuclear (n) and six chloroplast (cp) microsatellite (SSR) loci for 38 populations across the species range. As predicted from the expected reduction in effective population size (Ne ) caused by selfing, small-flowered, predominantly selfing (SF) populations had much lower nSSR diversity (but not cpSSR) than large-flowered, predominantly outcrossing (LF) populations. The reduction in nSSR diversity was greater than expected from the effects of selfing on Ne alone, but could not be accounted for by indirect effects of selfing on population density. Although selfing should reduce gene flow, SF populations were not more genetically differentiated than LF populations. We detected five clusters of nSSR genotypes and three groups of cpSSR haplotypes across the species range consisting of parapatric groups of populations that usually (but not always) differed in mating system, suggesting that selfing may often initiate ecogeographic isolation. However, lineage-wide genetic variation was not lower for selfing clusters, failing to support the hypothesis that selection for reproductive assurance spurred the evolution of selfing in this species. Within three populations where LF and SF plants coexist, we detected genetic differentiation among diverged floral phenotypes suggesting that reproductive isolation (probably postzygotic) may help maintain the striking mating-system differentiation observed across the range of this species.
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Affiliation(s)
| | - C G Eckert
- Department of Biology, Queen's University, Kingston, ON, Canada
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59
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Fujikura U, Jing R, Hanada A, Takebayashi Y, Sakakibara H, Yamaguchi S, Kappel C, Lenhard M. Variation in Splicing Efficiency Underlies Morphological Evolution in Capsella. Dev Cell 2018; 44:192-203.e5. [DOI: 10.1016/j.devcel.2017.11.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/10/2017] [Accepted: 11/27/2017] [Indexed: 12/21/2022]
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60
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Voillemot M, Rougemont Q, Roux C, Pannell JR. The divergence history of the perennial plant Linaria cavanillesii
confirms a recent loss of self-incompatibility. J Evol Biol 2017; 31:136-147. [DOI: 10.1111/jeb.13209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 11/03/2017] [Accepted: 11/07/2017] [Indexed: 11/30/2022]
Affiliation(s)
- M. Voillemot
- Department of Ecology and Evolution; Biophore/Sorge; University of Lausanne; Lausanne Switzerland
| | - Q. Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS); University of Laval; Québec City Québec Canada
| | - C. Roux
- Department of Ecology and Evolution; Biophore/Sorge; University of Lausanne; Lausanne Switzerland
- Unité Evo-Eco-Paléo (EEP) - UMR 8198; CNRS; Université de Lille Sciences et Technologies; Villeneuve d'Ascq Cedex France
| | - J. R. Pannell
- Department of Ecology and Evolution; Biophore/Sorge; University of Lausanne; Lausanne Switzerland
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61
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Wu Q, Han TS, Chen X, Chen JF, Zou YP, Li ZW, Xu YC, Guo YL. Long-term balancing selection contributes to adaptation in Arabidopsis and its relatives. Genome Biol 2017; 18:217. [PMID: 29141655 PMCID: PMC5686891 DOI: 10.1186/s13059-017-1342-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/16/2017] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND In contrast to positive selection, which reduces genetic variation by fixing beneficial alleles, balancing selection maintains genetic variation within a population or species and plays crucial roles in adaptation in diverse organisms. However, which genes, genome-wide, are under balancing selection and the extent to which these genes are involved in adaptation are largely unknown. RESULTS We performed a genome-wide scan for genes under balancing selection across two plant species, Arabidopsis thaliana and its relative Capsella rubella, which diverged about 8 million generations ago. Among hundreds of genes with shared coding-region polymorphisms, we find evidence for long-term balancing selection in five genes: AT1G35220, AT2G16570, AT4G29360, AT5G38460, and AT5G44000. These genes are involved in the response to biotic and abiotic stress and other fundamental biochemical processes. More intriguingly, for these genes, we detected significant ecological diversification between the two haplotype groups, suggesting that balancing selection has been very important for adaptation. CONCLUSIONS Our results indicate that beyond the well-known S-locus genes and resistance genes, many loci are under balancing selection. These genes are mostly correlated with resistance to stress or other fundamental functions and likely play a more important role in adaptation to diverse habitats than previously thought.
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Affiliation(s)
- Qiong Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ting-Shen Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- 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
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu-Pan Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zi-Wen Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- 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.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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62
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Takuno S, Seymour DK, Gaut BS. The Evolutionary Dynamics of Orthologs That Shift in Gene Body Methylation between Arabidopsis Species. Mol Biol Evol 2017; 34:1479-1491. [PMID: 28333248 DOI: 10.1093/molbev/msx099] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA methylation labels a specific subset of genes in plant genomes. Recent work has shown that this gene-body methylation (gbM) is a conserved feature of orthologs, because highly methylated genes in one species tend to be highly methylated in another. In this study, we examined the exceptions to that rule by identifying genes that differ in gbM status between two plant species-Arabidopsis thaliana and Arabidopsis lyrata. Using Capsella grandiflora as an outgroup, we polarized the loss and gain of gbM for orthologs in the Arabidopsis lineage. Our survey identified a few hundred genes that differed between ingroup species, out of ∼9,000 orthologs. The estimated rate of gbM gain was ∼2 × 10-9 per gene per year for both ingroup taxa and was similar to the loss rate in A. lyrata. In contrast, A. thaliana had a ∼3-fold higher estimated rate of gbM loss per gene, consistent with a recent diminishment of genome size. As in previous studies, we found that body-methylated genes were expressed broadly across tissues and were also longer than other genic sets. Genes that differed in gbM status exhibited higher variance in expression between species than genes that were body-methylated in both species. Moreover, the gain of gbM in one lineage tended to be associated with an increase of expression in that lineage. The genes that varied in gbM status between species varied more significantly in length between species than other sets of genes; we hypothesize that length is a key feature in the transition between body-methylated and nonmethylated genes.
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Affiliation(s)
- Shohei Takuno
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Danelle K Seymour
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
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63
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Kerbs B, Ressler J, Kelly JK, Mort ME, Santos-Guerra A, Gibson MJS, Caujapé-Castells J, Crawford DJ. The potential role of hybridization in diversification and speciation in an insular plant lineage: insights from synthetic interspecific hybrids. AOB PLANTS 2017; 9:plx043. [PMID: 29225761 PMCID: PMC5714139 DOI: 10.1093/aobpla/plx043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 08/25/2017] [Indexed: 05/17/2023]
Abstract
Hybridization is recognized as an important process in plant evolution, and this may be particularly true for island plants where several biotic and abiotic factors facilitate interspecific hybridization. Although rarely done, experimental studies could provide insights into the potential of natural hybridization to generate diversity when species come into contact in the dynamic island setting. The potential of hybridization to generate morphological variation was analysed within and among 12 families (inbred lines) of an F4 hybrid generation between two species of Tolpis endemic to the Canary Islands. Combinations of characters not seen in the parents were present in hybrids. Several floral and vegetative characters were transgressive relative to their parents. Morphometric studies of floral, vegetative and fruit characters revealed that several F4 families were phenotypically distinct from other families, and from their parents. The study demonstrates that morphologically distinct pollen-fertile lines, potentially worthy of taxonomic recognition if occurring in nature, can be generated in four generations. The ability of the hybrid lines to set self-seed would reduce gene flow among the lines, and among the hybrids and their parental species. Selfing would also facilitate the fixation of characters within each of the lines. Overall, the results show the considerable potential of hybridization for generating diversity and distinct phenotypes in island lineages.
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Affiliation(s)
- Benjamin Kerbs
- Department of Biological Sciences, Emporia State University, Emporia, KS 66801, USA
| | - Jacob Ressler
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - John K Kelly
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7534, USA
| | - Mark E Mort
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7534, USA
| | - Arnoldo Santos-Guerra
- Calle Guaidil 16, Urbanización Tamarco, 38280 Tegueste, Tenerife, Canary Islands, Spain
| | | | - Juli Caujapé-Castells
- Jardín Botánico 13 Canario “Viera y Clavijo”-Unidad Asociada al CSIC (Cabildo de Gran Canaria), Camino del palmeral 14 15 (Tafira Alta), 35017 Las Palmas de Gran Canaria, Spain
| | - Daniel J Crawford
- Department of Ecology & Evolutionary Biology, and the Biodiversity Institute, University of Kansas, Lawrence, KS 66045-7534, USA
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64
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Settepani V, Schou MF, Greve M, Grinsted L, Bechsgaard J, Bilde T. Evolution of sociality in spiders leads to depleted genomic diversity at both population and species levels. Mol Ecol 2017; 26:4197-4210. [DOI: 10.1111/mec.14196] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 12/21/2022]
Affiliation(s)
- V. Settepani
- Department of Bioscience; Aarhus University; Aarhus C Denmark
| | - M. F. Schou
- Department of Bioscience; Aarhus University; Aarhus C Denmark
| | - M. Greve
- Department of Plant Science; University of Pretoria; Hatfield South Africa
| | - L. Grinsted
- School of Biological Sciences; Royal Holloway University of London; Egham UK
| | - J. Bechsgaard
- Department of Bioscience; Aarhus University; Aarhus C Denmark
| | - T. Bilde
- Department of Bioscience; Aarhus University; Aarhus C Denmark
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65
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African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2017; 114:5213-5218. [PMID: 28473417 DOI: 10.1073/pnas.1616736114] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Over the past 20 y, many studies have examined the history of the plant ecological and molecular model, Arabidopsis thaliana, in Europe and North America. Although these studies informed us about the recent history of the species, the early history has remained elusive. In a large-scale genomic analysis of African A. thaliana, we sequenced the genomes of 78 modern and herbarium samples from Africa and analyzed these together with over 1,000 previously sequenced Eurasian samples. In striking contrast to expectations, we find that all African individuals sampled are native to this continent, including those from sub-Saharan Africa. Moreover, we show that Africa harbors the greatest variation and represents the deepest history in the A. thaliana lineage. Our results also reveal evidence that selfing, a major defining characteristic of the species, evolved in a single geographic region, best represented today within Africa. Demographic inference supports a model in which the ancestral A. thaliana population began to split by 120-90 kya, during the last interglacial and Abbassia pluvial, and Eurasian populations subsequently separated from one another at around 40 kya. This bears striking similarities to the patterns observed for diverse species, including humans, implying a key role for climatic events during interglacial and pluvial periods in shaping the histories and current distributions of a wide range of species.
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66
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Levin DA, Scarpino SV. On the young age of intraspecific herbaceous taxa. THE NEW PHYTOLOGIST 2017; 213:1513-1520. [PMID: 27726173 DOI: 10.1111/nph.14224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
Dated phylogenies rarely include the divergence times of sister intraspecific taxa, and when they do little is said about this subject. We show that over 90% of the intraspecific plant taxa found in a literature search are estimated to be 5 million yr old or younger, with only 4% of taxa estimated to be over 10 million yr old or older. A Bayesian analysis of intraspecific taxon ages indicates that indeed these taxa are expected to be < 10 million yr old. This result for the young age of intraspecific taxa is consistent with the earlier observation that post-pollination reproductive barriers develop between 5 and 10 million yr after lineage splitting, thus leading to species formation. If lineages have not graduated to the species level of divergence by 10 million yr or so, they are likely to have gone extinct by that time as a result of narrow geographical distributions, narrow niche breadths, and relatively small numbers across populations.
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Affiliation(s)
- Donald A Levin
- Department of Integrative Biology, University of Texas, Austin, TX 78713, USA
| | - Samuel V Scarpino
- Department of Mathematics & Statistics, University of Vermont, Burlington, VT 05401, USA
- Complex Systems Center, University of Vermont, Burlington, VT 05401, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
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68
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Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora. Proc Natl Acad Sci U S A 2017; 114:1087-1092. [PMID: 28096395 DOI: 10.1073/pnas.1612561114] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation (i) are under weaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis-regulatory variation in a wide range of plant species.
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69
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Voillemot M, Pannell JR. Maintenance of mixed mating after the loss of self-incompatibility in a long-lived perennial herb. ANNALS OF BOTANY 2017; 119:177-190. [PMID: 27941096 PMCID: PMC5218368 DOI: 10.1093/aob/mcw203] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/23/2016] [Accepted: 07/19/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Many hermaphroditic plants avoid self-fertilization by means of a molecular self-incompatibility (SI) system, a complex trait that is difficult to evolve but relatively easy to lose. Loss of SI is a prerequisite for an evolutionary transition from obligate outcrossing to self-fertilization, which may bring about rapid changes in the genetic diversity and structure of populations. Loss of SI is also often followed by the evolution of a 'selfing syndrome', with plants having small flowers, little nectar and few pollen grains per ovule. Here, we document the loss of SI in the long-lived Spanish toadflax Linaria cavanillesii, which has led to mixed mating rather than a transition to a high rate of selfing and in which an outcrossing syndrome has been maintained. METHODS We performed crosses within and among six populations of L. cavanillesii in the glasshouse, measured floral traits in a common-garden experiment, performed a pollen-limitation experiment in the field and conducted population genetic analyses using microsatellites markers. KEY RESULTS Controlled crosses revealed variation in SI from fully SI through intermediate SI to fully self-compatible (SC). Flowers of SC individuals showed no evidence of a selfing syndrome. Although the SC population of L. cavanillesii had lower within-population genetic diversity than SI populations, as expected, population differentiation among all populations was extreme and represents an FST outlier in the distribution for both selfing and outcrossing species of flowering plants. CONCLUSIONS Together, our results suggest that the transition to SC in L. cavanillesii has probably been very recent, and may have been aided by selection during or following a colonization bottleneck rather than in the absence of pollinators. We find little indication that the transition to SC has been driven by selection for reproductive assurance under conditions currently prevailing in natural populations.
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Affiliation(s)
- Marie Voillemot
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - John R Pannell
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, CH-1015 Lausanne, Switzerland
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70
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Kuester A, Fall E, Chang SM, Baucom RS. Shifts in outcrossing rates and changes to floral traits are associated with the evolution of herbicide resistance in the common morning glory. Ecol Lett 2017; 20:41-49. [PMID: 27905176 DOI: 10.1111/ele.12703] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/27/2016] [Accepted: 10/18/2016] [Indexed: 01/19/2023]
Abstract
Human-mediated selection can strongly influence the evolutionary response of natural organisms within ecological timescales. But what traits allow for, or even facilitate, adaptation to the strong selection humans impose on natural systems? Using a combination of laboratory and greenhouse studies of 32 natural populations of the common agricultural weed, Ipomoea purpurea, we show that herbicide-resistant populations self-fertilise more than susceptible populations. We likewise show that anther-stigma distance, a floral trait associated with self-fertilisation in this species, exhibits a nonlinear relationship with resistance such that the most and least resistant populations exhibit lower anther-stigma separation compared to populations with moderate levels of resistance. Overall, our results extend the general finding that plant mating can be impacted by human-mediated agents of selection to that of the extreme selection of the agricultural system. This work highlights the influence of human-mediated selection on rapid responses of natural populations that can lead to unexpected long-term evolutionary consequences.
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Affiliation(s)
- Adam Kuester
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Eva Fall
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Shu-Mei Chang
- Plant Biology Department, University of Georgia, Athens, GA, 30602, USA
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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71
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Sas C, Müller F, Kappel C, Kent TV, Wright SI, Hilker M, Lenhard M. Repeated Inactivation of the First Committed Enzyme Underlies the Loss of Benzaldehyde Emission after the Selfing Transition in Capsella. Curr Biol 2016; 26:3313-3319. [PMID: 27916528 DOI: 10.1016/j.cub.2016.10.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 01/05/2023]
Abstract
The enormous species richness of flowering plants is at least partly due to floral diversification driven by interactions between plants and their animal pollinators [1, 2]. Specific pollinator attraction relies on visual and olfactory floral cues [3-5]; floral scent can not only attract pollinators but also attract or repel herbivorous insects [6-8]. However, despite its central role for plant-animal interactions, the genetic control of floral scent production and its evolutionary modification remain incompletely understood [9-13]. Benzenoids are an important class of floral scent compounds that are generated from phenylalanine via several enzymatic pathways [14-17]. Here we address the genetic basis of the loss of floral scent associated with the transition from outbreeding to selfing in the genus Capsella. While the outbreeding C. grandiflora emits benzaldehyde as a major constituent of its floral scent, this has been lost in the selfing C. rubella. We identify the Capsella CNL1 gene encoding cinnamate:CoA ligase as responsible for this variation. Population genetic analysis indicates that CNL1 has been inactivated twice independently in C. rubella via different novel mutations to its coding sequence. Together with a recent study in Petunia [18], this identifies cinnamate:CoA ligase as an evolutionary hotspot for mutations causing the loss of benzenoid scent compounds in association with a shift in the reproductive strategy of Capsella from pollination by insects to self-fertilization.
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Affiliation(s)
- Claudia Sas
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam-Golm, Germany
| | - Frank Müller
- Institute of Biology, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Haderslebener Straße 9, 12163 Berlin, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam-Golm, Germany
| | - Tyler V Kent
- 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
| | - Monika Hilker
- Institute of Biology, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Haderslebener Straße 9, 12163 Berlin, Germany
| | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam-Golm, Germany.
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72
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Carleial S, van Kleunen M, Stift M. Small reductions in corolla size and pollen: ovule ratio, but no changes in flower shape in selfing populations of the North American Arabidopsis lyrata. Oecologia 2016; 183:401-413. [DOI: 10.1007/s00442-016-3773-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 11/08/2016] [Indexed: 12/31/2022]
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73
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Standing genetic variation in a tissue-specific enhancer underlies selfing-syndrome evolution in Capsella. Proc Natl Acad Sci U S A 2016; 113:13911-13916. [PMID: 27849572 DOI: 10.1073/pnas.1613394113] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mating system shifts recurrently drive specific changes in organ dimensions. The shift in mating system from out-breeding to selfing is one of the most frequent evolutionary transitions in flowering plants and is often associated with an organ-specific reduction in flower size. However, the evolutionary paths along which polygenic traits, such as size, evolve are poorly understood. In particular, it is unclear how natural selection can specifically modulate the size of one organ despite the pleiotropic action of most known growth regulators. Here, we demonstrate that allelic variation in the intron of a general growth regulator contributed to the specific reduction of petal size after the transition to selfing in the genus Capsella Variation within this intron affects an organ-specific enhancer that regulates the level of STERILE APETALA (SAP) protein in the developing petals. The resulting decrease in SAP activity leads to a shortening of the cell proliferation period and reduced number of petal cells. The absence of private polymorphisms at the causal region in the selfing species suggests that the small-petal allele was captured from standing genetic variation in the ancestral out-crossing population. Petal-size variation in the current out-crossing population indicates that several small-effect mutations have contributed to reduce petal-size. These data demonstrate how tissue-specific regulatory elements in pleiotropic genes contribute to organ-specific evolution. In addition, they provide a plausible evolutionary explanation for the rapid evolution of flower size after the out-breeding-to-selfing transition based on additive effects of segregating alleles.
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74
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Hatorangan MR, Laenen B, Steige KA, Slotte T, Köhler C. Rapid Evolution of Genomic Imprinting in Two Species of the Brassicaceae. THE PLANT CELL 2016; 28:1815-27. [PMID: 27465027 PMCID: PMC5006707 DOI: 10.1105/tpc.16.00304] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/16/2016] [Accepted: 07/21/2016] [Indexed: 05/21/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon occurring in mammals and flowering plants that causes genes to adopt a parent-of-origin-specific mode of expression. While the imprinting status of genes is well conserved in mammals, clear estimates for the degree of conservation were lacking in plants. We therefore analyzed the genome-wide imprinting status of Capsella rubella, which shared a common recent ancestor with Arabidopsis thaliana ∼10 to 14 million years ago. However, only ∼14% of maternally expressed genes (MEGs) and ∼29% of paternally expressed genes (PEGs) in C. rubella were commonly imprinted in both species, revealing that genomic imprinting is a rapidly evolving phenomenon in plants. Nevertheless, conserved PEGs exhibited signs of selection, suggesting that a subset of imprinted genes play an important functional role and are therefore maintained in plants. Like in Arabidopsis, PEGs in C. rubella are frequently associated with the presence of transposable elements that preferentially belong to helitron and MuDR families. Our data further reveal that MEGs and PEGs differ in their targeting by 24-nucleotide small RNAs and asymmetric DNA methylation, suggesting different mechanisms establishing DNA methylation at MEGs and PEGs.
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Affiliation(s)
- Marcelinus R Hatorangan
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750 07 Uppsala, Sweden
| | - Benjamin Laenen
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Kim A Steige
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750 07 Uppsala, Sweden
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75
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Ågren JA, Huang HR, Wright SI. Transposable element evolution in the allotetraploid Capsella bursa-pastoris. AMERICAN JOURNAL OF BOTANY 2016; 103:1197-1202. [PMID: 27440791 DOI: 10.3732/ajb.1600103] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/20/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Shifts in ploidy affect the evolutionary dynamics of genomes in a myriad of ways. Population genetic theory predicts that transposable element (TE) proliferation may follow because the genomewide efficacy of selection should be reduced and the increase in gene copies may mask the deleterious effects of TE insertions. Moreover, in allopolyploids, TEs may further accumulate because of hybrid breakdown of TE silencing. However, to date the evidence of TE proliferation following an increase in ploidy is mixed, and the relative importance of relaxed selection vs. silencing breakdown remains unclear. METHODS We used high-coverage whole-genome sequence data to evaluate the abundance, genomic distribution, and population frequencies of TEs in the self-fertilizing recent allotetraploid Capsella bursa-pastoris (Brassicaceae). We then compared the C. bursa-pastoris TE profile with that of its two parental diploid species, outcrossing C. grandiflora and self-fertilizing C. orientalis. KEY RESULTS We found no evidence that C. bursa-pastoris has experienced a large genomewide proliferation of TEs relative to its parental species. However, when centromeric regions are excluded, we found evidence of significantly higher abundance of retrotransposons in C. bursa-pastoris along the gene-rich chromosome arms compared with C. grandiflora and C. orientalis. CONCLUSIONS The lack of a genomewide effect of allopolyploidy on TE abundance, combined with the increases TE abundance in gene-rich regions, suggests that relaxed selection rather than hybrid breakdown of host silencing explains the TE accumulation in C. bursa-pastoris.
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Affiliation(s)
- J Arvid Ågren
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Hui-Run Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, China
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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76
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Indriolo E, Goring DR. Yeast two-hybrid interactions between Arabidopsis lyrata S Receptor Kinase and the ARC1 E3 ligase. PLANT SIGNALING & BEHAVIOR 2016; 11:e1188233. [PMID: 27175603 PMCID: PMC4973788 DOI: 10.1080/15592324.2016.1188233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Here we describe protein-protein interactions between signaling components in the conserved self-incompatibility pathway from Brassica spp. and Arabidopsis lyrata. Previously, we had demonstrated that ARC1 is necessary in A. lyrata for the rejection of self-pollen by the self-incompatibility pathway. The results described here demonstrate that A. lyrata ARC1 interacts with A. lyrata S Receptor Kinase (SRK1) in the yeast 2-hybrid system. A. lyrata ARC1 also interacted with B. napus SRK910 illustrating that interactions in this pathway are conserved across species. Finally, we discuss how the more widely occurring interactions between SRK and ARC1-related family members may be modulated in vivo by expression and subcellular localization patterns resulting in a particular response.
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Affiliation(s)
- Emily Indriolo
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- CONTACT Emily Indriolo ; Daphne Goring
| | - Daphne R. Goring
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
- CONTACT Emily Indriolo ; Daphne Goring
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77
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Herman AC, Schoen DJ. Recent selection for self-compatibility in a population of Leavenworthia alabamica. Evolution 2016; 70:1212-24. [PMID: 27139712 DOI: 10.1111/evo.12937] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 04/13/2016] [Accepted: 04/26/2016] [Indexed: 12/28/2022]
Abstract
The evolution of self-compatibility (SC) is the first step in the evolutionary transition in plants from outcrossing enforced by self-incompatibility (SI) to self-fertilization. In the Brassicaceae, SI is controlled by alleles of two tightly linked genes at the S-locus. Despite permitting inbreeding, mutations at the S-locus leading to SC may be selected if they provide reproductive assurance and/or gain a transmission advantage in a population when SC plants self- and outcross. Positive selection can leave a genomic signature in the regions physically linked to the focus of selection when selection has occurred recently. From an SC population of Leavenworthia alabamica with a known nonfunctional mutation at the S-locus, we collected sequence data from a ∼690 Kb region surrounding the S-locus, as well as from regions not linked to the S-locus. To test for recent positive selection acting at the S-locus, we examined polymorphism and the site-frequency spectra. Using forward simulations, we demonstrate that recent selection of the strength expected for SC at a locus formerly under balancing selection can generate patterns similar to those seen in our empirical data.
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Affiliation(s)
- Adam C Herman
- Department of Biology, McGill University, Montreal, Quebec, H3A 1B1, Canada. .,Current Address: Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, 55108.
| | - Daniel J Schoen
- Department of Biology, McGill University, Montreal, Quebec, H3A 1B1, Canada
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78
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Nicotra AB, Chong C, Bragg JG, Ong CR, Aitken NC, Chuah A, Lepschi B, Borevitz JO. Population and phylogenomic decomposition via genotyping-by-sequencing in Australian Pelargonium. Mol Ecol 2016; 25:2000-14. [PMID: 26864117 DOI: 10.1111/mec.13584] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 01/21/2016] [Accepted: 01/26/2016] [Indexed: 02/05/2023]
Abstract
Species delimitation has seen a paradigm shift as increasing accessibility of genomic-scale data enables separation of lineages with convergent morphological traits and the merging of recently diverged ecotypes that have distinguishing characteristics. We inferred the process of lineage formation among Australian species in the widespread and highly variable genus Pelargonium by combining phylogenomic and population genomic analyses along with breeding system studies and character analysis. Phylogenomic analysis and population genetic clustering supported seven of the eight currently described species but provided little evidence for differences in genetic structure within the most widely distributed group that containing P. australe. In contrast, morphometric analysis detected three deep lineages within Australian Pelargonium; with P. australe consisting of five previously unrecognized entities occupying separate geographic ranges. The genomic approach enabled elucidation of parallel evolution in some traits formerly used to delineate species, as well as identification of ecotypic morphological differentiation within recognized species. Highly variable morphology and trait convergence each contribute to the discordance between phylogenomic relationships and morphological taxonomy. Data suggest that genetic divergence among species within the Australian Pelargonium may result from allopatric speciation while morphological differentiation within and among species may be more strongly driven by environmental differences.
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Affiliation(s)
- Adrienne B Nicotra
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Caroline Chong
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia.,Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Jason G Bragg
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Chong Ren Ong
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Nicola C Aitken
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Aaron Chuah
- Genome Discovery Unit, Australian National University, Canberra, ACT, 0200, Australia
| | - Brendan Lepschi
- Australian National Herbarium, Centre for Australian National Biodiversity Research, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia.,Centre of Excellence in Plant Energy Biology, Australian National University, ACT, 2601, Australia
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79
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Buckley J, Kilbride E, Cevik V, Vicente JG, Holub EB, Mable BK. R-gene variation across Arabidopsis lyrata subspecies: effects of population structure, selection and mating system. BMC Evol Biol 2016; 16:93. [PMID: 27150007 PMCID: PMC4858910 DOI: 10.1186/s12862-016-0665-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/23/2016] [Indexed: 11/10/2022] Open
Abstract
Background Examining allelic variation of R-genes in closely related perennial species of Arabidopsis thaliana is critical to understanding how population structure and ecology interact with selection to shape the evolution of innate immunity in plants. We finely sampled natural populations of Arabidopsis lyrata from the Great Lakes region of North America (A. l. lyrata) and broadly sampled six European countries (A. l. petraea) to investigate allelic variation of two R-genes (RPM1 and WRR4) and neutral genetic markers (Restriction Associated DNA sequences and microsatellites) in relation to mating system, phylogeographic structure and subspecies divergence. Results Fine-scale sampling of populations revealed strong effects of mating system and population structure on patterns of polymorphism for both neutral loci and R-genes, with no strong evidence for selection. Broad geographic sampling revealed evidence of balancing selection maintaining polymorphism in R-genes, with elevated heterozygosity and diversity compared to neutral expectations and sharing of alleles among diverged subspecies. Codon-based tests detected both positive and purifying selection for both R-genes, as commonly found for animal immune genes. Conclusions Our results highlight that combining fine and broad-scale sampling strategies can reveal the multiple factors influencing polymorphism and divergence at potentially adaptive genes such as R-genes. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0665-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James Buckley
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK. .,Current address: Center for Adaptation to a Changing Environment, ETH Zurich, Zurich, 8092, Switzerland.
| | - Elizabeth Kilbride
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Volkan Cevik
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, CV359EF, UK.,Current address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR47UH, UK
| | - Joana G Vicente
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, CV359EF, UK
| | - Eric B Holub
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, CV359EF, UK
| | - Barbara K Mable
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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Kartzinel RY, Spalink D, Waller DM, Givnish TJ. Divergence and isolation of cryptic sympatric taxa within the annual legume Amphicarpaea bracteata. Ecol Evol 2016; 6:3367-79. [PMID: 27103991 PMCID: PMC4833626 DOI: 10.1002/ece3.2134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 11/22/2022] Open
Abstract
The amphicarpic annual legume Amphicarpaea bracteata is unusual in producing aerial and subterranean cleistogamous flowers that always self‐fertilize and, less commonly, aerial chasmogamous flowers that outcross. Although both morphologic and genetic variants are known in this highly selfing species, debate continues over whether this variation is continuous, reflecting the segregation of standing genetic variation, or discontinuous, reflecting distinct taxa that rarely intercross. We characterized SNP variation in 128 individuals in southern Wisconsin to assess within‐ and among‐population variation at 3928 SNPs. We also assessed genotype and leaf morphology in an additional 76 individuals to connect phenotypic variation with genetic variation. Genetic variation maps onto three strongly divergent and highly inbred genetic groups showing little relation to site location. Each group has a distinct phenotype, but the divergence of these groups differs from the varietal divisions previously identified based on morphological characters. Like previous authors, we argue that the taxonomy of this species should be revised. Despite extensive sympatry, estimates of among‐group migration rates are low, and hybrid individuals were at low frequency (<2%) in our dataset. Restricted gene flow likely results from high selfing rates and partial reproductive incompatibility as evidenced by the U‐shaped distribution of pairwise FST values reflecting “islands” of genomic divergence. These islands may be associated with hybrid incompatibility loci that arose in allopatry. The coexistence of lineages within sites may reflect density‐dependent attack by species‐specific strains of pathogenic fungi and/or root‐nodulating bacteria specializing on distinct genotypes.
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Affiliation(s)
- Rebecca Y Kartzinel
- Department of Botany University of Wisconsin-Madison 430 Lincoln Drive Madison Wisconsin 53706
| | - Daniel Spalink
- Department of Botany University of Wisconsin-Madison 430 Lincoln Drive Madison Wisconsin 53706
| | - Donald M Waller
- Department of Botany University of Wisconsin-Madison 430 Lincoln Drive Madison Wisconsin 53706
| | - Thomas J Givnish
- Department of Botany University of Wisconsin-Madison 430 Lincoln Drive Madison Wisconsin 53706
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81
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Noël E, Chemtob Y, Janicke T, Sarda V, Pélissié B, Jarne P, David P. Reduced mate availability leads to evolution of self-fertilization and purging of inbreeding depression in a hermaphrodite. Evolution 2016; 70:625-40. [DOI: 10.1111/evo.12886] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/02/2016] [Accepted: 02/05/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Elsa Noël
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS, Université de Montpellier; Université Paul Valéry Montpellier; EPHE, 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - Yohann Chemtob
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS, Université de Montpellier; Université Paul Valéry Montpellier; EPHE, 1919 route de Mende 34293 Montpellier Cedex 5 France
- Laboratoire Interdisciplinaire des Energies de Demain (LIED), UMR 8236; Université Paris Diderot; UFR Physique, Bâtiment Condorcet, 10 Rue A. Domon et L. Duquet 75205 Paris Cedex 13 France
| | - Tim Janicke
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS, Université de Montpellier; Université Paul Valéry Montpellier; EPHE, 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - Violette Sarda
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS, Université de Montpellier; Université Paul Valéry Montpellier; EPHE, 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - Benjamin Pélissié
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS, Université de Montpellier; Université Paul Valéry Montpellier; EPHE, 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - Philippe Jarne
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS, Université de Montpellier; Université Paul Valéry Montpellier; EPHE, 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - Patrice David
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS, Université de Montpellier; Université Paul Valéry Montpellier; EPHE, 1919 route de Mende 34293 Montpellier Cedex 5 France
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82
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Qiao Q, Wang Q, Han X, Guan Y, Sun H, Zhong Y, Huang J, Zhang T. Transcriptome sequencing of Crucihimalaya himalaica (Brassicaceae) reveals how Arabidopsis close relative adapt to the Qinghai-Tibet Plateau. Sci Rep 2016; 6:21729. [PMID: 26906946 PMCID: PMC4764839 DOI: 10.1038/srep21729] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/29/2016] [Indexed: 12/12/2022] Open
Abstract
The extreme environment of the Qinghai-Tibet Plateau (QTP) provides an ideal natural laboratory for studies on adaptive evolution. Few genome/transcriptome based studies have been conducted on how plants adapt to the environments of QTP compared to numerous studies on vertebrates. Crucihimalaya himalaica is a close relative of Arabidopsis with typical QTP distribution, and is hoped to be a new model system to study speciation and ecological adaptation in extreme environment. In this study, we de novo generated a transcriptome sequence of C. himalaica, with a total of 49,438 unigenes. Compared to five relatives, 10,487 orthogroups were shared by all six species, and 4,286 orthogroups contain putative single copy gene. Further analysis identified 487 extremely significantly positively selected genes (PSGs) in C. himalaica transcriptome. Theses PSGs were enriched in functions related to specific adaptation traits, such as response to radiation, DNA repair, nitrogen metabolism, and stabilization of membrane. These functions are responsible for the adaptation of C. himalaica to the high radiation, soil depletion and low temperature environments on QTP. Our findings indicate that C. himalaica has evolved complex strategies for adapting to the extreme environments on QTP and provide novel insights into genetic mechanisms of highland adaptation in plants.
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Affiliation(s)
- Qin Qiao
- School of Agriculture, Yunnan University, Kunming 650091, China
| | - Qia Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.,University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xi Han
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yanlong Guan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yang Zhong
- Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Ticao Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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83
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Pettengill JB, Briscoe Runquist RD, Moeller DA. Mating system divergence affects the distribution of sequence diversity within and among populations of recently diverged subspecies of Clarkia xantiana (Onagraceae). AMERICAN JOURNAL OF BOTANY 2016; 103:99-109. [PMID: 26643885 DOI: 10.3732/ajb.1500147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/14/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY The population biology of outcrossing and self-fertilizing taxa is thought to differ because of the advantage that selfers have in colonizing unoccupied sites where mates and pollinators may be limiting (Baker's Law). This reduced tendency for outcrossers to colonize new sites, along with their greater dependence on pollinators to disperse pollen, has the potential to differently influence the genetic diversity and structure of outcrossing and selfing populations. METHODS We conducted a comparative population genetic study of two sister outcrossing and selfing subspecies of Clarkia xantiana that have very recently diverged. We used DNA sequence variation (>40 kb from eight nuclear loci) from large samples of individuals from 14 populations to assess geographic patterns of genetic diversity and make inferences about the demographic and colonization histories of each subspecies. KEY RESULTS We show that sequence variation is strongly reduced across all selfing populations. The demographic history of selfing populations exhibits recent colonization bottlenecks, whereas such bottlenecks are rarely observed for the outcrosser. The greater effect of genetic drift in the selfer has resulted in strong population genetic structure, but with no pattern of isolation by distance. By contrast, the stronger effect of gene flow in the outcrosser has resulted in considerably less structure, but a significant pattern of isolation by distance. CONCLUSIONS Taken together, our results suggest that selfing populations are not at migration-drift equilibrium, are affected by strong episodes of genetic drift during colonization, and experience little or no subsequent gene flow from other populations after those founder events.
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Affiliation(s)
- James B Pettengill
- Department of Plant Biology, 1445 Gortner Avenue, University of Minnesota, Saint Paul, Minnesota 55108 USA
| | - Ryan D Briscoe Runquist
- Department of Plant Biology, 1445 Gortner Avenue, University of Minnesota, Saint Paul, Minnesota 55108 USA
| | - David A Moeller
- Department of Plant Biology, 1445 Gortner Avenue, University of Minnesota, Saint Paul, Minnesota 55108 USA
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84
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Grossenbacher D, Briscoe Runquist RD, Goldberg EE, Brandvain Y. No association between plant mating system and geographic range overlap. AMERICAN JOURNAL OF BOTANY 2016; 103:110-117. [PMID: 26643886 DOI: 10.3732/ajb.1500078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 06/15/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Automatic self-fertilization may influence the geography of speciation, promote reproductive isolation between incipient species, and lead to ecological differentiation. As such, selfing taxa are predicted to co-occur more often with their closest relatives than are outcrossing taxa. Despite suggestions that this pattern may be general, the extent to which mating system influences range overlap in close relatives has not been tested formally across a diverse group of plant species pairs. METHODS We tested for a difference in range overlap between species pairs for which zero, one, or both species are selfers, using data from 98 sister species pairs in 20 genera across 15 flowering plant families. We also used divergence time estimates from time-calibrated phylogenies to ask how range overlap changes with divergence time and whether this effect depends on mating system. KEY RESULTS We found no evidence that automatic self-fertilization influenced range overlap of closely related plant species. Sister pairs with more recent divergence times had modestly greater range overlap, but this effect did not depend on mating system. CONCLUSIONS The absence of a strong influence of mating system on range overlap suggests that mating system plays a minor or inconsistent role compared with many other mechanisms potentially influencing the co-occurrence of close relatives.
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Affiliation(s)
- Dena Grossenbacher
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 USA
| | | | - Emma E Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108 USA
| | - Yaniv Brandvain
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 USA
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85
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Shimizu KK, Tsuchimatsu T. Evolution of Selfing: Recurrent Patterns in Molecular Adaptation. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054249] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Selfing has evolved in animals, fungi, and plants, and since Darwin's pioneering study, it is considered one of the most frequent evolutionary trends in flowering plants. Generally, the evolution of selfing is characterized by a loss of self-incompatibility, the selfing syndrome, and changes in genome-wide polymorphism patterns. Recent interdisciplinary studies involving molecular functional experiments, genome-wide data, experimental evolution, and evolutionary ecology using Arabidopsis thaliana, Caenorhabditis elegans, and other species show that the evolution of selfing is not merely a degradation of outcrossing traits but a model for studying the recurrent patterns underlying adaptive molecular evolution. For example, in wild Arabidopsis relatives, self-compatibility evolved from mutations in the male specificity gene, S-LOCUS CYSTEINE-RICH PROTEIN/S-LOCUS PROTEIN 11 (SCR/SP11), rather than the female specificity gene, S-LOCUS RECEPTOR KINASE (SRK), supporting the theoretical prediction of sexual asymmetry. Prevalence of dominant self-compatible mutations is consistent with Haldane's sieve, which acts against recessive adaptive mutations. Time estimates based on genome-wide polymorphisms and self-incompatibility genes generally support the recent origin of selfing.
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Affiliation(s)
- Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Takashi Tsuchimatsu
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo 153-8902, Japan
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86
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Gamisch A, Fischer GA, Comes HP. Multiple independent origins of auto-pollination in tropical orchids (Bulbophyllum) in light of the hypothesis of selfing as an evolutionary dead end. BMC Evol Biol 2015; 15:192. [PMID: 26376901 PMCID: PMC4574068 DOI: 10.1186/s12862-015-0471-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/28/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The transition from outcrossing to selfing has long been portrayed as an 'evolutionary dead end' because, first, reversals are unlikely and, second, selfing lineages suffer from higher rates of extinction owing to a reduced potential for adaptation and the accumulation of deleterious mutations. We tested these two predictions in a clade of Madagascan Bulbophyllum orchids (30 spp.), including eight species where auto-pollinating morphs (i.e., selfers, without a 'rostellum') co-exist with their pollinator-dependent conspecifics (i.e., outcrossers, possessing a rostellum). Specifically, we addressed this issue on the basis of a time-calibrated phylogeny by means of ancestral character reconstructions and within the state-dependent evolution framework of BiSSE (Binary State Speciation and Extinction), which allowed jointly estimating rates of transition, speciation, and extinction between outcrossing and selfing. RESULTS The eight species capable of selfing occurred in scattered positions across the phylogeny, with two likely originating in the Pliocene (ca. 4.4-3.1 Ma), one in the Early Pleistocene (ca. 2.4 Ma), and five since the mid-Pleistocene (ca. ≤ 1.3 Ma). We infer that this scattered phylogenetic distribution of selfing is best described by models including up to eight independent outcrossing-to-selfing transitions and very low rates of speciation (and either moderate or zero rates of extinction) associated with selfing. CONCLUSIONS The frequent and irreversible outcrossing-to-selfing transitions in Madagascan Bulbophyllum are clearly congruent with the first prediction of the dead end hypothesis. The inability of our study to conclusively reject or support the likewise predicted higher extinction rate in selfing lineages might be explained by a combination of methodological limitations (low statistical power of our BiSSE approach to reliably estimate extinction in small-sized trees) and evolutionary processes (insufficient time elapsed for selfers to go extinct). We suggest that, in these tropical orchids, a simple genetic basis of selfing (via loss of the 'rostellum') is needed to explain the strikingly recurrent transitions to selfing, perhaps reflecting rapid response to parallel and novel selective environments over Late Quaternary (≤ 1.3 Ma) time scales.
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Affiliation(s)
- Alexander Gamisch
- Department of Ecology and Evolution, University of Salzburg, A-5020, Salzburg, Austria.
| | | | - Hans Peter Comes
- Department of Ecology and Evolution, University of Salzburg, A-5020, Salzburg, Austria.
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87
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Steige KA, Reimegård J, Koenig D, Scofield DG, Slotte T. Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella. Mol Biol Evol 2015; 32:2501-14. [PMID: 26318184 PMCID: PMC4576713 DOI: 10.1093/molbev/msv169] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The selfing syndrome constitutes a suite of floral and reproductive trait changes that have evolved repeatedly across many evolutionary lineages in response to the shift to selfing. Convergent evolution of the selfing syndrome suggests that these changes are adaptive, yet our understanding of the detailed molecular genetic basis of the selfing syndrome remains limited. Here, we investigate the role of cis-regulatory changes during the recent evolution of the selfing syndrome in Capsella rubella, which split from the outcrosser Capsella grandiflora less than 200 ka. We assess allele-specific expression (ASE) in leaves and flower buds at a total of 18,452 genes in three interspecific F1 C. grandiflora x C. rubella hybrids. Using a hierarchical Bayesian approach that accounts for technical variation using genomic reads, we find evidence for extensive cis-regulatory changes. On average, 44% of the assayed genes show evidence of ASE; however, only 6% show strong allelic expression biases. Flower buds, but not leaves, show an enrichment of cis-regulatory changes in genomic regions responsible for floral and reproductive trait divergence between C. rubella and C. grandiflora. We further detected an excess of heterozygous transposable element (TE) insertions near genes with ASE, and TE insertions targeted by uniquely mapping 24-nt small RNAs were associated with reduced expression of nearby genes. Our results suggest that cis-regulatory changes have been important during the recent adaptive floral evolution in Capsella and that differences in TE dynamics between selfing and outcrossing species could be important for rapid regulatory divergence in association with mating system shifts.
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Affiliation(s)
- Kim A Steige
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Johan Reimegård
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Daniel Koenig
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Douglas G Scofield
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala Sweden
| | - Tanja Slotte
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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88
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Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella. Nat Commun 2015; 6:7960. [PMID: 26268845 PMCID: PMC4539569 DOI: 10.1038/ncomms8960] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/01/2015] [Indexed: 11/13/2022] Open
Abstract
In the Bateson–Dobzhansky–Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles. A hybrid incompatibility between Capsella plant species is due to an interaction between two immune regulators. Here, the authors show that highly divergent haplotypes result from balancing selection in the ancestral lineage and their sorting into derived lineages facilitated the evolution of the incompatibility.
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89
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Tedder A, Carleial S, Gołębiewska M, Kappel C, Shimizu KK, Stift M. Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae). PLoS One 2015; 10:e0126618. [PMID: 26039362 PMCID: PMC4454584 DOI: 10.1371/journal.pone.0126618] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 04/04/2015] [Indexed: 12/03/2022] Open
Abstract
Introduction The transition from cross-fertilisation (outcrossing) to self-fertilisation (selfing) frequently coincides with changes towards a floral morphology that optimises self-pollination, the selfing syndrome. Population genetic studies have reported the existence of both outcrossing and selfing populations in Arabis alpina (Brassicaceae), which is an emerging model species for studying the molecular basis of perenniality and local adaptation. It is unknown whether its selfing populations have evolved a selfing syndrome. Methods Using macro-photography, microscopy and automated cell counting, we compared floral syndromes (size, herkogamy, pollen and ovule numbers) between three outcrossing populations from the Apuan Alps and three selfing populations from the Western and Central Alps (Maritime Alps and Dolomites). In addition, we genotyped the plants for 12 microsatellite loci to confirm previous measures of diversity and inbreeding coefficients based on allozymes, and performed Bayesian clustering. Results and Discussion Plants from the three selfing populations had markedly smaller flowers, less herkogamy and lower pollen production than plants from the three outcrossing populations, whereas pistil length and ovule number have remained constant. Compared to allozymes, microsatellite variation was higher, but revealed similar patterns of low diversity and high Fis in selfing populations. Bayesian clustering revealed two clusters. The first cluster contained the three outcrossing populations from the Apuan Alps, the second contained the three selfing populations from the Maritime Alps and Dolomites. Conclusion We conclude that in comparison to three outcrossing populations, three populations with high selfing rates are characterised by a flower morphology that is closer to the selfing syndrome. The presence of outcrossing and selfing floral syndromes within a single species will facilitate unravelling the genetic basis of the selfing syndrome, and addressing which selective forces drive its evolution.
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Affiliation(s)
- Andrew Tedder
- Institute of Evolutionary Biology and Environmental studies, University of Zurich, Zurich, Switzerland
| | - Samuel Carleial
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martyna Gołębiewska
- Institute of Evolutionary Biology and Environmental studies, University of Zurich, Zurich, Switzerland
| | - Christian Kappel
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam-Golm, Germany
| | - Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental studies, University of Zurich, Zurich, Switzerland
- * E-mail: (KKS); (MS)
| | - Marc Stift
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
- * E-mail: (KKS); (MS)
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90
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Rebernig CA, Lafon-Placette C, Hatorangan MR, Slotte T, Köhler C. Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm. PLoS Genet 2015; 11:e1005295. [PMID: 26086217 PMCID: PMC4472357 DOI: 10.1371/journal.pgen.1005295] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/21/2015] [Indexed: 11/18/2022] Open
Abstract
The transition to selfing in Capsella rubella accompanies its recent divergence from the ancestral outcrossing C. grandiflora species about 100,000 years ago. Whether the change in mating system was accompanied by the evolution of additional reproductive barriers that enforced species divergence remained unknown. Here, we show that C. rubella and C. grandiflora are reproductively separated by an endosperm-based, non-reciprocal postzygotic hybridization barrier. While hybridizations of C. rubella maternal plants with C. grandiflora pollen donors resulted in complete seed abortion caused by endosperm cellularization failure, the reciprocal hybridization resulted in the formation of small seeds with precociously cellularized endosperm. Strikingly, the transcriptomic response of both hybridizations mimicked respectively the response of paternal and maternal excess hybridizations in Arabidopsis thaliana, suggesting unbalanced genome strength causes hybridization failure in both species. These results provide strong support for the theory that crosses between plants of different mating systems will be unbalanced, with the outcrosser behaving like a plant of increased ploidy, evoking a response that resembles an interploidy-type seed failure. Seed incompatilibity of C. rubella pollinated by C. grandiflora followed the Bateson-Dobzhansky-Muller model, involving negative genetic interaction of multiple paternal C. grandiflora loci with at least one maternal C. rubella locus. Given that both species only recently diverged, our data suggest that a fast evolving mechanism underlies the post-zygotic hybridization barrier(s) separating both species.
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Affiliation(s)
- Carolin A. Rebernig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
| | - Clément Lafon-Placette
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
| | - Marcelinus R. Hatorangan
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
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91
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Koenig D, Weigel D. Beyond the thale: comparative genomics and genetics of Arabidopsis relatives. Nat Rev Genet 2015; 16:285-98. [DOI: 10.1038/nrg3883] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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92
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Thomas CG, Wang W, Jovelin R, Ghosh R, Lomasko T, Trinh Q, Kruglyak L, Stein LD, Cutter AD. Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis. Genome Res 2015; 25:667-78. [PMID: 25783854 PMCID: PMC4417115 DOI: 10.1101/gr.187237.114] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/12/2015] [Indexed: 12/19/2022]
Abstract
The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans. We estimate that a diaspora of at least six distinct C. briggsae lineages separated from one another approximately 200,000 generations ago, including the “Temperate” and “Tropical” phylogeographic groups that dominate most samples worldwide. Moreover, an ancient population split in its history approximately 2 million generations ago, coupled with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes.
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Affiliation(s)
- Cristel G Thomas
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Wei Wang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Rajarshi Ghosh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA; Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Tatiana Lomasko
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada, M5G 0A3
| | - Quang Trinh
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada, M5G 0A3
| | - Leonid Kruglyak
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA; Departments of Human Genetics and Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, California 90095, USA
| | - Lincoln D Stein
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada, M5G 0A3; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 3B2; Bioinformatics and Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2; Center for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
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93
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Pannell JR. Evolution of the mating system in colonizing plants. Mol Ecol 2015; 24:2018-37. [DOI: 10.1111/mec.13087] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/12/2015] [Accepted: 01/15/2015] [Indexed: 12/16/2022]
Affiliation(s)
- John R. Pannell
- Department of Ecology and Evolution; University of Lausanne; Biophore Building 1015 Lausanne Switzerland
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94
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Han TS, Wu Q, Hou XH, Li ZW, Zou YP, Ge S, Guo YL. Frequent introgressions from diploid species contribute to the adaptation of the tetraploid Shepherd's purse (Capsella bursa-pastoris). MOLECULAR PLANT 2015; 8:427-438. [PMID: 25661060 DOI: 10.1016/j.molp.2014.11.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/19/2014] [Accepted: 11/30/2014] [Indexed: 06/04/2023]
Abstract
Adaptation is the most important ability for organisms to survive in diverse habitats. Animals have the option to escape from stressful environments, but plants do not. In plants, polyploids consist of about 30%-70% angiosperms and 95% ferns, of which some are important crops such as cotton and wheat. How polyploid plants adapt to various habitats has been a fundamental question remained largely unanswered. The tetraploid Shepherd's purse (Capsella bursa-pastoris) is one of the most successful plants on earth and has been distributed across the world, thus being an ideal model system for studying the adaptation of polyploids. We found that there are frequent introgressions from congeneric diploids to Shepherd's purse. Ecological niche modeling suggests that ecological differentiation is evident between the introgressed and non-introgressed C. bursa-pastoris, and the introgressions are a source of adaptation. This result links an evolutionary process to the adaptation of polyploids, and sheds light on the breeding strategy of polyploids as well. We conclude that frequent introgressions from congeneric diploids contributed to the acquisition of adequate genetic variations, thereby allowing C. bursa-pastoris to adapt to various habitats across the world. Our results highlight how a polyploid could have successfully established after it originated.
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Affiliation(s)
- Ting-Shen Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiong Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xing-Hui Hou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Wen Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yu-Pan Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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95
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Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris. Proc Natl Acad Sci U S A 2015; 112:2806-11. [PMID: 25691747 DOI: 10.1073/pnas.1412277112] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Whole-genome duplication (WGD) events have occurred repeatedly during flowering plant evolution, and there is growing evidence for predictable patterns of gene retention and loss following polyploidization. Despite these important insights, the rate and processes governing the earliest stages of diploidization remain poorly understood, and the relative importance of genetic drift, positive selection, and relaxed purifying selection in the process of gene degeneration and loss is unclear. Here, we conduct whole-genome resequencing in Capsella bursa-pastoris, a recently formed tetraploid with one of the most widespread species distributions of any angiosperm. Whole-genome data provide strong support for recent hybrid origins of the tetraploid species within the past 100,000-300,000 y from two diploid progenitors in the Capsella genus. Major-effect inactivating mutations are frequent, but many were inherited from the parental species and show no evidence of being fixed by positive selection. Despite a lack of large-scale gene loss, we observe a decrease in the efficacy of natural selection genome-wide due to the combined effects of demography, selfing, and genome redundancy from WGD. Our results suggest that the earliest stages of diploidization are associated with quantitative genome-wide decreases in the strength and efficacy of selection rather than rapid gene loss, and that nonfunctionalization can receive a "head start" through a legacy of deleterious variants and differential expression originating in parental diploid populations.
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96
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Roux C, Pannell JR. Inferring the mode of origin of polyploid species from next-generation sequence data. Mol Ecol 2015; 24:1047-59. [DOI: 10.1111/mec.13078] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 01/06/2015] [Accepted: 01/08/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Camille Roux
- Department of Ecology and Evolution; University of Lausanne; Lausanne 1015 Switzerland
| | - John R. Pannell
- Department of Ecology and Evolution; University of Lausanne; Lausanne 1015 Switzerland
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97
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Fishman L, Beardsley PM, Stathos A, Williams CF, Hill JP. The genetic architecture of traits associated with the evolution of self-pollination in Mimulus. THE NEW PHYTOLOGIST 2015; 205:907-917. [PMID: 25306861 DOI: 10.1111/nph.13091] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/26/2014] [Indexed: 06/04/2023]
Abstract
Quantitative trait locus (QTL) mapping is a first step toward understanding the genetic basis of adaptive evolution and may also reveal reproductive incompatibilities unique to hybrids. In plants, the shift from outcrossing to self-pollination is common, providing the opportunity for comparisons of QTL architecture among parallel evolutionary transitions. We used QTL mapping in hybrids between the bee-pollinated monkeyflower Mimulus lewisii and the closely related selfer Mimulus parishii to determine the genetic basis of divergence in floral traits and flowering time associated with mating-system evolution, and to characterize hybrid anther sterility. We found a moderately polygenic and highly directional basis for floral size evolution, suggesting adaptation from standing variation or in pursuit of a moving optimum, whereas only a few major loci accounted for substantial flowering-time divergence. Cytonuclear incompatibilities caused hybrid anther sterility, confounding estimation of reproductive organ QTLs. The genetic architecture of floral traits associated with selfing in M. parishii was primarily polygenic, as in other QTL studies of this transition, but in contrast to the previously characterized oligogenic basis of a pollinator shift in close relatives. Hybrid anther sterility appeared parallel at the molecular level to previously characterized incompatibilities, but also raised new questions about cytonuclear co-evolution in plants.
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Affiliation(s)
- Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
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98
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Brodie JF, Aslan CE, Rogers HS, Redford KH, Maron JL, Bronstein JL, Groves CR. Secondary extinctions of biodiversity. Trends Ecol Evol 2014; 29:664-72. [PMID: 25445878 DOI: 10.1016/j.tree.2014.09.012] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 09/25/2014] [Accepted: 09/26/2014] [Indexed: 10/24/2022]
Abstract
Extinctions beget further extinctions when species lose obligate mutualists, predators, prey, or hosts. Here, we develop a conceptual model of species and community attributes affecting secondary extinction likelihood, incorporating mechanisms that buffer organisms against partner loss. Specialized interactors, including 'cryptic specialists' with diverse but nonredundant partner assemblages, incur elevated risk. Risk is also higher for species that cannot either evolve new traits following partner loss or obtain novel partners in communities reorganizing under changing environmental conditions. Partner loss occurs alongside other anthropogenic impacts; multiple stressors can circumvent ecological buffers, enhancing secondary extinction risk. Stressors can also offset each other, reducing secondary extinction risk, a hitherto unappreciated phenomenon. This synthesis suggests improved conservation planning tactics and critical directions for research on secondary extinctions.
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Affiliation(s)
- Jedediah F Brodie
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Biodiversity Research Centre, University of British Columbia, Vancouver BC, V6T 1Z4, Canada.
| | - Clare E Aslan
- Conservation Education and Science Department, Arizona-Sonora Desert Museum, Tucson, AZ 85743, USA
| | - Haldre S Rogers
- Department of Ecology and Evolutionary Biology, Rice University, Houston, TX 77005, USA
| | | | - John L Maron
- Division of Biological Sciences, University of Montana, Missoula, MT 59803, USA
| | - Judith L Bronstein
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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99
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Sicard A, Thamm A, Marona C, Lee YW, Wahl V, Stinchcombe JR, Wright SI, Kappel C, Lenhard M. Repeated evolutionary changes of leaf morphology caused by mutations to a homeobox gene. Curr Biol 2014; 24:1880-6. [PMID: 25127212 DOI: 10.1016/j.cub.2014.06.061] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 06/24/2014] [Accepted: 06/24/2014] [Indexed: 10/24/2022]
Abstract
Elucidating the genetic basis of morphological changes in evolution remains a major challenge in biology. Repeated independent trait changes are of particular interest because they can indicate adaptation in different lineages or genetic and developmental constraints on generating morphological variation. In animals, changes to "hot spot" genes with minimal pleiotropy and large phenotypic effects underlie many cases of repeated morphological transitions. By contrast, only few such genes have been identified from plants, limiting cross-kingdom comparisons of the principles of morphological evolution. Here, we demonstrate that the REDUCED COMPLEXITY (RCO) locus underlies more than one naturally evolved change in leaf shape in the Brassicaceae. We show that the difference in leaf margin dissection between the sister species Capsella rubella and Capsella grandiflora is caused by cis-regulatory variation in the homeobox gene RCO-A, which alters its activity in the developing lobes of the leaf. Population genetic analyses in the ancestral C. grandiflora indicate that the more-active C. rubella haplotype is derived from a now rare or lost C. grandiflora haplotype via additional mutations. In Arabidopsis thaliana, the deletion of the RCO-A and RCO-B genes has contributed to its evolutionarily derived smooth leaf margin, suggesting the RCO locus as a candidate for an evolutionary hot spot. We also find that temperature-responsive expression of RCO-A can explain the phenotypic plasticity of leaf shape to ambient temperature in Capsella, suggesting a molecular basis for the well-known negative correlation between temperature and leaf margin dissection.
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Affiliation(s)
- Adrien Sicard
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam-Golm, Germany
| | - Anna Thamm
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam-Golm, Germany
| | - Cindy Marona
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam-Golm, Germany
| | - Young Wha Lee
- Department of Ecology & Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Vanessa Wahl
- Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - John R Stinchcombe
- Department of Ecology & Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology & Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Christian Kappel
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam-Golm, Germany
| | - Michael Lenhard
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam-Golm, Germany.
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100
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Crawford DJ, Doyle JJ, Soltis DE, Soltis PS, Wendel JF. Contemporary and future studies in plant speciation, morphological/floral evolution and polyploidy: honouring the scientific contributions of Leslie D. Gottlieb to plant evolutionary biology. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130341. [PMID: 24958916 PMCID: PMC4071516 DOI: 10.1098/rstb.2013.0341] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Daniel J Crawford
- Department of Ecology and Evolutionary Biology, and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Jeffrey J Doyle
- L. H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 17 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 17 32611, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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