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Lipánová V, Kabátová KN, Zeisek V, Kolář F, Chrtek J. Evolution of the Sabulina verna group (Caryophyllaceae) in Europe: A deep split, followed by secondary contacts, multiple allopolyploidization and colonization of challenging substrates. Mol Phylogenet Evol 2023; 189:107940. [PMID: 37820762 DOI: 10.1016/j.ympev.2023.107940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 08/10/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
One of the major goals of contemporary evolutionary biology is to elucidate the relative roles of allopatric and ecological differentiation and polyploidy in speciation. In this study, we address the taxonomically intricate Sabulina verna group, which has a disjunct Arctic-alpine postglacial range in Europe and occupies a broad range of ecological niches, including substrates toxic to plants. Using genome-wide ddRAD sequencing combined with morphometric analyses based on extensive sampling of 111 natural populations, we aimed to disentangle internal evolutionary relationships and examine their correspondence with the pronounced edaphic and ploidy diversity within the group. We identified two spatially distinct groups of diploids: a widespread Arctic-alpine group and a spatially restricted yet diverse Balkan group. Most tetraploids exhibited a considerably admixed ancestry derived from both these groups, suggesting their allopolyploid origin. Four genetic clusters in congruence with geography and mostly supported by morphological traits were recognized in the diploid Arctic-alpine group. Tetraploids are split into two distinct and geographically vicariant groups, indicating their repeated polytopic origin. Furthermore, our results also revealed at least five-fold parallel colonization of toxic substrates (serpentine and metalliferous), altogether demonstrating a complex interaction between geography, challenging substrates and polyploidy in the evolution of the group. Finally, we propose a new taxonomic treatment of this complex.
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Affiliation(s)
- Veronika Lipánová
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | | | - Vojtěch Zeisek
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
| | - Jindřich Chrtek
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic.
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2
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Barton S, Broad Z, Ortiz-Barrientos D, Donovan D, Lefevre J. Hypergraphs and centrality measures identifying key features in gene expression data. Math Biosci 2023; 366:109089. [PMID: 37914024 DOI: 10.1016/j.mbs.2023.109089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
Multidisciplinary approaches can significantly advance our understanding of complex systems. For instance, gene co-expression networks align prior knowledge of biological systems with studies in graph theory, emphasising pairwise gene to gene interactions. In this paper, we extend these ideas, promoting hypergraphs as an investigative tool for studying multi-way interactions in gene expression data. Additional freedoms are achieved by representing individual genes with hyperedges, and simultaneously testing each gene against many features/vertices. Further gene/hyperedge interactions can be captured and explored using the line graph representations, a technique that reduces the complexity of dense hypergraphs. Such an approach provides access to graph centrality measures, which identifies salient features within a data set. For instance dominant or hub-like hyperedges, leading to key knowledge on gene expression. The validity of this approach is established through the study of gene expression data for the plant species Senecio lautus and results will be interpreted within this biological setting.
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Affiliation(s)
- Samuel Barton
- School of Mathematics and Physics, ARC Centre of Excellence, Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072, Australia.
| | - Zoe Broad
- School of the Environment, ARC Centre of Excellence, Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072, Australia
| | - Daniel Ortiz-Barrientos
- School of the Environment, ARC Centre of Excellence, Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072, Australia
| | - Diane Donovan
- School of Mathematics and Physics, ARC Centre of Excellence, Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072, Australia
| | - James Lefevre
- School of Mathematics and Physics, ARC Centre of Excellence, Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072, Australia
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3
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James ME, Allsopp RN, Groh JS, Kaur A, Wilkinson MJ, Ortiz-Barrientos D. Uncovering the genetic architecture of parallel evolution. Mol Ecol 2023; 32:5575-5589. [PMID: 37740681 DOI: 10.1111/mec.17134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/25/2023]
Abstract
Identifying the genetic architecture underlying adaptive traits is exceptionally challenging in natural populations. This is because associations between traits not only mask the targets of selection but also create correlated patterns of genomic divergence that hinder our ability to isolate causal genetic effects. Here, we examine the repeated evolution of components of the auxin pathway that have contributed to the replicated loss of gravitropism (i.e. the ability of a plant to bend in response to gravity) in multiple populations of the Senecio lautus species complex in Australia. We use a powerful approach which combines parallel population genomics with association mapping in a Multiparent Advanced Generation Inter-Cross (MAGIC) population to break down genetic and trait correlations to reveal how adaptive traits evolve during replicated evolution. We sequenced auxin and shoot gravitropism-related gene regions in 80 individuals from six natural populations (three parallel divergence events) and 133 individuals from a MAGIC population derived from two of the recently diverged natural populations. We show that artificial tail selection on gravitropism in the MAGIC population recreates patterns of parallel divergence in the auxin pathway in the natural populations. We reveal a set of 55 auxin gene regions that have evolved repeatedly during the evolution of the species, of which 50 are directly associated with gravitropism divergence in the MAGIC population. Our work creates a strong link between patterns of genomic divergence and trait variation contributing to replicated evolution by natural selection, paving the way to understand the origin and maintenance of adaptations in natural populations.
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Affiliation(s)
- Maddie E James
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Robin N Allsopp
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jeffrey S Groh
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Avneet Kaur
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Melanie J Wilkinson
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
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4
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Schlötterer C. How predictable is adaptation from standing genetic variation? Experimental evolution in Drosophila highlights the central role of redundancy and linkage disequilibrium. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220046. [PMID: 37004724 PMCID: PMC10067264 DOI: 10.1098/rstb.2022.0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Experimental evolution is well-suited to test the predictability of evolution without the confounding effects of inaccurate forecasts about future environments. Most of the literature about parallel (and thus predictable) evolution has been carried out in asexual microorganisms, which adapt by de novo mutations. Nevertheless, parallel evolution has also been studied in sexual species at the genomic level. Here, I review the evidence for parallel evolution in Drosophila, the best-studied obligatory outcrossing model for adaptation from standing genetic variation in the laboratory. Similar to asexual microorganisms, evidence for parallel evolution varies between the focal hierarchical levels. Selected phenotypes consistently respond in a very predicable way, but the underlying allele frequency changes are much less predictable. The most important insight is that the predictability of the genomic selection response for polygenic traits depends highly on the founder population and to a much lesser extent on the selection regime. This implies that predicting adaptive genomic response is challenging and requires a good understanding of the adaptive architecture (including linkage disequilibrium) in the ancestral populations. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
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5
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Szukala A, Lovegrove‐Walsh J, Luqman H, Fior S, Wolfe TM, Frajman B, Schönswetter P, Paun O. Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae). Mol Ecol 2023; 32:1832-1847. [PMID: 35152499 PMCID: PMC10946620 DOI: 10.1111/mec.16393] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/29/2021] [Accepted: 02/02/2022] [Indexed: 11/28/2022]
Abstract
Understanding how organisms adapt to the environment is a major goal of modern biology. Parallel evolution-the independent evolution of similar phenotypes in different populations-provides a powerful framework to investigate the evolutionary potential of populations, the constraints of evolution, its repeatability and therefore its predictability. Here, we quantified the degree of gene expression and functional parallelism across replicated ecotype formation in Heliosperma pusillum (Caryophyllaceae), and gained insights into the architecture of adaptive traits. Population structure analyses and demographic modelling support a previously formulated hypothesis of parallel polytopic divergence of montane and alpine ecotypes. We detect a large proportion of differentially expressed genes (DEGs) underlying divergence within each replicate ecotype pair, with a strikingly low number of shared DEGs across pairs. Functional enrichment of DEGs reveals that the traits affected by significant expression divergence are largely consistent across ecotype pairs, in strong contrast to the nonshared genetic basis. The remarkable redundancy of differential gene expression indicates a polygenic architecture for the diverged adaptive traits. We conclude that polygenic traits appear key to opening multiple routes for adaptation, widening the adaptive potential of organisms.
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Affiliation(s)
- Aglaia Szukala
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | | | - Hirzi Luqman
- Department of Environmental System ScienceETH ZürichZürichSwitzerland
| | - Simone Fior
- Department of Environmental System ScienceETH ZürichZürichSwitzerland
| | - Thomas M. Wolfe
- Institute for Forest EntomologyForest Pathology and Forest Protection, BOKUViennaAustria
| | - Božo Frajman
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | | | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
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6
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Johnson SE, Tittes S, Franks SJ. Rapid, nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought. J Evol Biol 2023; 36:550-562. [PMID: 36721268 DOI: 10.1111/jeb.14152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/22/2022] [Accepted: 12/08/2022] [Indexed: 02/02/2023]
Abstract
While we know that climate change can potentially cause rapid phenotypic evolution, our understanding of the genetic basis and degree of genetic parallelism of rapid evolutionary responses to climate change is limited. In this study, we combined the resurrection approach with an evolve-and-resequence design to examine genome-wide evolutionary changes following drought. We exposed genetically similar replicate populations of the annual plant Brassica rapa derived from a field population in southern California to four generations of experimental drought or watered conditions in a greenhouse. Genome-wide sequencing of ancestral and descendant population pools identified hundreds of SNPs that showed evidence of rapidly evolving in response to drought. Several of these were in stress response genes, and two were identified in a prior study of drought response in this species. However, almost all genetic changes were unique among experimental populations, indicating that the evolutionary changes were largely nonparallel, despite the fact that genetically similar replicates of the same founder population had experienced controlled and consistent selection regimes. This nonparallelism of evolution at the genetic level is potentially because of polygenetic adaptation allowing for multiple different genetic routes to similar phenotypic outcomes. Our findings help to elucidate the relationship between rapid phenotypic and genomic evolution and shed light on the degree of parallelism and predictability of genomic evolution to environmental change.
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Affiliation(s)
- Stephen E Johnson
- Department of Biological Sciences and Louis Calder Center, Fordham University, Bronx, New York, USA
| | - Silas Tittes
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Steven J Franks
- Department of Biological Sciences and Louis Calder Center, Fordham University, Bronx, New York, USA
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7
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Wang MZ, Fan XK, Zhang YH, Wu J, Mao LM, Zhang SL, Cai MQ, Li MH, Zhu ZSC, Zhao MS, Liu LX, Cameron KM, Li P. Phylogenomics and integrative taxonomy reveal two new species of Amana (Liliaceae). Plant Divers 2023; 45:54-68. [PMID: 36876315 PMCID: PMC9975474 DOI: 10.1016/j.pld.2022.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/01/2022] [Accepted: 03/01/2022] [Indexed: 05/07/2023]
Abstract
Until now the genus Amana (Liliaceae), known as 'East Asian tulips', has contained just seven species. In this study, a phylogenomic and integrative taxonomic approach was used to reveal two new species, Amana nanyueensis from Central China and A. tianmuensis from East China. A. nanyueensis resembles Amana edulis in possessing a densely villous-woolly bulb tunic and two opposite bracts, but differs in its leaves and anthers. Amana tianmuensis resembles Amana erythronioides in possessing three verticillate bracts and yellow anthers, but differs in aspects of its leaves and bulbs. These four species are clearly separated from each other in principal components analysis based on morphology. Phylogenomic analyses based on plastid CDS further support the species delimitation of A. nanyueensis and A. tianmuensis and suggests they are closely related to A. edulis. Cytological analysis shows that A. nanyueensis and A. tianmuensis are both diploid (2n = 2x = 24), different from A. edulis, which is either diploid (northern populations) or tetraploid (southern populations, 2n = 4x = 48). The pollen morphology of A. nanyueensis is similar to other Amana species (single-groove germination aperture), but A. tianmuensis is quite different because of the presence of a sulcus membrane, which creates the illusion of double grooves. Ecological niche modelling also revealed a niche differentiation between A. edulis, A. nanyueensis and A. tianmuensis.
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Affiliation(s)
- Mei-Zhen Wang
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xiao-Kai Fan
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yong-Hua Zhang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
- Corresponding author.
| | - Jing Wu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Li-Mi Mao
- Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China
| | - Sheng-Lu Zhang
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Min-Qi Cai
- Shanghai Science and Technology Museum, Shanghai, 200127, China
| | - Ming-Hong Li
- Nanyue Hengshan National Nature Reserve Administration, Hengyang 421900, Hunan, China
| | - Zhang-Shi-Chang Zhu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Ming-Shui Zhao
- Zhejiang Tianmushan National Nature Reserve Management Bureau, Hangzhou, 311311, China
| | - Lu-Xian Liu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475001, Henan, China
| | | | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Corresponding author.
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8
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Zhu W, Yang C, Yong B, Wang Y, Li B, Gu Y, Wei S, An Z, Sun W, Qiu L, He C. An enhancing effect attributed to a nonsynonymous mutation in SOYBEAN SEED SIZE 1, a SPINDLY-like gene, is exploited in soybean domestication and improvement. New Phytol 2022; 236:1375-1392. [PMID: 36068955 DOI: 10.1111/nph.18461] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/12/2022] [Indexed: 05/26/2023]
Abstract
Soybean (Glycine max) was domesticated from its wild relative Glycine soja. One-hundred-seed weight is one of the most important domesticated traits determining soybean yield; however, its underlying genetic basis remains elusive. We characterized a soybean seed size 1 (sss1) mutant featuring large seeds compared to its wild-type background. Positional cloning revealed that the candidate gene GmSSS1 encoded a SPINDLY homolog and was co-located in a well-identified quantitative trait locus (QTL)-rich region on chromosome 19. Knocking out GmSSS1 resulted in small seeds, while overexpressing GmSSS1/Gmsss1 induced large seeds. Modulating GmSSS1/Gmsss1 in transgenic plants can positively influence cell expansion and cell division. Relative to GmSSS1, one mutation leading to an E to Q substitution at the 182nd residue in Gmsss1 conferred an enhancing effect on seed weight. GmSSS1 underwent diversification in wild-type and cultivated soybean, and the alleles encoding the Gmsss1-type substitution of 182nd -Q, which originated along the central and downstream parts of the Yellow River, were selected and expanded during soybean domestication and improvement. We cloned the causative gene for the sss1 mutant, which is linked with a seed weight QTL, identified an elite allele of this gene for increasing seed weight, and provided new insights into soybean domestication and breeding.
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Affiliation(s)
- Weiwei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Ce Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Bin Yong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
| | - Bingbing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Yongzhe Gu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Siming Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Zhenghong An
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Wenkai Sun
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Lijuan Qiu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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9
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Konečná V, Šustr M, Požárová D, Čertner M, Krejčová A, Tylová E, Kolář F. Genomic basis and phenotypic manifestation of (non-)parallel serpentine adaptation in Arabidopsis arenosa. Evolution 2022; 76:2315-2331. [PMID: 35950324 DOI: 10.1111/evo.14593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/15/2022] [Accepted: 07/23/2022] [Indexed: 01/22/2023]
Abstract
Parallel evolution is common in nature and provides one of the most compelling examples of rapid environmental adaptation. In contrast to the recent burst of studies addressing genomic basis of parallel evolution, integrative studies linking genomic and phenotypic parallelism are scarce. Edaphic islands of toxic serpentine soils provide ideal systems for studying rapid parallel adaptation in plants, imposing strong, spatially replicated selection on recently diverged populations. We leveraged threefold independent serpentine adaptation of Arabidopsis arenosa and combined reciprocal transplants, ion uptake phenotyping, and available genome-wide polymorphisms to test if parallelism is manifested to a similar extent at both genomic and phenotypic levels. We found pervasive phenotypic parallelism in functional traits yet with varying magnitude of fitness differences that was congruent with neutral genetic differentiation between populations. Limited costs of serpentine adaptation suggest absence of soil-driven trade-offs. On the other hand, the genomic parallelism at the gene level was significant, although relatively minor. Therefore, the similarly modified phenotypes, for example, of ion uptake arose possibly by selection on different loci in similar functional pathways. In summary, we bring evidence for the important role of genetic redundancy in rapid adaptation involving traits with polygenic architecture.
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Affiliation(s)
- Veronika Konečná
- Department of Botany, Faculty of Science, Charles University, Prague, 128 00, Czech Republic.,Institute of Botany, Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
| | - Marek Šustr
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, 128 00, Czech Republic
| | - Doubravka Požárová
- Department of Botany, Faculty of Science, Charles University, Prague, 128 00, Czech Republic
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Prague, 128 00, Czech Republic.,Institute of Botany, Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
| | - Anna Krejčová
- Faculty of Chemical Technology, University of Pardubice, Pardubice, 532 10, Czech Republic
| | - Edita Tylová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, 128 00, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, 128 00, Czech Republic.,Institute of Botany, Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
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10
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Kolis KM, Berg CS, Nelson TC, Fishman L. Population genomic consequences of life-history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers. Evolution 2022; 76:765-781. [PMID: 35266558 DOI: 10.1111/evo.14469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 01/13/2022] [Accepted: 01/26/2022] [Indexed: 01/21/2023]
Abstract
Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in Mimulus guttatus (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life-history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200 m geographical gap of no intermediate habitat. Individual inbreeding coefficients (FIS ) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1 km) scales. Finally, YNP adaptation does not reuse a widespread inversion that underlies M. guttatus life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life-history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.
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Affiliation(s)
- Kory M Kolis
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812.,Current Address: O'Connor Center for the Rocky Mountain West, University of Montana, Missoula, MT, 59812
| | - Colette S Berg
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
| | - Thomas C Nelson
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812.,Current Address: Embark Veterinary, Inc., Boston, Massachusetts, 02210
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
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11
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Abstract
Parallelism between evolutionary trajectories in a trait space is often seen as evidence for repeatability of phenotypic evolution, and angles between trajectories play a pivotal role in the analysis of parallelism. However, properties of angles in multidimensional spaces have not been widely appreciated by biologists. To remedy this situation, this study provides a brief overview on geometric and statistical aspects of angles in multidimensional spaces. Under the null hypothesis that trajectory vectors have no preferred directions (i.e. uniform distribution on hypersphere), the angle between two independent vectors is concentrated around the right angle, with a more pronounced peak in a higher-dimensional space. This probability distribution is closely related to t- and beta distributions, which can be used for testing the null hypothesis concerning a pair of trajectories. A recently proposed method with eigenanalysis of a vector correlation matrix can be connected to the test of no correlation or concentration of multiple vectors, for which simple test procedures are available in the statistical literature. Concentration of vectors can also be examined by tools of directional statistics such as the Rayleigh test. These frameworks provide biologists with baselines to make statistically justified inferences for (non)parallel evolution.
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Affiliation(s)
- Junya Watanabe
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
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DeWitt TJ, Troendle NJ, Mateos M, Mauricio R. Population genetics and independently replicated evolution of predator-associated burst speed ecophenotypy in mosquitofish. Heredity (Edinb) 2022; 128:45-55. [PMID: 34876658 DOI: 10.1038/s41437-021-00487-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 01/03/2023] Open
Abstract
Many species show replicated ecophenotypy due to recurring patterns of natural selection. Based on the presence or absence of pursuit predators, at least 17 species of fish repeatedly differentiated in body shape in a manner that increases burst swimming speed and the likelihood of predator escape. The predator-associated burst speed (PABS) ecophenotype is characterized by a small head and trunk and enlarged caudal region. Mechanisms promoting replicated phenotype-environment association include selection (without evolution), a single instance of adaptive evolution followed by biased habitat occupation, repeated instances of local adaptation, or adaptive phenotypic plasticity. Common garden rearing of mosquitofish, Gambusia affinis, demonstrated a likely heritable basis for PABS phenotypy, but it is unknown whether populations are otherwise genetically distinct or whether replicated ecophenotypy represents a single or replicated instances of adaptation. To genetically characterize the populations and test hypotheses of single or multiple adaptations, we characterized variation in 12 polymorphic DNA microsatellites in the previously studied G. affinis populations. Populations were genetically distinct by multilocus analysis, exhibited high allelic diversity, and were heterozygote deficient, which effects were attributed to G. affinis's shoaling nature and habitat patchiness. Genetic and phenotypic distances among populations were correlated for non-PABS but not PABS morphology. Multilocus analysis demonstrated ecophenotype polyphyly and scattered multivariate genetic structure which support only the replicated-adaptation model. As all of the diverse tests performed demonstrated lack of congruence between patterns of molecular genetic and PABS differentiation, it is likely that divergent natural selection drove multiple instances of adaptive evolution.
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Wong ELY, Hiscock SJ, Filatov DA. The Role of Interspecific Hybridisation in Adaptation and Speciation: Insights From Studies in Senecio. Front Plant Sci 2022; 13:907363. [PMID: 35812981 PMCID: PMC9260247 DOI: 10.3389/fpls.2022.907363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/03/2022] [Indexed: 05/08/2023]
Abstract
Hybridisation is well documented in many species, especially plants. Although hybrid populations might be short-lived and do not evolve into new lineages, hybridisaiton could lead to evolutionary novelty, promoting adaptation and speciation. The genus Senecio (Asteraceae) has been actively used to unravel the role of hybridisation in adaptation and speciation. In this article, we first briefly describe the process of hybridisation and the state of hybridisation research over the years. We then discuss various roles of hybridisation in plant adaptation and speciation illustrated with examples from different Senecio species, but also mention other groups of organisms whenever necessary. In particular, we focus on the genomic and transcriptomic consequences of hybridisation, as well as the ecological and physiological aspects from the hybrids' point of view. Overall, this article aims to showcase the roles of hybridisation in speciation and adaptation, and the research potential of Senecio, which is part of the ecologically and economically important family, Asteraceae.
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Affiliation(s)
- Edgar L. Y. Wong
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- *Correspondence: Edgar L. Y. Wong,
| | - Simon J. Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- Oxford Botanic Garden and Arboretum, Oxford, United Kingdom
| | - Dmitry A. Filatov
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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