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Osterman WHA, Hill A, Hagan JG, Whitton J, Bacon CD, Bjorkman AD. Rethinking pathways to the dioecy-polyploidy association: Genera with many dioecious species have fewer polyploids. AMERICAN JOURNAL OF BOTANY 2024:e16318. [PMID: 38654555 DOI: 10.1002/ajb2.16318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024]
Abstract
PREMISE Numerous studies have found a positive association between dioecy and polyploidy; however, this association presents a theoretical conflict: While polyploids are predicted to benefit from self-reproduction for successful establishment, dioecious species cannot self-reproduce. We propose a theoretical framework to resolve this apparent conflict. We hypothesize that the inability of dioecious species to self-reproduce hinders their establishment as polyploids. We therefore expect that genera with many dioecious species have fewer polyploids, leading to a negative association between polyploidy and dioecy across genera. METHODS We used three publicly available databases to determine ploidy and sexual systems for 131 genera and 546 species. We quantified (1) the relationship between the frequency of polyploid species and the frequency of dioecious species across genera, and (2) the proportion of polyploids with hermaphroditism and dioecy across species, adjusting for phylogenetic history. RESULTS Across genera, we found a negative relationship between the proportion of polyploids and the proportion of dioecious species, a consistent trend across clades. Across all species, we found that sexual system (dioecious or not) was not associated with polyploidy. CONCLUSIONS Polyploids are rare in genera in which the majority of species are dioecious, consistent with the theory that self-reproduction favors polyploid establishment. The low frequency of polyploidy among dioecious species indicates the association is not as widespread as previously suggested. Our findings are consistent with previous studies identifying a positive relationship between the two traits, but only if polyploidy promotes a transition to dioecy, and not the reverse.
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Affiliation(s)
- Wilhelm H A Osterman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Adrian Hill
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - James G Hagan
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Jeannette Whitton
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, Vancouver, Canada
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Anne D Bjorkman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
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2
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Halabi K, Shafir A, Mayrose I. PloiDB: the plant ploidy database. THE NEW PHYTOLOGIST 2023; 240:918-927. [PMID: 37337836 DOI: 10.1111/nph.19057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/16/2023] [Indexed: 06/21/2023]
Abstract
See also the Commentary on this article by Spoelhof et al., 240: 909–911.
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Affiliation(s)
- Keren Halabi
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-Yafo, 69978, Israel
| | - Anat Shafir
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-Yafo, 69978, Israel
| | - Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-Yafo, 69978, Israel
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3
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Masuda K, Akagi T. Evolution of sex in crops: recurrent scrap and rebuild. BREEDING SCIENCE 2023; 73:95-107. [PMID: 37404348 PMCID: PMC10316312 DOI: 10.1270/jsbbs.22082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/20/2022] [Indexed: 07/06/2023]
Abstract
Sexuality is the main strategy for maintaining genetic diversity within a species. In flowering plants (angiosperms), sexuality is derived from ancestral hermaphroditism and multiple sexualities can be expressed in an individual. The mechanisms conferring chromosomal sex determination in plants (or dioecy) have been studied for over a century by both biologists and agricultural scientists, given the importance of this field for crop cultivation and breeding. Despite extensive research, the sex determining gene(s) in plants had not been identified until recently. In this review, we dissect plant sex evolution and determining systems, with a focus on crop species. We introduced classic studies with theoretical, genetic, and cytogenic approaches, as well as more recent research using advanced molecular and genomic techniques. Plants have undergone very frequent transitions into, and out of, dioecy. Although only a few sex determinants have been identified in plants, an integrative viewpoint on their evolutionary trends suggests that recurrent neofunctionalization events are potentially common, in a "scrap and (re)build" cycle. We also discuss the potential association between crop domestication and transitions in sexual systems. We focus on the contribution of duplication events, which are particularly frequent in plant taxa, as a trigger for the creation of new sexual systems.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
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4
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Wang R, Xing S, Bourke PM, Qi X, Lin M, Esselink D, Arens P, Voorrips RE, Visser RG, Sun L, Zhong Y, Gu H, Li Y, Li S, Maliepaard C, Fang J. Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:369-380. [PMID: 36333116 PMCID: PMC9884011 DOI: 10.1111/pbi.13958] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/22/2022] [Accepted: 10/31/2022] [Indexed: 05/11/2023]
Abstract
Kiwifruit (Actinidia spp) is a woody, perennial and deciduous vine. In this genus, there are multiple ploidy levels but the main cultivated cultivars are polyploid. Despite the availability of many genomic resources in kiwifruit, SNP genotyping is still a challenge given these different levels of polyploidy. Recent advances in SNP array technologies have offered a high-throughput genotyping platform for genome-wide DNA polymorphisms. In this study, we developed a high-density SNP genotyping array to facilitate genetic studies and breeding applications in kiwifruit. SNP discovery was performed by genome-wide DNA sequencing of 40 kiwifruit genotypes. The identified SNPs were stringently filtered for sequence quality, predicted conversion performance and distribution over the available Actinidia chinensis genome. A total of 134 729 unique SNPs were put on the array. The array was evaluated by genotyping 400 kiwifruit individuals. We performed a multidimensional scaling analysis to assess the diversity of kiwifruit germplasm, showing that the array was effective to distinguish kiwifruit accessions. Using a tetraploid F1 population, we constructed an integrated linkage map covering 3060.9 cM across 29 linkage groups and performed QTL analysis for the sex locus that has been identified on Linkage Group 3 (LG3) in Actinidia arguta. Finally, our dataset presented evidence of tetrasomic inheritance with partial preferential pairing in A. arguta. In conclusion, we developed and evaluated a 135K SNP genotyping array for kiwifruit. It has the advantage of a comprehensive design that can be an effective tool in genetic studies and breeding applications in this high-value crop.
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Affiliation(s)
- Ran Wang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Siyuan Xing
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Peter M. Bourke
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Xiuquan Qi
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Miaomiao Lin
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Danny Esselink
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Paul Arens
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | | | | | - Leiming Sun
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Yunpeng Zhong
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Hong Gu
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Yukuo Li
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Sikai Li
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Chris Maliepaard
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Jinbao Fang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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5
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Godin VN. Trioecy in Flowering Plants. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2022; 507:301-311. [PMID: 36781527 DOI: 10.1134/s0012496622060023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 02/15/2023]
Abstract
Populations of trioecious plants consists of individuals with staminate, pistillate, and hermaphrodite flowers. Trioecy is extremely rare in angiosperms, and relevant data are scarce. A list of trioecious plants found in the global flora was compiled on the basis of literature data and original research. The list includes 80 species of 46 genera, which represent 33 families and 21 orders of flowering plants. Trioecy is found in 7.9% of families, 0.3% of genera, and 0.03% of species in angiosperms. Trioecious species are now unknown in basal angiosperms, uncommon in magnoliids, and rather rare in monocots. The overwhelming majority (87.5%) of trioecious plants belong to Superrosids (30 species) and Superasterids (40 species). The greatest numbers of trioecious species are found in the families Rosaceae (nine species of two genera), Caprifoliaceae (seven species of one genus), Scrophulariaceae (seven species of one genus), Caryophyllaceae (six species of two genera), and Celastraceae (six species of two genera). Almost half of the identified trioecious species represent five genera: Fragaria L. (eight species), Valeriana L. (seven species), Buddleja L. (seven species), Maytenus Molina (five species), and Silene L. (five species). An association with trioecy was analyzed for several biological and ecological factors, such as the life form, the method of pollination, the perianth color, the pericarp consistency, the presence of related dioecious species in the same genus, the latitudinal position, and the distribution through floristic phytochoria. A lability of sex differentiation in certain trioecious plants, the proportion of sex forms in a population, a possible association with polyploidy, and mechanisms of trioecy maintenance and evolution in flowering plants are discussed.
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Affiliation(s)
- V N Godin
- Moscow Pedagogical State University, Moscow, Russia. .,Central Siberian Botanical Garden, Novosibirsk, Russia.
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6
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He L, Hörandl E. Does polyploidy inhibit sex chromosome evolution in angiosperms? FRONTIERS IN PLANT SCIENCE 2022; 13:976765. [PMID: 36212292 PMCID: PMC9541106 DOI: 10.3389/fpls.2022.976765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Dioecy is rare in flowering plants (5-6% of species), but is often controlled genetically by sex-linked regions (SLRs). It has so far been unclear whether, polyploidy affects sex chromosome evolution, as it does in animals, though polyploidy is quite common in angiosperms, including in dioecious species. Plants could be different, as, unlike many animal systems, degenerated sex chromosomes, are uncommon in plants. Here we consider sex determination in plants and plant-specific factors, and propose that constraints created at the origin of polyploids limit successful polyploidization of species with SLRs. We consider the most likely case of a polyploid of a dioecious diploid with an established SLR, and discuss the outcome in autopolyploids and allopolyploids. The most stable system possibly has an SLR on just one chromosome, with a strongly dominant genetic factor in the heterogametic sex (e.g., xxxY male in a tetraploid). If recombination occurs with its homolog, this will prevent Y chromosome degeneration. Polyploidy may also allow for reversibility of multiplied Z or X chromosomes into autosomes. Otherwise, low dosage of Y-linked SLRs compared to their multiple homologous x copies may cause loss of reliable sex-determination at higher ploidy levels. We discuss some questions that can be studied using genome sequencing, chromosome level-assemblies, gene expression studies and analysis of loci under selection.
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Affiliation(s)
- Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Göttingen, Germany
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7
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Meissner ST. Plant sexual reproduction: perhaps the current plant two-sex model should be replaced with three- and four-sex models? PLANT REPRODUCTION 2021; 34:175-189. [PMID: 34213647 PMCID: PMC8360875 DOI: 10.1007/s00497-021-00420-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
The two-sex model makes the assumption that there are only two sexual reproductive states: male and female. However, in land plants (embryophytes) the application of this model to the alternation of generations life cycle requires the subtle redefinition of several common terms related to sexual reproduction, which seems to obscure aspects of one or the other plant generation: For instance, the homosporous sporophytic plant is treated as being asexual, and the gametophytes of angiosperms treated like mere gametes. In contrast, the proposal is made that the sporophytes of homosporous plants are indeed sexual reproductive organisms, as are the gametophytes of heterosporous plants. This view requires the expansion of the number of sexual reproductive states we accept for these plant species; therefore, a three-sex model for homosporous plants and a four-sex model for heterosporous plants are described and then contrasted with the current two-sex model. These new models allow the use of sexual reproductive terms in a manner largely similar to that seen in animals, and may better accommodate the plant alternation of generations life cycle than does the current plant two-sex model. These new models may also help stimulate new lines of research, and examples of how they might alter our view of events in the flower, and may lead to new questions about sexual determination and differentiation, are presented. Thus it is suggested that land plant species have more than merely two sexual reproductive states and that recognition of this may promote our study and understanding of them.
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Affiliation(s)
- Scott T Meissner
- Institute of Biology, University of the Philippines Diliman, 1101, Quezon City, NCR, Philippines.
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8
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Domínguez-Delgado JJ, López-Jurado J, Mateos-Naranjo E, Balao F. Phenotypic diploidization in plant functional traits uncovered by synthetic neopolyploids in Dianthus broteri. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5522-5533. [PMID: 33909906 PMCID: PMC8760854 DOI: 10.1093/jxb/erab179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/26/2021] [Indexed: 05/27/2023]
Abstract
Whole-genome duplication and post-polyploidization genome downsizing play key roles in the evolution of land plants; however, the impact of genomic diploidization on functional traits still remains poorly understood. Using Dianthus broteri as a model, we compared the ecophysiological behaviour of colchicine-induced neotetraploids (4xNeo) to diploids (2x) and naturally occurring tetraploids (4xNat). Leaf gas-exchange and chlorophyll fluorescence analyses were performed in order to asses to what extent post-polyploidization evolutionary processes have affected 4xNat. Genomic diploidization and phenotypic novelty were evident. Distinct patterns of variation revealed that post-polyploidization processes altered the phenotypic shifts directly mediated by genome doubling. The photosynthetic phenotype was affected in several ways but the main effect was phenotypic diploidization (i.e. 2x and 4xNat were closer to each other than to 4xNeo). Overall, our results show the potential benefits of considering experimentally synthetized versus naturally established polyploids when exploring the role of polyploidization in promoting functional divergence.
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Affiliation(s)
| | - Javier López-Jurado
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080-Sevilla, Spain
| | - Enrique Mateos-Naranjo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080-Sevilla, Spain
| | - Francisco Balao
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080-Sevilla, Spain
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9
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Kučera J, Svitok M, Gbúrová Štubňová E, Mártonfiová L, Lafon Placette C, Slovák M. Eunuchs or Females? Causes and Consequences of Gynodioecy on Morphology, Ploidy, and Ecology of Stellaria graminea L. (Caryophyllaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:589093. [PMID: 33912199 PMCID: PMC8072285 DOI: 10.3389/fpls.2021.589093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Plant speciation results from intricate processes such as polyploidization, reproductive strategy shifts and adaptation. These evolutionary processes often co-occur, blurring their respective contributions and interactions in the speciation continuum. Here, relying on a large-scale study, we tested whether gynodioecy triggers the divergent evolution of flower morphology and genome between sexes, and contributes to the establishment of polyploids and colonization of ecological niches in Stellaria graminea. We found that gynodioecy in S. graminea leads to flower morphology divergence between females and hermaphrodites, likely due to sexual selection. Contrary to our expectations, gynodioecy occurs evenly in diploids and tetraploids, suggesting that this reproductive strategy was not involved in the establishment of polyploids. Both diploid and tetraploid females have a larger genome size than hermaphrodites, suggesting the presence of sex chromosomes. Finally, ecology differs between cytotypes and to a lesser extent between sexes, suggesting that the link between environment and presence of females is indirect and likely explained by other aspects of the species' life history. Our study shows that gynodioecy leads to the consistent evolution of sexual traits across a wide range of populations, cytotypes and environments within a given species, and this likely contributes to the phenotypic and genetic distinctiveness of the species from its sister clades.
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Affiliation(s)
- Jaromír Kučera
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Marek Svitok
- Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, Zvolen, Slovakia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Eliška Gbúrová Štubňová
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
- Slovak National Museum, Natural History Museum, Bratislava, Slovakia
| | | | | | - Marek Slovák
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Charles University, Prague, Czechia
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10
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Azouri D, Abadi S, Mansour Y, Mayrose I, Pupko T. Harnessing machine learning to guide phylogenetic-tree search algorithms. Nat Commun 2021; 12:1983. [PMID: 33790270 PMCID: PMC8012635 DOI: 10.1038/s41467-021-22073-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/26/2021] [Indexed: 02/01/2023] Open
Abstract
Inferring a phylogenetic tree is a fundamental challenge in evolutionary studies. Current paradigms for phylogenetic tree reconstruction rely on performing costly likelihood optimizations. With the aim of making tree inference feasible for problems involving more than a handful of sequences, inference under the maximum-likelihood paradigm integrates heuristic approaches to evaluate only a subset of all potential trees. Consequently, existing methods suffer from the known tradeoff between accuracy and running time. In this proof-of-concept study, we train a machine-learning algorithm over an extensive cohort of empirical data to predict the neighboring trees that increase the likelihood, without actually computing their likelihood. This provides means to safely discard a large set of the search space, thus potentially accelerating heuristic tree searches without losing accuracy. Our analyses suggest that machine learning can guide tree-search methodologies towards the most promising candidate trees.
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Affiliation(s)
- Dana Azouri
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, Tel-Aviv, Israel
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Tel-Aviv, Israel
| | - Shiran Abadi
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, Tel-Aviv, Israel
| | - Yishay Mansour
- Balvatnik School of Computer Science, Tel-Aviv University, Ramat Aviv, Tel-Aviv, Israel
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, Tel-Aviv, Israel.
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Tel-Aviv, Israel.
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11
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Rice A, Mayrose I. Model adequacy tests for probabilistic models of chromosome-number evolution. THE NEW PHYTOLOGIST 2021; 229:3602-3613. [PMID: 33226654 DOI: 10.1111/nph.17106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/18/2020] [Indexed: 05/29/2023]
Abstract
Chromosome number is a central feature of eukaryote genomes. Deciphering patterns of chromosome-number change along a phylogeny is central to the inference of whole genome duplications and ancestral chromosome numbers. ChromEvol is a probabilistic inference tool that allows the evaluation of several models of chromosome-number evolution and their fit to the data. However, fitting a model does not necessarily mean that the model describes the empirical data adequately. This vulnerability may lead to incorrect conclusions when model assumptions are not met by real data. Here, we present a model adequacy test for likelihood models of chromosome-number evolution. The procedure allows us to determine whether the model can generate data with similar characteristics as those found in the observed ones. We demonstrate that using inadequate models can lead to inflated errors in several inference tasks. Applying the developed method to 200 angiosperm genera, we find that in many of these, the best-fitting model provides poor fit to the data. The inadequacy rate increases in large clades or in those in which hybridizations are present. The developed model adequacy test can help researchers to identify phylogenies whose underlying evolutionary patterns deviate substantially from current modelling assumptions and should guide future methods development.
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Affiliation(s)
- Anna Rice
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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12
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Porturas LD, Segraves KA. Whole genome duplication does not promote common modes of reproductive isolation in Trifolium pratense. AMERICAN JOURNAL OF BOTANY 2020; 107:833-841. [PMID: 32329070 DOI: 10.1002/ajb2.1466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 02/10/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Although polyploidy has been studied since the early 1900s, fundamental aspects of polyploid ecology and evolution remain unexplored. In particular, surprisingly little is known about how newly formed polyploids (neopolyploids) become demographically established. Models predict that most polyploids should go extinct within the first few generations as a result of reproductive disadvantages associated with being the minority in a primarily diploid population (i.e., the minority cytotype principle), yet polyploidy is extremely common. Therefore, a key goal in the study of polyploidy is to determine the mechanisms that promote polyploid establishment in nature. Because premating isolation is critical in order for neopolylpoids to avoid minority cytotype exclusion and thus facilitate establishment, we examined floral morphology and three common premating barriers to determine their importance in generating reproductive isolation of neopolyploids from diploids. METHODS We induced neopolyploidy in Trifolium pratense and compared their floral traits to the diploid progenitors. In addition to shifts in floral morphology, we examined three premating barriers: isolation by self-fertilization, flowering-time asynchrony, and pollinator-mediated isolation. RESULTS We found significant differences in the morphology of diploid and neopolyploid flowers, but these changes did not facilitate premating barriers that would generate reproductive isolation of neopolyploids from diploids. There was no difference in flowering phenology, pollinator visitation, or selfing between the cytotypes. CONCLUSIONS Our results indicate that barriers other than the ones tested in this study-such as geographic isolation, vegetative reproduction, and pistil-stigma incompatibilities-may be more important in facilitating isolation and establishment of neopolyploid T. pratense.
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Affiliation(s)
- Laura D Porturas
- Penn State University, Frost Entomological Museum, 501 ASI, University Park, Pennsylvania, 16802, USA
- Syracuse University, Biology, 107 College Place, Syracuse, New York, 13244, USA
| | - Kari A Segraves
- Syracuse University, Biology, 107 College Place, Syracuse, New York, 13244, USA
- Archbold Biological Station, 123 Main Drive, Venus, Florida, 33960, USA
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13
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Guerrero PC, Majure LC, Cornejo-Romero A, Hernández-Hernández T. Phylogenetic Relationships and Evolutionary Trends in the Cactus Family. J Hered 2020; 110:4-21. [PMID: 30476167 DOI: 10.1093/jhered/esy064] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/21/2018] [Indexed: 12/29/2022] Open
Abstract
Members of the cactus family are keystone species of arid and semiarid biomes in the Americas, as they provide shelter and resources to support other members of ecosystems. Extraordinary examples are the several species of flies of the genus Drosophila that lay eggs and feed in their rotting stems, which provide a model system for studying evolutionary processes. Although there is significant progress in understanding the evolution of Drosophila species, there are gaps in our knowledge about the cactus lineages hosting them. Here, we review the current knowledge about the evolution of Cactaceae, focusing on phylogenetic relationships and trends revealed by the study of DNA sequence data. During the last several decades, the availability of molecular phylogenies has considerably increased our understanding of the relationships, biogeography, and evolution of traits in the family. Remarkably, although succulent cacti have very low growth rates and long generation times, they underwent some of the fastest diversifications observed in the plant kingdom, possibly fostered by strong ecological interactions. We have a better understanding of the reproductive biology, population structure and speciation mechanisms in different clades. The recent publication of complete genomes for some species has revealed the importance of phenomena such as incomplete lineage sorting. Hybridization and polyploidization are common in the family, and have been studied using a variety of phylogenetic methods. We discuss potential future avenues for research in Cactaceae, emphasizing the need of a concerted effort among scientists in the Americas, together with the analyses of data from novel sequencing techniques.
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Affiliation(s)
- Pablo C Guerrero
- Departamento de Botánica, Universidad de Concepción, Chile, Concepción, Chile
| | - Lucas C Majure
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ.,Florida Museum of Natural History, University of Florida, Gainesville, FL
| | - Amelia Cornejo-Romero
- Departamento de Botánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
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14
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Wang LL, Zhang ZQ, Yang YP, Duan YW. The coexistence of hermaphroditic and dioecious plants is associated with polyploidy and gender dimorphism in Dasiphora fruticosa. PLANT DIVERSITY 2019; 41:323-329. [PMID: 31934677 PMCID: PMC6951273 DOI: 10.1016/j.pld.2019.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 06/10/2023]
Abstract
Dasiphora fruticosa comprises male, female and hermaphrodite plants, which are distributed sympatrically in some populations on the Qinghai-Tibet Plateau. To explore what governs the coexistence of these three sexual phenotypes, we investigated the DNA contents, pollen and ovule production, pollen deposition, and performed hand-pollination in both hermaphroditic and dioecious individuals of D. fruticosa. Flow cytometry confirmed that the DNA content of males and females were almost twice as much as that of the hermaphrodites. Male and female flowers produced more pollen grains and ovules than hermaphroditic flowers. Hand-pollinated treatments showed that unisexual flowers were sterile in one sexual function and bisexual flowers were fertile for both functions, but no sterile seeds were produced between unisexual and bisexual flowers. Our findings imply that polyploidy is related to gender dimorphism, and both are likely to play a strong role in the coexistence of two cryptic biological species of D. fruticosa (low ploidy hermaphroditic species and high ploidy dioecious species) in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Lin-Lin Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Germplasm Bank of Wild Species, Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Qiang Zhang
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, Yunnan, 650091, China
| | - Yong-Ping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Germplasm Bank of Wild Species, Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Yuan-Wen Duan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Germplasm Bank of Wild Species, Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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15
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Abadi S, Azouri D, Pupko T, Mayrose I. Model selection may not be a mandatory step for phylogeny reconstruction. Nat Commun 2019; 10:934. [PMID: 30804347 PMCID: PMC6389923 DOI: 10.1038/s41467-019-08822-w] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 01/29/2019] [Indexed: 11/29/2022] Open
Abstract
Determining the most suitable model for phylogeny reconstruction constitutes a fundamental step in numerous evolutionary studies. Over the years, various criteria for model selection have been proposed, leading to debate over which criterion is preferable. However, the necessity of this procedure has not been questioned to date. Here, we demonstrate that although incongruency regarding the selected model is frequent over empirical and simulated data, all criteria lead to very similar inferences. When topologies and ancestral sequence reconstruction are the desired output, choosing one criterion over another is not crucial. Moreover, skipping model selection and using instead the most parameter-rich model, GTR+I+G, leads to similar inferences, thus rendering this time-consuming step nonessential, at least under current strategies of model selection.
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Affiliation(s)
- Shiran Abadi
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel
| | - Dana Azouri
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel
- School of Molecular Cell Biology & Biotechnology, Tel Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel
| | - Tal Pupko
- School of Molecular Cell Biology & Biotechnology, Tel Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel.
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel.
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16
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Blackmon H, Justison J, Mayrose I, Goldberg EE. Meiotic drive shapes rates of karyotype evolution in mammals. Evolution 2019; 73:511-523. [PMID: 30690715 PMCID: PMC6590138 DOI: 10.1111/evo.13682] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/07/2019] [Indexed: 02/06/2023]
Abstract
Chromosome number is perhaps the most basic characteristic of a genome, yet generalizations that can explain the evolution of this trait across large clades have remained elusive. Using karyotype data from over 1000 mammals, we developed and applied a phylogenetic model of chromosome evolution that links chromosome number changes with karyotype morphology. Using our model, we infer that rates of chromosome number evolution are significantly lower in species with karyotypes that consist of either all bibrachial or all monobrachial chromosomes than in species with a mix of both types of morphologies. We suggest that species with homogeneous karyotypes may represent cases where meiotic drive acts to stabilize the karyotype, favoring the chromosome morphologies already present in the genome. In contrast, rapid bouts of chromosome number evolution in taxa with mixed karyotypes may indicate that a switch in the polarity of female meiotic drive favors changes in chromosome number. We do not find any evidence that karyotype morphology affects rates of speciation or extinction. Furthermore, we document that switches in meiotic drive polarity are likely common and have occurred in most major clades of mammals, and that rapid remodeling of karyotypes may be more common than once thought.
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Affiliation(s)
- Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Joshua Justison
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108
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17
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Rice A, Šmarda P, Novosolov M, Drori M, Glick L, Sabath N, Meiri S, Belmaker J, Mayrose I. The global biogeography of polyploid plants. Nat Ecol Evol 2019; 3:265-273. [PMID: 30697006 DOI: 10.1038/s41559-018-0787-9] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 12/11/2018] [Indexed: 11/09/2022]
Abstract
Deciphering the global distribution of polyploid plants is fundamental for understanding plant evolution and ecology. Many factors have been hypothesized to affect the uneven distribution of polyploid plants across the globe. Nevertheless, the lack of large comparative datasets has restricted such studies to local floras and to narrow taxonomical scopes, limiting our understanding of the underlying drivers of polyploid plant distribution. We present a map portraying the worldwide polyploid frequencies, based on extensive spatial data coupled with phylogeny-based polyploidy inference for tens of thousands of species. This allowed us to assess the potential global drivers affecting polyploid distribution. Our data reveal a clear latitudinal trend, with polyploid frequency increasing away from the equator. Climate, especially temperature, appears to be the most influential predictor of polyploid distribution. However, we find this effect to be mostly indirect, mediated predominantly by variation in plant lifeforms and, to a lesser extent, by taxonomical composition and species richness. Thus, our study presents an emerging view of polyploid distribution that highlights attributes that facilitate the establishment of new polyploid lineages by providing polyploids with sufficient time (that is, perenniality) and space (low species richness) to compete with pre-adapted diploid relatives.
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Affiliation(s)
- Anna Rice
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv, Israel
| | - Petr Šmarda
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Maria Novosolov
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel.,Steinhardt Museum of Natural History, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Drori
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv, Israel
| | - Lior Glick
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv, Israel
| | - Niv Sabath
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv, Israel
| | - Shai Meiri
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel.,Steinhardt Museum of Natural History, Tel-Aviv University, Tel-Aviv, Israel
| | - Jonathan Belmaker
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel.,Steinhardt Museum of Natural History, Tel-Aviv University, Tel-Aviv, Israel
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv, Israel.
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18
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Layman NC, Busch JW. Bottlenecks and inbreeding depression in autotetraploids. Evolution 2018; 72:2025-2037. [PMID: 30136722 DOI: 10.1111/evo.13587] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/14/2018] [Indexed: 12/30/2022]
Abstract
Inbreeding depression is dependent on the ploidy of populations and can inhibit the evolution of selfing. While polyploids should generally harbor less inbreeding depression than diploids at equilibrium, it has been unclear whether this pattern holds in non-equilibrium conditions following bottlenecks. We use stochastic individual-based simulations to determine the effects of population bottlenecks on inbreeding depression in diploids and autotetraploids, in addition to cases where neo-autotetraploids form from the union of unreduced gametes. With a ploidy-independent dominance function based on enzyme kinetics, inbreeding depression is generally lower in autotetraploids for fully and partially recessive mutations. Due to the sampling of more chromosomes during reproduction, bottlenecks generally reduce inbreeding depression to a lesser extent in autotetraploids. All else being equal, population bottlenecks may have ploidy-dependent effects for another reason-in some cases matings between close relatives temporarily increase inbreeding depression in autotetraploids by increasing the frequency of the heterozygous genotype harboring the most harmful mutations. When neo-autotetraploids are formed by few individuals, inbreeding depression is dramatically reduced, given extensive masking of harmful mutations following whole genome duplication. This effect persists as nascent tetraploids reach mutation-selection-drift balance, providing a transient period of permissive conditions favoring the evolution of selfing.
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Affiliation(s)
- Nathan C Layman
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Jeremiah W Busch
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
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19
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Zhou R, Macaya-Sanz D, Rodgers-Melnick E, Carlson CH, Gouker FE, Evans LM, Schmutz J, Jenkins JW, Yan J, Tuskan GA, Smart LB, DiFazio SP. Characterization of a large sex determination region in Salix purpurea L. (Salicaceae). Mol Genet Genomics 2018; 293:1437-1452. [PMID: 30022352 DOI: 10.1007/s00438-018-1473-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/09/2018] [Indexed: 12/30/2022]
Abstract
Dioecy has evolved numerous times in plants, but heteromorphic sex chromosomes are apparently rare. Sex determination has been studied in multiple Salix and Populus (Salicaceae) species, and P. trichocarpa has an XY sex determination system on chromosome 19, while S. suchowensis and S. viminalis have a ZW system on chromosome 15. Here we use whole genome sequencing coupled with quantitative trait locus mapping and a genome-wide association study to characterize the genomic composition of the non-recombining portion of the sex determination region. We demonstrate that Salix purpurea also has a ZW system on chromosome 15. The sex determination region has reduced recombination, high structural polymorphism, an abundance of transposable elements, and contains genes that are involved in sex expression in other plants. We also show that chromosome 19 contains sex-associated markers in this S. purpurea assembly, along with other autosomes. This raises the intriguing possibility of a translocation of the sex determination region within the Salicaceae lineage, suggesting a common evolutionary origin of the Populus and Salix sex determination loci.
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Affiliation(s)
- Ran Zhou
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - David Macaya-Sanz
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - Eli Rodgers-Melnick
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Fred E Gouker
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Luke M Evans
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA.,Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Juying Yan
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Gerald A Tuskan
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.,Biosciences Division, Oak Ridge National Lab, Oak Ridge, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA.
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20
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Henry IM, Akagi T, Tao R, Comai L. One Hundred Ways to Invent the Sexes: Theoretical and Observed Paths to Dioecy in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:553-575. [PMID: 29719167 DOI: 10.1146/annurev-arplant-042817-040615] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Dioecy, the presence of male and female flowers on separate individuals, is both widespread and uncommon within flowering plants, with only a few percent of dioecious species spread across most major phylogenetic taxa. It is therefore safe to assume that dioecy evolved independently in these different groups, which allows us to ask questions regarding the molecular and developmental mechanisms underlying these independent transitions to dioecy. We start this review by examining the problem from the standpoint of a genetic engineer trying to develop dioecy, discuss various potential solutions, and compare them to models proposed in the past and based on genetic and evolutionary considerations. Next, we present recent information regarding candidate sex determinants in three species, acquired using newly established genomic approaches. Although such specific information is still scarce, it is slowly becoming apparent that various genes or pathways can be altered to evolve dioecy.
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Affiliation(s)
- Isabelle M Henry
- Department of Plant Biology, University of California, Davis, California 95616, USA; ,
- Genome Center, University of California, Davis, California 95616, USA
| | - Takashi Akagi
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; ,
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; ,
| | - Luca Comai
- Department of Plant Biology, University of California, Davis, California 95616, USA; ,
- Genome Center, University of California, Davis, California 95616, USA
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21
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Wei N, Govindarajulu R, Tennessen JA, Liston A, Ashman TL. Genetic Mapping and Phylogenetic Analysis Reveal Intraspecific Variation in Sex Chromosomes of the Virginian Strawberry. J Hered 2018; 108:731-739. [PMID: 29036451 DOI: 10.1093/jhered/esx077] [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: 03/27/2017] [Accepted: 09/20/2017] [Indexed: 11/12/2022] Open
Abstract
With their extraordinary diversity in sexual systems, flowering plants offer unparalleled opportunities to understand sex determination and to reveal generalities in the evolution of sex chromosomes. Comparative genetic mapping of related taxa with good phylogenetic resolution can delineate the extent of sex chromosome diversity within plant groups, and lead the way to understanding the evolutionary drivers of such diversity. The North American octoploid wild strawberries provide such an opportunity. We performed linkage mapping using targeted sequence capture for the subdioecious western Fragaria virginiana ssp. platypetala and compared the location of its sex-determining region (SDR) to those of 2 other (sub)dioecious species, the eastern subspecies, F. virginiana ssp. virginiana (whose SDR is at 0-5.5 Mb on chromosome VI of the B2 subgenome), and the sister species F. chiloensis (whose SDR is at 37 Mb on chromosome VI of the Av subgenome). Male sterility was dominant in F. virginiana ssp. platypetala and mapped to a chromosome also in homeologous group VI. Likewise, one major quantitative trait locus (QTL) for female fertility overlapped the male sterility region. However, the SDR mapped to yet another subgenome (B1), and to a different location (13 Mb), but similar to the location inferred in one population of the naturally occurring hybrid between F. chiloensis and F. virginiana (F. ×ananassa ssp. cuneifolia). Phylogenetic analysis of chromosomes across the octoploid taxa showed consistent subgenomic composition reflecting shared evolutionary history but also reinforced within-species variation in the SDR-carrying chromosome, suggesting either repeated evolution, or recent turnovers in SDR.
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Affiliation(s)
- Na Wei
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Rajanikanth Govindarajulu
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260.,Department of Biology, West Virginia University, Morgantown, WV 26505
| | - Jacob A Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
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22
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Alix K, Gérard PR, Schwarzacher T, Heslop-Harrison JS(P. Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants. ANNALS OF BOTANY 2017; 120:183-194. [PMID: 28854567 PMCID: PMC5737848 DOI: 10.1093/aob/mcx079] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/31/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND Polyploidy or whole-genome duplication is now recognized as being present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridization events are found in about half of the world's crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this review, consider genomic aspects of polyploidy. APPROACHES Discovery of the evolutionary consequences of new, evolutionarily recent and ancient polyploidy requires a range of approaches. Large-scale studies of both single species and whole ecosystems, with hundreds to tens of thousands of individuals, sometimes involving 'garden' or transplant experiments, are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical. CONCLUSIONS The success of polyploidy, displacing the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidization events. Strikingly, polyploidization often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting the concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole-genome duplication act as drivers of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution.
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Affiliation(s)
- Karine Alix
- GQE – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- For correspondence. E-mail
| | - Pierre R. Gérard
- GQE – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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23
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Segraves KA. The effects of genome duplications in a community context. THE NEW PHYTOLOGIST 2017; 215:57-69. [PMID: 28418074 DOI: 10.1111/nph.14564] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/16/2017] [Indexed: 06/07/2023]
Abstract
Contents 57 I. 57 II. 59 III. 59 IV. 63 V. 64 VI. 64 VII. 66 66 References 66 SUMMARY: Whole-genome duplication (WGD), or polyploidy, has important effects on the genotype and phenotype of plants, potentially altering ecological interactions with other organisms. Even though the connections between polyploidy and species interactions have been recognized for some time, we are only just beginning to test whether WGD affects community context. Here I review the sparse information on polyploidy and community context and then present a set of hypotheses for future work. Thus far, community-level studies of polyploids suggest an array of outcomes, from no changes in community context to shifts in the abundance and composition of interacting species. I propose a number of mechanisms for how WGD could alter community context and how the emergence of polyploids in populations could also alter the community context of parental diploids and other plant species. Resolving how and when these changes are expected to occur will require a deeper understanding of the connections among WGD, phenotypic changes, and the direct and indirect effects of species interactions.
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Affiliation(s)
- Kari A Segraves
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA
- Archbold Biological Station, Venus, FL, 33960, USA
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24
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Zenil‐Ferguson R, Ponciano JM, Burleigh JG. Testing the association of phenotypes with polyploidy: An example using herbaceous and woody eudicots. Evolution 2017; 71:1138-1148. [DOI: 10.1111/evo.13226] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/17/2017] [Indexed: 01/08/2023]
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25
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Barker MS, Husband BC, Pires JC. Spreading Winge and flying high: The evolutionary importance of polyploidy after a century of study. AMERICAN JOURNAL OF BOTANY 2016; 103:1139-45. [PMID: 27480249 DOI: 10.3732/ajb.1600272] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 05/10/2023]
Affiliation(s)
- Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1 Canada
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 USA
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