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Mezzasalma M, Brunelli E, Odierna G, Guarino FM. Evolutionary and Genomic Diversity of True Polyploidy in Tetrapods. Animals (Basel) 2023; 13:ani13061033. [PMID: 36978574 PMCID: PMC10044425 DOI: 10.3390/ani13061033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/02/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
True polyploid organisms have more than two chromosome sets in their somatic and germline cells. Polyploidy is a major evolutionary force and has played a significant role in the early genomic evolution of plants, different invertebrate taxa, chordates, and teleosts. However, the contribution of polyploidy to the generation of new genomic, ecological, and species diversity in tetrapods has traditionally been underestimated. Indeed, polyploidy represents an important pathway of genomic evolution, occurring in most higher-taxa tetrapods and displaying a variety of different forms, genomic configurations, and biological implications. Herein, we report and discuss the available information on the different origins and evolutionary and ecological significance of true polyploidy in tetrapods. Among the main tetrapod lineages, modern amphibians have an unparalleled diversity of polyploids and, until recently, they were considered to be the only vertebrates with closely related diploid and polyploid bisexual species or populations. In reptiles, polyploidy was thought to be restricted to squamates and associated with parthenogenesis. In birds and mammals, true polyploidy has generally been considered absent (non-tolerated). These views are being changed due to an accumulation of new data, and the impact as well as the different evolutionary and ecological implications of polyploidy in tetrapods, deserve a broader evaluation.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
- Correspondence: (M.M.); (E.B.)
| | - Elvira Brunelli
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
- Correspondence: (M.M.); (E.B.)
| | - Gaetano Odierna
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy (F.M.G.)
| | - Fabio Maria Guarino
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy (F.M.G.)
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Fujiwara T, Egashira T, Gutiérrez-Ortega JS, Hori K, Ebihara A, Watano Y. Establishment of an allotetraploid fern species, Lepisorus yamaokae Seriz., between two highly niche-differentiated parental species. AMERICAN JOURNAL OF BOTANY 2022; 109:1456-1471. [PMID: 35938973 DOI: 10.1002/ajb2.16043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The successful establishment of polyploid species is hypothesized to be promoted by niche differentiation from the parental species or by range shifts during climate oscillations. However, few studies have considered both of these factors simultaneously. We resolved the origin of a tetraploid fern, Lepisorus yamaokae, and explored a pattern of niche differentiation among the allotetraploid and parental species in past and current climates. METHODS We reconstructed phylogenetic trees based on plastid marker and single-copy nuclear genes to resolve the allopolyploid origin of L. yamaokae. We also evaluated climatic niche differentiation among L. yamaokae and its two parental species using species distribution models in geographic space and principal component analysis. RESULTS We infer that L. yamaokae had a single allotetraploid origin from L. annuifrons and L. uchiyamae. Climatic niche analyses show that the parental species currently occupy different niche spaces. The predicted distribution of the parental species at the Last Glacial Maximum (LGM) suggests more opportunities for hybridization during the LGM or during other recent temporary range shifts. Lepisorus yamaokae has a narrower niche than the additive niche of the parental species. We also observed niche conservatism in L. yamaokae. CONCLUSIONS Range shifts of the parental species during climatic oscillations in the Quaternary likely facilitated the formation and establishment of L. yamaokae. Further, the genetic intermediacy of L. yamaokae may have enabled a niche shift in its microenvironment, resulting in its successful establishment without a macroclimatic niche shift in L. yamaokae.
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Affiliation(s)
- Tao Fujiwara
- Makino Herbarium, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji, Tokyo, 192-0397, Japan
| | - Tsubasa Egashira
- Department of Biology, Faculty of Science, Chiba University, Yayoi-cho, Inage, Chiba, 263-8522, Japan
| | | | - Kiyotaka Hori
- The Kochi Prefectural Makino Botanical Garden, 4200-6 Godaisan, Kochi, 781-8125, Japan
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage, Chiba, 263-8522, Japan
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Van de Peer Y, Ashman TL, Soltis PS, Soltis DE. Polyploidy: an evolutionary and ecological force in stressful times. THE PLANT CELL 2021; 33:11-26. [PMID: 33751096 PMCID: PMC8136868 DOI: 10.1093/plcell/koaa015] [Citation(s) in RCA: 273] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/07/2020] [Indexed: 05/10/2023]
Abstract
Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.
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Affiliation(s)
- Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB - UGent Center for Plant Systems Biology, B-9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
- Department of Biology, University of Florida, Gainesville, Florida 32611
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Duchoslav M, Jandová M, Kobrlová L, Šafářová L, Brus J, Vojtěchová K. Intricate Distribution Patterns of Six Cytotypes of Allium oleraceum at a Continental Scale: Niche Expansion and Innovation Followed by Niche Contraction With Increasing Ploidy Level. FRONTIERS IN PLANT SCIENCE 2020; 11:591137. [PMID: 33362819 PMCID: PMC7755979 DOI: 10.3389/fpls.2020.591137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/06/2020] [Indexed: 05/23/2023]
Abstract
The establishment and success of polyploids are thought to often be facilitated by ecological niche differentiation from diploids. Unfortunately, most studies compared diploids and polyploids, ignoring variation in ploidy level in polyploids. To fill this gap, we performed a large-scale study of 11,163 samples from 1,283 populations of the polyploid perennial geophyte Allium oleraceum with reported mixed-ploidy populations, revealed distribution ranges of cytotypes, assessed their niches and explored the pattern of niche change with increasing ploidy level. Altogether, six ploidy levels (3x-8x) were identified. The most common were pentaploids (53.6%) followed by hexaploids (22.7%) and tetraploids (21.6%). Higher cytotype diversity was found at lower latitudes than at higher latitudes (>52° N), where only tetraploids and pentaploids occurred. We detected 17.4% of mixed-ploidy populations, usually as a combination of two, rarely of three, cytotypes. The majority of mixed-ploidy populations were found in zones of sympatry of the participating cytotypes, suggesting they have arisen through migration (secondary contact zone). Using coarse-grained variables (climate, soil), we found evidence of both niche expansion and innovation in tetraploids related to triploids, whereas higher ploidy levels showed almost zero niche expansion, but a trend of increased niche unfilling of tetraploids. Niche unfilling in higher ploidy levels was caused by a contraction of niche envelopes toward lower continentality of the climate and resulted in a gradual decrease of niche breadth and a gradual shift in niche optima. Field-recorded data indicated wide habitat breadth of tetraploids and pentaploids, but also a pattern of increasing synanthropy in higher ploidy levels. Wide niche breadth of tetra- and pentaploids might be related to their multiple origins from different environmental conditions, higher "age", and retained sexuality, which likely preserve their adaptive potential. In contrast, other cytotypes with narrower niches are mostly asexual, probably originating from a limited range of contrasting environments. Persistence of local ploidy mixtures could be enabled by the perenniality of A. oleraceum and its prevalence of vegetative reproduction, facilitating the establishment and decreasing exclusion of minority cytotype due to its reproductive costs. Vegetative reproduction might also significantly accelerate colonization of new areas, including recolonization of previously glaciated areas.
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Affiliation(s)
- Martin Duchoslav
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Michaela Jandová
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
- Institute of Botany, Czech Academy of Sciences, Pruhonice, Czechia
| | - Lucie Kobrlová
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Lenka Šafářová
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jan Brus
- Department of Geoinformatics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Kateřina Vojtěchová
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
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Stevens AV, Nicotra AB, Godfree RC, Guja LK. Polyploidy affects the seed, dormancy and seedling characteristics of a perennial grass, conferring an advantage in stressful climates. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:500-513. [PMID: 32011086 DOI: 10.1111/plb.13094] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 12/30/2019] [Indexed: 06/10/2023]
Abstract
Polyploidy (the state of having more than two genome copies) is widely distributed in flowering plants and can vary within species, with polyploid races often associated with broad ecological tolerances. Polyploidy may influence within-species variation in seed development, germination and establishment. We hypothesized that interactions between polyploidy and the seed developmental environment would affect subsequent dormancy, germination and early growth traits, particularly in stressful environments. Using seeds developed in a common garden under ambient and warmed conditions, we conducted germination trials under drought and temperature stress, and monitored the subsequent growth of seedlings. The study species, Themeda triandra, is a widespread, keystone, Australian native grass and a known polyploid complex. Tetraploid plants produced heavier, more viable seeds than diploids. Tetraploids were significantly more dormant than diploids, regardless of seed developmental environment. Non-dormant tetraploids were more sensitive to germination stress compared to non-dormant diploids. Finally, tetraploid seedlings were larger and grew faster than diploids, usually when maternal plants were exposed to developmental temperatures atypical to the source environment. Seed and seedling traits suggest tetraploids are generally better adapted to stressful environments than diploids. Because tetraploid seeds of T. triandra are more dormant they are less likely to germinate under stress, and when they do germinate, seedling growth is rapid and independent of seed developmental environment. These novel results demonstrate that polyploidy, sometimes in interaction with developmental environment and possibly also asexuality, can have within-species variation in seed and seedling traits that increase fitness in stressful environments.
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Affiliation(s)
- A V Stevens
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
- National Seed Bank, Australian National Botanic Gardens, Canberra, ACT, Australia
- Centre for Australian National Biodiversity Research, CSIRO, Canberra, ACT, Australia
| | - A B Nicotra
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - R C Godfree
- Centre for Australian National Biodiversity Research, CSIRO, Canberra, ACT, Australia
| | - L K Guja
- National Seed Bank, Australian National Botanic Gardens, Canberra, ACT, Australia
- Centre for Australian National Biodiversity Research, CSIRO, Canberra, ACT, Australia
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Decanter L, Colling G, Elvinger N, Heiðmarsson S, Matthies D. Ecological niche differences between two polyploid cytotypes of Saxifraga rosacea. AMERICAN JOURNAL OF BOTANY 2020; 107:423-435. [PMID: 32067225 PMCID: PMC7216898 DOI: 10.1002/ajb2.1431] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/04/2019] [Indexed: 05/30/2023]
Abstract
PREMISE Different cytotypes of a species may differ in their morphology, phenology, physiology, and their tolerance of extreme environments. We studied the ecological niches of two subspecies of Saxifraga rosacea with different ploidy levels: the hexaploid Central European endemic subspecies sponhemica and the more widely distributed octoploid subspecies rosacea. METHODS For both cytotypes, we recorded local environmental conditions and mean plant trait values in populations across their areas of distribution, analyzed their distributions by niche modeling, studied their performance at two transplant sites with contrasting conditions, and experimentally tested their cold resistance. RESULTS Mean annual temperature was higher in hexaploid than in octoploid populations and experiments indicated that frost tolerance of the hexaploid is lower than that of the octoploid. Reproduction of octoploids from Central Europe was higher than that of hexaploids at a transplant site in subarctic Iceland, whereas the opposite was true in temperate Luxembourg, indicating adaptation of the octoploids to colder conditions. Temperature variables were also most important in niche models predicting the distribution of the two cytotypes. Genetic differences in survival among populations were larger for the octoploids than for the hexaploids in both field gardens, suggesting that greater genetic variability may contribute to the octoploid's larger distributional range. CONCLUSIONS Our results support the hypotheses that different cytotypes may have different niches leading to spatial segregation, and that higher ploidy levels can result in a broader ecological niche and greater tolerance of more extreme conditions.
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Affiliation(s)
- Lucile Decanter
- Fondation Faune‐Flore c/o Musée national d'histoire naturelle25 rue MünsterL‐2160LuxembourgLuxembourg
- Population Biology and EvolutionMusée national d'histoire naturelle25 rue MunsterL‐2160LuxembourgLuxembourg
- Unit of Plant EcologyDepartment of BiologyUniversity of MarburgKarl‐von‐Frisch‐Straße 8D‐35043MarburgGermany
| | - Guy Colling
- Population Biology and EvolutionMusée national d'histoire naturelle25 rue MunsterL‐2160LuxembourgLuxembourg
| | - Nora Elvinger
- Population Biology and EvolutionMusée national d'histoire naturelle25 rue MunsterL‐2160LuxembourgLuxembourg
| | - Starri Heiðmarsson
- The Icelandic Institute of Natural HistoryBorgir vid Nordurslod600AkureyriIceland
| | - Diethart Matthies
- Unit of Plant EcologyDepartment of BiologyUniversity of MarburgKarl‐von‐Frisch‐Straße 8D‐35043MarburgGermany
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López-Jurado J, Mateos-Naranjo E, Balao F. Niche divergence and limits to expansion in the high polyploid Dianthus broteri complex. THE NEW PHYTOLOGIST 2019; 222:1076-1087. [PMID: 30585629 DOI: 10.1111/nph.15663] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/14/2018] [Indexed: 05/25/2023]
Abstract
Niche evolution in plant polyploids remains controversial and evidence for alternative patterns has been reported. Using the autopolyploid Dianthus broteri complex (2×, 4×, 6× and 12×) as a model, we aimed to integrate three scenarios - competitive exclusion, recurrent origins of cytotypes and niche filling - into a single framework of polyploid niche evolution. We hypothesized that high polyploids would tend to evolve towards extreme niches when low ploidy cytotypes have nearly filled the niche space. We used several ecoinformatics and phylogenetic comparative analyses to quantify differences in the ecological niche of each cytotype and to evaluate alternative models of niche evolution. Each cytotype in this complex occupied a distinct ecological niche. The distributions were mainly constrained by soil characteristics, temperature and drought stress imposed by the Mediterranean climate. Tetraploids had the highest niche breadth and overlap due to their multiple origins, whereas the higher ploidy cytotypes were found in different, restricted, nonoverlapping niches. Niche evolution analyses suggested a scenario with one niche optimum for each ploidy, including the two independent tetraploid lineages. Our results suggest that the fate of nascent polyploids could not be predicted without accounting for phylogenetic relatedness, recurrent origins or the niche occupied by ancestors.
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Affiliation(s)
- Javier López-Jurado
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, E-41080, Seville, Spain
| | - Enrique Mateos-Naranjo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, E-41080, Seville, Spain
| | - Francisco Balao
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, E-41080, Seville, Spain
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DeWoody J, Rogers DL, Hipkins VD, Endress BA. Spatially explicit and multi-sourced genetic information is critical for conservation of an endangered plant species, San Diego thornmint (Acanthomintha ilicifolia). CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1062-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Blaine Marchant D, Soltis DE, Soltis PS. Patterns of abiotic niche shifts in allopolyploids relative to their progenitors. THE NEW PHYTOLOGIST 2016; 212:708-718. [PMID: 27399976 DOI: 10.1111/nph.14069] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/23/2016] [Indexed: 05/05/2023]
Abstract
Polyploidy has extensive genetic, physiological, morphological, and ecological ramifications. While the patterns underlying the genetic and morphological consequences of polyploidy are being rapidly elucidated, the effects on ecological niche are still largely unknown. This study investigated 13 allopolyploid systems in North America (10 ferns and three angiosperms) using digitized natural history museum specimens. The abiotic niches of the allopolyploids were compared with those of their diploid progenitors using ecological niche modeling, niche analyses, and multivariate analyses. We identified four patterns of niche shifts through our analyses: niche expansion, niche contraction, niche intermediacy, and niche novelty. The classification of these shifts depended on the amount of niche overlap and breadth between the polyploid and progenitors. The most common niche shift was niche intermediacy in which the polyploid inhabited a geographic range between that of the progenitors and had a high degree of niche overlap. Each polyploid had at least partial geographic sympatry and abiotic niche overlap with one of its progenitors, suggesting that biotic and/or microclimate factors may play a larger role in polyploid establishment than previously hypothesized. This study provides a baseline for future comparisons of the diverse outcomes of genome merger and duplication on abiotic niche preference.
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Affiliation(s)
- D Blaine Marchant
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
- Florida Museum of Natural History, Gainesville, FL, 32611, USA.
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
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Guo W, Yang J, Sun XD, Chen GJ, Yang YP, Duan YW. Divergence in Eco-Physiological Responses to Drought Mirrors the Distinct Distribution of Chamerion angustifolium Cytotypes in the Himalaya-Hengduan Mountains Region. FRONTIERS IN PLANT SCIENCE 2016; 7:1329. [PMID: 27630654 PMCID: PMC5005327 DOI: 10.3389/fpls.2016.01329] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 08/18/2016] [Indexed: 05/08/2023]
Abstract
Polyploid species generally occupy harsher habitats (characterized by cold, drought and/or high altitude) than diploids, but the converse was observed for Chamerion angustifolium, in which diploid plants generally inhabit higher altitudes than their polyploid derivatives. Plants at high altitudes may experience cold-induced water stress, and we therefore examined the physiological responses of diploid and hexaploid C. angustifolium to water stress to better understand the ecological differentiation of plants with different ploidy levels. We conducted a common garden experiment by subjecting seedlings of different ploidy levels to low, moderate, and severe water stress. Fourteen indicators of physiological fitness were measured, and the anatomical characteristics of the leaves of each cytotype were determined. Both cytotypes were influenced by drought, and diploids exhibited higher fitness in terms of constant root:shoot ratio (R:S ratio) and maximum quantum yield of PS II (Fv/Fm ), less reduced maximal photosynthetic rate (A max), transpiration rate (E), intercellular CO2 concentration (C i) and stomatal conductance (g s), and higher long-term water use efficiency (WUEL) under severe water stress than did hexaploids. Analysis of leaf anatomy revealed morphological adjustments for tolerating water deficiency in diploids, in the form of closely packed mesophyll cells and small conduits in the midvein. Our results indicate that diploid C. angustifolium is more tolerant of drought than hexaploid plants, ensuring the successful survival of the diploid at high altitudes. This eco-physiological divergence may facilitate the species with different cytotypes to colonize new and large geographic ranges with heterogeneous environmental conditions.
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Affiliation(s)
- Wen Guo
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of the Chinese Academy of SciencesBeijing, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Jie Yang
- School of Life Sciences, Yunnan Normal UniversityKunming, China
| | - Xu-Dong Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Guang-Jie Chen
- Key Laboratory of Plateau Lake Ecology and Global Change, School of Tourism and Geography, Yunnan Normal UniversityKunming, China
| | - Yong-Ping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Yuan-Wen Duan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
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Soltis DE, Visger CJ, Marchant DB, Soltis PS. Polyploidy: Pitfalls and paths to a paradigm. AMERICAN JOURNAL OF BOTANY 2016; 103:1146-66. [PMID: 27234228 DOI: 10.3732/ajb.1500501] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/25/2016] [Indexed: 05/22/2023]
Abstract
Investigators have long searched for a polyploidy paradigm-rules or principles that might be common following polyploidization (whole-genome duplication, WGD). Here we attempt to integrate what is known across the more thoroughly investigated polyploid systems on topics ranging from genetics to ecology. We found that while certain rules may govern gene retention and loss, systems vary in the prevalence of gene silencing vs. homeolog loss, chromosomal change, the presence of a dominant genome (in allopolyploids), and the relative importance of hybridization vs. genome doubling per se. In some lineages, aspects of polyploidization are repeated across multiple origins, but in other species multiple origins behave more stochastically in terms of genetic and phenotypic change. Our investigation also reveals that the path to synthesis is hindered by numerous gaps in our knowledge of even the best-known systems. Particularly concerning is the absence of linkage between genotype and phenotype. Moreover, most recent studies have focused on the genetic and genomic attributes of polyploidy, but rarely is there an ecological or physiological context. To promote a path to a polyploidy paradigm (or paradigms), we propose a major community goal over the next 10-20 yr to fill the gaps in our knowledge of well-studied polyploids. Before a meaningful synthesis is possible, more complete data sets are needed for comparison-systems that include comparable genetic, genomic, chromosomal, proteomic, as well as morphological, physiological, and ecological data. Also needed are more natural evolutionary model systems, as most of what we know about polyploidy continues to come from a few crop and genetic models, systems that often lack the ecological context inherent in natural systems and necessary for understanding the drivers of biodiversity.
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Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - D Blaine Marchant
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
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