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268 results for “polyploid”
Reference datasets for consistency tests of GENAPOPOP 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms.
<p>Datasets companion of the manuscript entitled GenAPoPop 1.0: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms, used to achieve consistency test with Spagedi 1.5 software, and used as reference datasets to demonstrate the new possibilities allowed by GenAPoPop software.</p> <p>Raw datasets used for testing GenAPoPop 1.0, A user-friendly software for easily compute genetic analyses of autopolyploid populations packaged for Linux, MacOS and Windows; Results obtained from Spagedi 1.5 (Hardy & Vekemans 2001) and GenAPoPop1.0.</p> <p>Four pseudo-observed genotyping autotetrapolyploid SNP datasets, corresponding respectively to panmictic (A), highly clonal (B), highly selfed (C) and half-clonal-half-selfed (D) reproductive mode scenario. In all these four scenarios, we simulated two populations of 100 individuals each, connected with a migration rate of 0.01 and mutating at a rate of 0.01, genotyped at 10 SNPs. Datasets were recorded 1000 generations after an initial randomly drawing population with equal allele frequencies.</p> <p>One SNP tetraploid genotyping dataset from two French <em>Ludwigia grandiflora subsp. hexapetala</em> populations (aquatic plant from the Angiosperm clade): two populations in which we collected 75 individuals, each genotyped with 36 SNPs using the Hiplex method allowing confident allele dosage (Delord et al. 2018).</p> <p>One microsatellite tetraploid genotyping dataset on two Aulactinia stella populations (sea-anemone from the Cnidaria phylum), sampled on the coast of the arctic ocean. One population of 21 individuals and one population of 15 individuals, both genotyped with 10 microsatellites.</p> <p>We also report here the consistency tests with GenAlex and Spagedi, results of analyses (GPP tab) on 6300 independant simulations and inferences of the quantitative reproductive modes using the bayesian method on CEMP tab made on 6300 another independant simulations.</p>
Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation (Part 1/2)
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Data from: Dispersal and establishment traits provide a colonization advantage for a polyploid apomictic plant
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Sensitivity analysis script for: Why so many polyploids?
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Phenotypic plasticity and genetic diversity in a polyploid Arabidopsis complex
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Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation (Part 2/2)
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Inbreeding depression in polyploid species: a meta-analysis
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Investigating historical drivers of latitudinal gradients in polyploid plant biogeography: A multi-clade perspective
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Synergistic polyploidization and long-distance dispersal enable the global diversification of yellowcress herbs
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The genetic consequences of range expansion and its influence on diploidization in polyploids
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Data from: Genome duplication effects on functional traits and fitness are genetic context and species dependent: studies of synthetic polyploid Fragaria
PREMISE OF THE STUDY Divergence in functional traits and adaptive responses to environmental change underlies the ecological advantage of polyploid plants in the wild. While established polyploids may benefit from combined outcomes of genome doubling, hybridization and polyploidy-enabled adaptive evolution, it remains less clear whether genome doubling alone can drive ecological divergence or whether the outcome is genetically variable.METHODS Using synthetic, colchicine-induced, autotetraploid (4x) plants derived from self-pollinated diploid (2x) seeds, and their colchicine-treated but unconverted diploid (2x.nc) full sibs from two diploid wild strawberry taxa (Fragaria vesca ssp. vesca and F. vesca ssp. bracteata), we examined the effects of genome doubling on functional traits, heat stress tolerance and fitness components across taxa and maternal families (i.e. genetic families) within taxa.KEY RESULTS Comparisons between 2x and 2x.nc plants indicated a negligible effect of colchicine treatment on functional traits. Genome doubling increased stomatal length, and decreased stomatal density, specific leaf area and leaf vein density, recapitulating patterns observed in wild polyploid Fragaria. Trichome density, heat stress tolerance and relative growth rate were not significantly affected by genome doubling. Although a reduction in clonal reproduction was observed in response to genome doubling, this effect was strongly genetic family dependent.CONCLUSIONS The results suggest that genome doubling during incipient speciation alone can generate ecological divergence and variation among genetic lineages. This response potentially allows for rapid short-term evolutionary adaptation and fuels genomic diversity and independent origins of polyploidy.
Data from: Substantially adaptive potential in polyploid cyprinid fishes: evidence from biogeographic, phylogenetic and genomic studies
<p>Whole genome duplication is commonly believed to play key roles in vertebrate evolution. However, nowadays polyploidy exists in a few fish, amphibian, and reptile groups only, and seems to be an evolutionary dead-end in vertebrates. We investigate the evolutionary significance of polyploidization in Cyprinidae – a fish family that contains more polyploid species than any other vertebrate groups with integrating biogeographic, phylogenetic, and genomic analyses. First, polyploid species are found to be significantly frequent in higher altitude and lower mean annual temperature areas compared to diploid species in Cyprinidae. Second, a polyploidy-related diversification rate shift is observed in Cyprinidae. It is that increased net diversification rate is only seen in three polyploid lineages, and other polyploid lineages have similar net diversification rate as well as diploid lineages in Cyprinidae. Interestingly, significant 'lag-times' existed between polyploidization and radiation in Cyprinidae. Multiple polyploid lineages were established ~15 Mya through recurrent allopolyploidization events but net diversification rate did not start to increase until ~5 Mya – long after polyploidization events. Environmental changes associated with the continuous uplift of Tibetan Plateau and climate change have likely promoted the initial establishment and subsequent radiation of polyploidy in Cyprinidae. Finally, unique retention of duplicated genes in polyploid cyprinids adapted to harsh environments is found. Taken together, our results suggest that polyploidy in Cyprinidae is far more than an evolutionary dead-end, but rather shows substantially adaptive potential. Polyploid cyprinids thus constitute an ideal model system for unveiling largely unexplored consequences of whole genome duplication in vertebrates, from genomic evolution to species diversification.</p>
Pioneering polyploids: the impact of whole-genome duplication on biome shifting in New Zealand Coprosma (Rubiaceae) and Veronica (Plantaginaceae)
<p>The role of whole-genome duplication in facilitating shifts into novel biomes remains unknown. Focusing on two diverse woody plant groups in New Zealand, <i>Coprosma </i>(Rubiaceae) and <i>Veronica </i>(Plantaginaceae), we investigate how biome occupancy varies with ploidy level, and test the hypothesis that whole-genome duplication increases the rate of biome shifting.</p> <p>Ploidy levels and biome occupancy (forest, open, and alpine) were determined for indigenous species in both clades. The distribution of low ploidy (<i>Coprosma</i>: 2<i>x</i>, <i>Veronica</i>: 6<i>x</i>) vs high ploidy (<i>Coprosma</i>: 4–10<i>x</i>, <i>Veronica</i>: 12–18<i>x</i>) species across biomes was tested statistically. Estimation of the phylogenetic history of biome occupancy and whole-genome duplication was performed using time-calibrated phylogenies and the R package BioGeoBEARS. Trait-dependent dispersal models were implemented to determine support for an increased rate of biome shifting among high ploidy lineages.</p> <p>We find support for a greater than random portion of high ploidy species occupying multiple biomes. We also find strong support for high ploidy taxa showing a three to eight-fold increase in the rate of biome shifts. These results suggest that whole-genome duplication promotes ecological expansion into new biomes.</p>
Data from: Polyploid plants obtain greater fitness benefits from a nutrient acquisition mutualism
<p>Polyploidy is a key driver of ecological and evolutionary processes in plants, yet little is known about its effects on biotic interactions. This gap in knowledge is especially profound for nutrient acquisition mutualisms, despite the fact that they regulate global nutrient cycles and structure ecosystems. Generalism in mutualistic interactions depends on the range of potential partners (niche breadth), the benefits obtained, and ability to maintain benefits across a variety of partners (fitness plasticity). Here, we determine how each of these is influenced by polyploidy in the legume-rhizobium mutualism. We inoculated a broad geographic sample of natural diploid and autotetraploid alfalfa (<i>Medicago sativa</i>)<i> </i>lineages with a diverse panel of <i>Sinorhizobium </i>bacterial symbionts. To analyze the extent and mechanism of generalism, we measured host growth benefits and functional traits. Autotetraploid plants obtained greater fitness enhancement from mutualistic interactions and were better able to maintain this across diverse rhizobial partners (i.e., low plasticity in fitness) relative to diploids. These benefits were not attributed to increases in niche breadth, but instead reflect increased rewards from investment in the mutualism. Polyploid plants displayed greater generalization in bacterial mutualisms relative to diploids illustrating another axis of advantage for polyploids over diploids.</p>
Shared single copy genes are generally reliable for inferring phylogenetic relationships among polyploid taxa
<p>Polyploidy, or whole-genome duplication, is expected to confound the inference of species trees with phylogenetic methods for two reasons. First, the presence of retained duplicated genes requires the reconciliation of the inferred gene trees to a proposed species tree. Second, even if the analyses are restricted to shared single copy genes, the occurrence of reciprocal gene loss, where the surviving genes in different species are paralogs from the polyploidy rather than orthologs, will mean that such genes will not have evolved under the corresponding species tree and may not have gene trees that allow inference of the species tree. Here we analyze three different ancient polyploidy events, using synteny-based inferences of orthology and paralogy to infer gene trees from more than 17,000 sets of homologous genes. We find that the simple use of single copy genes from polyploid organisms provides reasonably robust phylogenetic signals, despite the presence of reciprocal gene losses. Such gene trees are also most often in accord with the inferred species relationships inferred from maximum likelihood models of gene loss after polyploidy: a completely distinct phylogenetic signal present in these genomes. As seen in other studies, however, we find that methods for inferring phylogenetic confidence yield high support values even in cases where the underlying data suggest meaningful conflict in the phylogenetic signals.</p>
High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species
<p>With populations of threatened and endangered species declining worldwide, efforts are being made to generate high-quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high-quality <em>de novo</em> plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus <em>Fraxinus</em> (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a whole genome triplication at the base of the Oleaceae as well as a subsequent whole genome duplication shared by <em>Syringa</em>, <em>Osmanthus</em>, <em>Olea, and Fraxinus</em>. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.</p>
Divergence in cold tolerance promotes niche differentiation between diploid and polyploid kiwifruits along an altitudinal gradient in Southwest China
<p>Polyploidization is hypothesized to improve the freezing resistance of plants in cold regions. However, adaptive strategies and key physiological mechanisms involved in the freezing resistant ability of polyploids remain unclear. In <em>Actinidia chinensis</em> (kiwifruits), the tetraploids and hexaploids occupy higher altitude habitats with colder climates than the diploids, providing a study system to investigate mechanisms responsible for differentiation in freezing resistance between cytotypes. We characterized environmental conditions of their natural distribution areas, and measured leaf-level traits of cold damages and water relations at typical sites of each cytotype along an altitudinal gradient. Polyploids showed lower semi-lethal temperature (LT<sub>50</sub>) than ice nucleation temperature (INT), reflecting a tolerance strategy to cope with freezing events in the plateau regions. More negative turgor loss points and larger cell elastic modulus of polyploids could help to alleviate damages from freezing-induced cell dehydration, thus strengthening their tolerance to lower subzero temperatures (lower LT<sub>50</sub>). The increased supercooling capacity of polyploids (lower INT) might correlate with less extracellular ice formation due to lower osmotic potential at full turgor, apoplastic water fraction and tissue capacitance. Our study uncovers a greater cold tolerance in polyploid kiwifruits than diploids, and suggests the potential linkage between freezing tolerance and water relations. Taken together, such a divergence in stress resistance may underlie the niche shift of polyploid plants towards harsh environments.</p>
Extensive polyploid clonality was a successful strategy for seagrass to expand into a newly submerged environment
<p>Polyploidy has the potential to allow organisms to outcompete their diploid progenitor(s) and occupy new environments. Shark Bay, Western Australia, is a World Heritage Area dominated by temperate seagrass meadows including Poseidon's ribbon weed, Posidonia australis. This seagrass is at the northern extent of its natural geographic range and experiences extreme temperatures and salinities. Our genomic and cytogenetic assessments of ten meadows identified geographically restricted, diploid clones (2n = 20) in a single location, and widespread, high heterozygosity, polyploid clones (2n = 40) in all other locations. A single polyploid clone spanned at least 180 km, making it the largest known example of a clone in any environment on earth. Whole genome duplication through polyploidy, combined with clonality, may have provided the mechanism for P. australis to expand into new habitats and adapt to new environments that became increasingly stressful for its diploid progenitor(s). The new polyploid clones likely formed in the shallow waters after inundation of Shark Bay < 8,500 years ago and subsequently expanded via vegetative growth into newly submerged habitats.</p>
Variation in reproduction and gene flow between cytotypes in a polyploid complex: one size does not fit all
<p>Whole-genome duplication is considered an important speciation mechanism in plants. However, its effect on reproductive isolation between higher cytotypes is not well understood. We used backcrosses between different ploidy levels and surveys of mixed-ploidy contact zones to determine how reproductive barriers differed with cytotype across a polyploid complex. We backcrossed F1 hybrids derived from 2X-4X and 4X-6X crosses in the Campanula rotundifolia autopolyploid complex, measured backcross fitness, and estimated backcross DNA cytotype. We then sampled four natural mixed-ploidy contact zones (two 2X-4X and two 4X-6X), estimated ploidy, and genotyped individuals across each contact zone. Reproductive success and capacity for gene flow was markedly lower for 2X-4X than 4X-6X hybrids. In fact, 3X hybrids could not backcross; all 2X-4X backcross progeny resulted from neotetraploid F1 hybrids. Further, no 3X individuals were found in 2X-4X contact zones, and 2X and 4X individuals were genetically distinct. By contrast, backcrosses of 5X hybrids were relatively successful, particularly when crossed to 6X individuals. In 4X-6X contact zones, 5X individuals and aneuploids were common and all cytotypes were largely genetically similar and spatially intermixed. Taken together, these results provide strong evidence that reproduction is low between 2X and 4X cytotypes, primarily occurring via unreduced gamete production, but that reproduction and gene flow are ongoing between 4X and 6X cytotypes. Further, it suggests whole genome duplication can result in speciation between diploids and polyploids, but is less likely to create reproductive barriers between different polyploid cytotypes, resulting in two fundamentally different potentials for speciation across polyploid complexes.</p>
Polyploidization-enhanced effective clonal reproduction endows the successful invasion of Solidago canadensis
Clonality and ploidy levels are positively associated with plant invasiveness. However, there is still no consensus on whether polyploidization can promote the invasion of alien plants by enhancing clonality. Our recent long-term community succession study found that the more vigorous clone of introduced polyploid Solidago canadensis succeeded into mono-dominant community, which seems to be a positive correlationship between polyploidization and clonal reproduction. However, how polyploidization improves the clonal reproduction of S. canadensis remains unknown. Here, we compared clonal growth ability among diploids and polyploids of S. canadensis from native and introduced ranges in a common garden. Results showed that the rhizomes of S. canadensis originated from axillary buds of dense nodes at the basal stem of seedling and then produced into clonal ramets. Diploids had denser nodes and more buds, developed more rhizomes per unit mass and produced more clonal propagules at the early growth stage compared with polyploids. However, the number of juvenile and secondary rhizomes, as well as the diameter and length of rhizomes in polyploid populations was significant higher than those of diploids, and those clonal traits in introduced polyploids were significant higher than in native polyploids. Moreover, a phalanx growth form was observed in native and introduced diploid populations, which allocated about 3% and 5% of the total biomass to rhizomes, respectively, resulting in short and weak rhizomes. However, native and introduced polyploids allocated about 35% and 40%, respectively, of the total biomass to rhizomes, resulting in long and strong rhizomes, which were guerrilla growth forms. This study firstly shows that polyploidization enhanced the effective clonal reproduction of S. canadensis through pre-adaptation and rapid post-adaptation evolution, and consequently contributed to its successful invasion.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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