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104 results for “allopolyploid”
Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus
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Data from: Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species
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The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars
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Eco-genetic additivity of diploids in allopolyploid wild wheats
Underpinnings of the distribution of allopolyploid species (hybrids with duplicated genome) along spatial and ecological gradients are elusive. As allopolyploid speciation combines the range of genetic and ecological characteristics of divergent diploids, allopolyploids initially show their additivity and are predicted to evolve differentiated ecological niches to establish in face of their competition. Here, we use four diploid wild wheats that differentially combined into four independent allopolyploid species to test for such additivity and assess the impact of ecological constraints on species ranges. Divergent genetic variation from diploids being fixed in heterozygote allopolyploids supports their genetic additivity. Spatial integration of comparative phylogeography and modeling of climatic niches supports ecological additivity of locally adapted diploid progenitors into allopolyploid species which subsequently colonized wide ranges. Allopolyploids fill suitable range to a larger extent than diploids and conservative evolution following the combination of divergent species appears to support their expansion under environmental changes.
Data from: Widespread generalist clones are associated with range and niche expansion in allopolyploids of Pacific Northwest Hawthorns (Crataegus L.)
Range and niche expansion are commonly associated with transitions to asexuality, polyploidy, and hybridity (allopolyploidy) in plants. The ability of asexual polyploids to colonize novel habitats may be due to widespread generalist clones, multiple ecologically specialized clones, or may be a neutral byproduct of multiple, independent origins of asexual polyploids throughout the range. We have quantified niche size and divergence for hawthorns of the Pacific Northwest using data from herbarium vouchers with known cytotypes. We find that all polyploid niches diverge from that of the diploid range, and allopolyploids have the broadest niches. Allotetraploids have the largest niche and the widest geographic distribution. We then assessed the genetic mechanism of range expansion by surveying the ecological and geographic distribution of genotypes within each cytotype from sites in which fine-scale habitat assessments were completed. We find no isolation by either geographic or ecological distance in allopolyploids, suggesting high dispersal and colonization ability. In contrast, autotriploids and diploids show patterns of isolation by geographic distance. We also compared the geographic and ecological distributions of clonal genotypes with those of randomly drawn sites of the most widespread cytotype. We found that most clones are geographically widespread and occur in a variety of habitats. We interpret these findings to suggest that patterns of range and niche expansion in Pacific Northwest Hawthorns may stem from these widespread, ecologically generalist clones of hybrid origin.
Data from: Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex
Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.s. and D. traunsteineri s.l. and their parents at localities across Europe. We make use in our inference of the distinct distribution ranges of the polyploids, including areas in which they are sympatric (that is, the Alps) or allopatric (for example, Pyrenees with D. majalis only and Britain with D. traunsteineri only). Our results show a phylogeographic signal, but no clear genetic differentiation between the allopolyploids, despite the visible phenotypic divergence between them. The results indicate that gene flow between sibling Dactylorhiza allopolyploids is frequent in sympatry, with potential implications for the genetic patterns across their entire distribution range. Limited interploidal introgression is also evidenced, in particular between D. incarnata and D. traunsteineri. Altogether the allopolyploid genomes appear to be porous for introgression from related diploids and polyploids. We conclude that the observed phenotypic divergence between D. majalis and D. traunsteineri is maintained by strong divergent selection on specific genomic areas with strong penetrance, but which are short enough to remain undetected by genotyping dispersed neutral markers.
Data from: Genetic structure reveals a history of multiple independent origins followed by admixture in the allopolyploid weed Salsola ryanii
It has recently become clear that many invasive species have evolved in situ via hybridization or polyploidy from progenitors which themselves are introduced species. For species formed by hybridization or polyploidy, genetic diversity within the newly formed species is influenced by the number of independent evolutionary origins of the species. For recently formed species, an analysis of genetic structure can provide insight into the number of independent origin events involved in the formation of the species. For a putative invasive allopolyploid species, the number of origins involved in the species formation, the genetic diversity present within these origins, and the level of gene flow between independent origins determines the genetic composition of the neospecies. Here we analyze the genetic structure of the newly formed allopolyploid species, Salsola ryanii, a tumbleweed which evolved within the last 20–100 years in California. We utilize the genetic structure analysis to determine that this new species is the result of at least three independent allopolyplodization events followed by gene flow between the descendants of independent origins.
Data from: Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris)
Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the inter-population diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C. bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C. bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4,274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centered on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C. bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C. bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.
Data from: From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae)
Allopolyploidisation acounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabelled genome tree and its corresponding network, resolved at the section (not the species) level. Reconstructing the 'correct' network for a set of polyploids depends on recovering all homoeologs, i.e. all subgenomes, in these polyploids. Assuming the presence of Viola subgenome lineages that were not detected by the nuclear gene phylogenies ('ghost subgenome lineages'), significantly reduced the number of inferred polyploidisation events. We identified the most parsimonious network topology from a set of five competing scenarios differing in the interpretation of homoeolog extinctions and lineage sorting, based on (1) fewest possible ghost subgenome lineages, (2) fewest possible polyploidisation events, and (3) least possible deviation from expected ploidy as inferred from available chromosome counts of the involved polyploid taxa. Finally, we estimated the homoploid and polyploid speciation times of the most parsimonious network. Homoploid speciation times were estimated by coalescent analysis of gene tree node ages. Polyploid speciation times were estimated by comparing branch lengths and speciation rates of lineages with and without ploidy shifts. Our analyses recognise Viola as an old genus (crown age 31 Ma) whose evolutionary history has been profoundly affected by allopolyploidy. Between 16 and 21 allopolyploidisations are necessary to explain the diversification of the 16 major lineages (sections) of Viola, suggesting that allopolyploidy has accounted for a high percentage – between 67% and 88% – of the speciation events at this level. The theoretical and methodological approaches presented here for (1) constructing networks and (2) dating speciation events within a network, have general applicability for phylogenetic studies of groups where allopolyploidisation has occurred. They make explicit use of a hitherto underexplored source of ploidy information from chromosome counts to help resolve phylogenetic cases where incomplete sequence data hampers network inference. Importantly, the coalescent-based method used herein circumvents the assumption of tree-like evolution required by most techniques for dating speciation events.
Data from: Stable epigenetic effects impact adaptation in allopolyploid orchids (Dactylorhiza: Orchidaceae)
Epigenetic information includes heritable signals that modulate gene expression but are not encoded in the primary nucleotide sequence. We have studied natural epigenetic variation in three allotetraploid sibling orchid species that differ radically in geography/ecology. The epigenetic variation released by genome doubling has been restructured in species-specific patterns that reflect their recent evolutionary history, and have an impact on their ecology and evolution, hundreds of generations after their formation. Epigenome scans pinpointed epiloci under divergent selection that correlate with eco-environmental variables, mainly related to water availability and temperature. The stable epigenetic divergence in this group is largely responsible for persistent ecological differences, which then set the stage for species-specific genetic patterns to accumulate in response to further selection and/or drift. Our results strongly suggest a need to expand our current evolutionary framework to encompass a complementary epigenetic dimension when seeking to understand population processes that drive phenotypic evolution and adaptation.
Data from: Fitness of an allopolyploid rupicolous fern compared to its diploid progenitors: From sporogenesis to sporophyte formation
PREMISE OF THE STUDY: When two populations of related cytotypes grow in sympatry, the rarer cytotype tends to be excluded due to a frequency-dependent mating disadvantage. Evolutionary models predict that polyploids, which are typically the rarer cytotype upon first formation, should have higher relative fitness and/or higher selfing rates to establish and then coexist with diploid parents. METHODS: We compared performance in early recruitment among three co-occurring rupicolous fern species: the allotetraploid Cheilanthes tinaei and its diploid ancestors, C. hispanica and C. maderensis. We made culture experiments with fresh spores and samples of soil spore banks to test for variation among cytotypes in germination, survival, growth and fecundity, and mating system of gametophytes. KEY RESULTS: Compared to its diploid parents, C. tinaei fresh spores had: higher abortion percentages, worselower dispersal ability due to larger spores, and similar vigor at germination. As for gametophytes from soil spore banks, C. tinaei showed high survival as C. maderensis, but its , similar germination percentage and similar time taken to germinate at each incubation temperature. Regarding soil spore banks, C. tinaei showed more abundant germination than both diploids, which supports greater spore deposition under sporophytes of the allotetraploid. Its gender expression resembles that of C. hispanica, with a high proportion of males. Patterns of sporophyte formation by females and bisexuals indicate that the polyploid does not have increased intragametophytic selfing rates. Gametophytes were larger in C. tinaei, but its reproductive success (sporophyte formation) was intermediate relative to diploids. CONCLUSIONS: Our results indicate that the allopolyploid show similar or even lower fitness than diploid progenitors show no evidence of higher selfing or fitness advantage of the allopolyploid over both diploid parents at any stage of early recruitment. In addition, all three species may have similar selfing rates. These two unexpected findings suggest that further factors, such as niche differentiation, play a more important role in cytotype coexistence.
Data from: Genetic architecture of adaptation to novel environmental conditions in a predominantly selfing allopolyploid plant
Genetic architecture of adaptation is traditionally studied in the context of local adaptation, viz. spatially varying conditions experienced by the species. However, human made changes in the natural environment pose a new context to this issue, i.e. adaptation to an environment that is new for the species. In this study, we used crossbreeding to analyze genetic architecture of adaptation to conditions not currently experienced by the species but with high probability of encounter in the near future due to the global climate change. We performed targeted inter-population crossing using genotypes from two core and two peripheral Triticum dicoccoides populations and grew up the parents and three generations of hybrids in a greenhouse under simulated desert conditions to analyze the genetic architecture of adaptation to these conditions and an effect of gene flow from plants having different origin. The observed in allopolyploid T. dicoccoides low importance of epistatic gene interactions and low probability of hybrid breakdown appear to be the result of permanent fixation of heterozygosity and lack of inter-genomic recombination in this species. At the same time, predominant but not complete selfing combined with an advantage of bivalent pairing of homologous chromosomes appear to maintain high genetic variability in T. dicoccoides, greatly enhancing its adaptive ability.
Data from: Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)
Background: Whole genome duplication plays a central role in plant evolution. There are two main classes of polyploid formation: autopolyploids which arise within one species by doubling of similar homologous genomes; in contrast, allopolyploidy (hybrid polyploidy) arise via hybridization and subsequent doubling of nonhomologous (homoeologous) genomes. The distinction between polyploid origins can be made using gene phylogenies, if alleles from each genome can be correctly retrieved. We examined whether two closely related tetraploid Mediterranean shrubs (Medicago arborea and M. strasseri) have an allopolyploid origin - a question that has remained unsolved despite substantial previous research. We sequenced and analyzed ten low-copy nuclear genes from these and related species, phasing all alleles. To test the efficacy of allele phasing on the ability to recover the evolutionary origin of polyploids, we compared these results to analyses using unphased sequences. Results: In eight of the gene trees the alleles inferred from the tetraploids formed two clades, in a non-sister relationship. Each of these clades was more closely related to alleles sampled from other species of Medicago, a pattern typical of allopolyploids. However, we also observed that alleles from one of the remaining genes formed two clades that were sister to one another, as is expected for autopolyploids. Trees inferred from unphased sequences were very different, with the tetraploids often placed in poorly supported and different positions compared to results obtained using phased alleles. Conclusions: The complex phylogenetic history of M. arborea and M. strasseri is explained predominantly by shared allotetraploidy. We also observed that an increase in woodiness is correlated with polyploidy in this group of species and present a new possibility that woodiness could be a transgressive phenotype. Correctly phased homoeologues are likely to be critical for inferring the hybrid origin of allopolyploid species, when most genes retain more than one homoeologue. Ignoring homoeologous variation by merging the homoeologues can obscure the signal of hybrid polyploid origins and produce inaccurate results.
Data from: Rapid allopolyploid radiation of moonwort ferns (Botrychium ; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions
Polyploidy is a major speciation process in vascular plants, and is postulated to be particularly important in shaping the diversity of extant ferns. However, limitations in the availability of bi-parental markers for ferns have greatly limited phylogenetic investigation of polyploidy in this group. With a large number of allopolyploid species, the genus Botrychium is a classic example in ferns where recurrent polyploidy is postulated to have driven frequent speciation events. Here, we use PacBio sequencing and the PURC bioinformatics pipeline to capture all homeologous or allelic copies of four long (∼1kb) low-copy nuclear regions from a sample of 45 specimens (25 diploids and 20 polyploids) representing 37 Botrychium taxa, and three outgroups. This sample includes most currently recognized Botrychium species in Europe and North America, and the majority of our specimens were genotyped with co-dominant nuclear allozymes to ensure species identification. We analyzed the sequence data using maximum likelihood (ML) and Bayesian inference (BI) concatenated-data ("gene tree") approaches to explore the relationships among Botrychium species. Finally, we estimated divergence times among Botrychium lineages and inferred the multi-labeled polyploid species tree showing the origins of the polyploid taxa, and their relationships to each other and to their diploid progenitors. We found strong support for the monophyly of the major lineages within Botrychium and identified most of the parental donors of the polyploids; these results largely corroborate earlier morphological and allozyme-based investigations. Each polyploid had at least two distinct homeologs, indicating that all sampled polyploids are likely allopolyploids (rather than autopolyploids). Our divergence-time analyses revealed that these allopolyploid lineages originated recently—within the last two million years—and thus that the genus has undergone a recent radiation, correlated with multiple independent allopolyploidizations across the phylogeny. Also, we found strong parental biases in the formation of allopolyploids, with individual diploid species participating multiple times as either the maternal or paternal donor (but not both). Finally, we discuss the role of polyploidy in the evolutionary history of Botrychium and the interspecific reproductive barriers possibly involved in these parental biases.
Evolution of the Sabulina verna group (Caryophyllaceae) in Europe: A deep split, followed by secondary contacts, multiple allopolyploidization and colonization of challenging substrates
<p>One of the major goals of contemporary evolutionary biology is to elucidate the relative roles of allopatric and ecological differentiation and polyploidy in speciation. In this study, we address the taxonomically intricate <em>Sabulina verna</em> group, which has a disjunct Arctic–alpine postglacial range in Europe and occupies a broad range of ecological niches, including substrates toxic to plants. Using genome-wide ddRAD sequencing combined with morphometric analyses based on extensive sampling of 111 natural populations, we aimed to disentangle internal evolutionary relationships and examine their correspondence with the pronounced edaphic and ploidy diversity within the group. We identified two spatially distinct groups of diploids: a widespread Arctic–alpine group and a spatially restricted yet diverse Balkan group. Most tetraploids exhibited a considerably admixed ancestry derived from both these groups, suggesting their allopolyploid origin. Four genetic clusters in congruence with geography and mostly supported by morphological traits were recognized in the diploid Arctic–alpine group. Tetraploids are split into two distinct and geographically vicariant groups, indicating their repeated polytopic origin. Furthermore, our results also revealed at least five-fold parallel colonization of toxic substrates (serpentine and metalliferous), altogether demonstrating a complex interaction between geography, challenging substrates, and polyploidy in the evolution of the group. Finally, we propose a new taxonomic treatment of this intricate complex.</p>
Fig. 6 in Cryptic and repeated "allopolyploid" speciation within Allium przewalskianum Regel. (Alliaceae) from the Qinghai-Tibet Plateau
Fig. 6 Origin of different tetraploid groups in A. przewalskianum inferred from AFLP, ITS, and CHS phylogenetic analyses. a A hypothesized origin of different tetraploid groups; b distributional patterns of tetraploid groups and differentiated diploid groups
Fig. 5 a in Cryptic and repeated "allopolyploid" speciation within Allium przewalskianum Regel. (Alliaceae) from the Qinghai-Tibet Plateau
Fig. 5 a Predicted distributions of the northern tetraploid group (NTP), the diploid populations (DP), and the southern tetraploid group (STP) of A. przewalskianum based on ecological niche modeling using MaxEnt. Predicted distributions are shown for (1) the present time, (2) at the LGM
Fig. 1 in Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences
Fig. 1 Phylogenetic tree for Ranunculus species based on internal transcribed spacer (ITS) sequences. a Consensus tree inferred from the six most parsimonious trees (CI=0.72; RI=0.93). Numbers above branches show bootstrap values (3,000 replicates). b Majority-rule consensus of
Fig. 6. Structural relationship between flavonoids 1–20 in Flavonoid pattern inheritance in the allopolyploid Spartina anglica - Comparison with the parental species S. maritima and S. alterniflora
Fig. 6. Structural relationship between flavonoids 1–20 identified in the three Spartina species (MW: molecular weight).
Fig. 2 in Flavonoid pattern inheritance in the allopolyploid Spartina anglica - Comparison with the parental species S. maritima and S. alterniflora
Fig. 2. Comparison of the HPLC chromatograms obtained on HTec (top) and Polartec (bottom) column: (a) S. maritima; (b) S. alterniflora; (c) S. anglica.
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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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
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.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.