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19 results for “allopolyploidy”
Data from: Embracing discordance: phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean Campanula (Campanulaceae) clade
The Mediterranean Basin harbors a remarkable amount of biodiversity, a high proportion of which is endemic to this region. Here, we present an in-depth study of an angiosperm species complex, in which cryptic taxonomic diversity has been hypothesized. Specifically, we focus on four currently recognized species in the Roucela complex, a well-supported clade in the Campanulaceae/Campanuloideae: Campanula creutzburgii, C. drabifolia, C. erinus, and C. simulans. This study takes a phylogenomic approach, utilizing near-complete plastomes and 130 nuclear loci, to uncover cryptic diversity and test hypotheses regarding hybridization and polyploidy within this clade. Genome size estimates recovered tetraploid and octoploid lineages within the currently recognized, widespread species C. erinus, showing an east-west geographic pattern. Though genomic data clearly differentiate these two cytotypes, we failed to discern morphological differences. The formation of a cryptic octoploid lineage, distributed across the eastern Mediterranean, is hypothesized to be the result of an allopolyploid event in which one parental morphology is retained. The tetraploid C. erinus and C. creutzburgii (also a tetraploid) are implicated as parental lineages. Our results highlight the utility of target-enrichment approaches for obtaining genomic datasets for thorough assessments of species diversity and the importance of carefully considering gene-tree discordance within such datasets.
Data from: Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events
• Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. • We assembled a dataset of transcriptomes and genomes from 169 species in Caryophyllales, of which 43 were newly generated for this study, representing one of the densest sampled genomic-scale datasets available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped phylogenetic distribution of polyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for allopolyploidy. • We identified twenty-six ancient and more recent polyploidy events distributed throughout Caryophyllales. Two of these events were inferred to be allopolyploidy. • Through dense phylogenomic sampling, we show the propensity of polyploidy throughout the evolutionary history of Caryophyllales. We also provide a framework for utilizing transcriptome data to detect allopolyploidy, which is important as it may have different macro-evolutionary implications compared to autopolyploidy.
Data from: Allopolyploidy in the Wintergreen Group of tribe Gaultherieae (Ericaceae) inferred from low-copy nuclear genes
DNA sequence data from the low-copy nuclear genes waxy (GBSSI) and leafy were compared with plastid sequence data from prior studies to reconstruct phylogenetic relationships in the Wintergreen Group of tribe Gaultherieae (Ericaceae). We conducted phylogenetic analysis with 109 species that includes representatives of all 15 major clades previously diagnosed in the Wintergreen Group and that together span its circum-Pacific distribution. Results yielded two distinct homeologous copies of waxy for two of the clades, each in widely separated parts of the tree. It also yielded two copies of leafy for one of the clades; only one copy of leafy was found for the other clade, but it was placed in the same major clade as its waxy counterpart and well away from its placement in a prior plastid analysis. A combined four-locus (waxy, leafy, ITS, and plastid loci) phylogenetic analysis of all available relevant data placed the copies of each of the clades in two distinct positions in the phylogeny with strong overall statistical support. In combination with evidence from morphology, reproductive biology, and cytology, the results suggest that these clades arose through allopolyploid hybridization between lineages deep in the phylogeny but relatively close geographically. This finding confirms previous assumptions that hybridization plays an important role in the evolution of the Gaultherieae.
Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere
<p>Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus <em>Malus</em> sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of <em>Malus</em> s.l. (including <em>Docynia</em>); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (<em>Malus doumeri)</em> and one recent event (<em>Malus</em> coronaria) were detected in <em>Malus</em> s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of <em>Malus</em> s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming datasets.</p>
Data from: Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes
<p>Polyploids represent a new frontier in species discovery among embryophytes. Within mosses, polyploid discovery is challenged by low morphological complexity. The rapid expansion of sub-genome sequencing approaches in addition to computational approaches to identifying whole genome duplication using allelic variation among nuclear markers has allowed for increased polyploid discovery among mosses. We confirm the intergeneric hybrid nature of <em>E. hungaricus</em>, and the allopolyploid origin of <em>P. eurystomum </em>and of one population of <em>P. collenchymatum</em>. We also reveal that hybridization gave rise to <em>P. immersum, </em>as well as to yet unrecognized lineages sharing the phenotype of <em>P. pyriforme</em>,<em> P. sphaericum</em> and <em>P. collenchymatum. </em>Our findings and methods demonstrate the utility of a novel approach to allele phasing and subgenome assignment, called homologizer, when working with polyploid genomes, and its value in identifying progenitor species using target capture data.</p>
Data from: Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes
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Data from: Allopolyploidy in the Wintergreen Group of tribe Gaultherieae (Ericaceae) inferred from low-copy nuclear genes
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Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere
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Data from: Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR ‐based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics
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Data from: Embracing discordance: phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean Campanula (Campanulaceae) clade
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Data from: Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events
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Data from: Allopolyploidy, diversification, and the Miocene grassland expansion
The role of polyploidy, particularly allopolyploidy, in plant diversification is a subject of debate. Whole-genome duplications precede the origins of many major clades (e.g., angiosperms, Brassicaceae, Poaceae), suggesting that polyploidy drives diversification. However, theoretical arguments and empirical studies suggest that polyploid lineages may actually have lower speciation rates and higher extinction rates than diploid lineages. We focus here on the grass tribe Andropogoneae, an economically and ecologically important group of C4 species with a high frequency of polyploids. A phylogeny was constructed for ca. 10% of the species of the clade, based on sequences of four concatenated low-copy nuclear loci. Genetic allopolyploidy was documented using the characteristic pattern of double-labeled gene trees. At least 32% of the species sampled are the result of genetic allopolyploidy and result from 28 distinct tetraploidy events plus an additional six hexaploidy events. This number is a minimum, and the actual frequency could be considerably higher. The parental genomes of most Andropogoneae polyploids diverged in the Late Miocene coincident with the expansion of the major C4 grasslands that dominate the earth today. The well-documented whole-genome duplication in Zea mays ssp. mays occurred after the divergence of Zea and Sorghum. We find no evidence that polyploidization is followed by an increase in net diversification rate; nonetheless, allopolyploidy itself is a major mode of speciation.
Data from: Allopolyploidy and the evolution of plant virus resistance
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Data from: Allopolyploidy, diversification, and the Miocene grassland expansion
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Data from: Dating the species network: allopolyploidy and repetitive DNA evolution in American daisies (Melampodium sect. Melampodium, Asteraceae)
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Data from: Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae)
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Accumulation of small RNA populations in response to allopolyploidy: analysis of small RNA sequencing data from resynthesized Brassica napus allotetraploid in comparison to their diploid progenitors
GEO Series GSE94076. Brassica napus; Brassica rapa; Brassica oleracea var. botrytis; Brassica oleracea; Brassica rapa subsp. oleifera. 11 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Datasets for "Allopolyploidy expanded gene content but not pangenomic variation in the hexaploid oilseed Camelina sativa"
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Transcriptomic changes following hybridization and allopolyploidy in two salt marsh species
GEO Series GSE18961. Oryza sativa Japonica Group; Sporobolus maritimus; Sporobolus alterniflorus; Sporobolus anglicus; Sporobolus x townsendii. 20 samples. Type: Expression profiling by array.
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