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104 results for “allopolyploid”
Benefits and limits of phasing alleles for network inference of allopolyploid complexes
<p>Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hindered by the complexities of homology determination in polyploid taxa. We use simulations to show that phasing alleles from allopolyploid individuals can improve phylogenetic network inference under the multispecies coalescent by obtaining the true network with fewer loci compared to haplotype consensus sequences or sequences with heterozygous bases represented as ambiguity codes. Phased allelic data can also improve divergence time estimates for networks, which is helpful for evaluating allopolyploid speciation hypotheses and proposing mechanisms of speciation. To achieve these outcomes in empirical data, we present a novel pipeline that leverages a recently developed phasing algorithm to reliably phase alleles from polyploids. This pipeline is especially appropriate for target enrichment data, where depth of coverage is typically high enough to phase entire loci. We provide an empirical example in the North American <em>Dryopteris </em>fern complex that demonstrates insights from phased data as well as the challenges of network inference. We establish that our pipeline (PATÉ: Phased Alleles from Target Enrichment data) is capable of recovering a high proportion of phased loci from both diploids and polyploids. These data may improve network estimates compared to using haplotype consensus assemblies by accurately inferring the direction of gene flow, but statistical non-identifiability of phylogenetic networks poses a barrier to inferring the evolutionary history of reticulate complexes.</p>
Benefits and limits of phasing alleles for network inference of allopolyploid complexes
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Data from: Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis
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Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species
<ul> <li>Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine-scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors.</li> <li> We quantified soil properties and light availability of habitats of an allotetraploid <i>Cardamine flexuosa</i> and its diploid progenitors <i>C. amara</i> and <i>C. hirsuta</i> in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA-seq.</li> <li>We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in <i>C. flexuosa</i> varied spatially and temporally. </li> <li>These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.</li> </ul>
Data from: Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species
Quantifying introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what drives the longevity of putatively asexual groups. Here, we capitalize on three recent innovations—ultraconserved element (UCE) sequencing, bioinformatic techniques for identifying genome-specific variation in polyploids, and model-based methods for evaluating historical gene flow—to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all-female salamanders and two ancestral sexual species. Our analyses support a scenario in which the genomes sampled in unisexual salamanders last shared a common ancestor with genomes in their parental species ~3.4 million years ago, followed by a period of divergence between homologous genomes. Recently, secondary introgression has occurred at different times with each sexual species during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage is the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have undergone long periods of divergence without introgression. Unlike other sperm-dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could explain why these salamanders are among the oldest described unisexual animals.
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars
<div> <p><em>Coffea arabica</em>, an allotetraploid hybrid of <em>C. eugenioides</em> and <em>C. canephora</em>, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid <em>C. arabica</em> accession and modern representatives of its diploid progenitors, <em>C. eugenioides</em> and <em>C. canephora</em>. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ∼30.5 kya, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with <em>C. canephora</em>, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of <em>C. arabica</em>.</p> </div>
Target capture methods offer insight into the evolution of rapidly diverged taxa and resolve allopolyploid homeologs in the fern genus Polypodium s.s.
<p><span></span></p> <p>Like many fern lineages comprising reticulate species complexes, <em>Polypodium</em> s.s. (Polypodiacaeae) has a history shaped by rapid diversification, hybridization, and polyploidy that poses substantial challenges for phylogenetic inference with plastid and single-locus nuclear loci. Using target capture probes for 408 nuclear loci developed by the GOFlag project and a custom bioinformatic pipeline, SORTER, we constructed multi-locus nuclear datasets for diploid temperate and Mesoamerican species of <em>Polypodium</em> and five allotetraploid species belonging to the well-studied <em>Polypodium</em> <em>vulgare</em> complex. SORTER employs a clustering approach to separate putatively paralogous copies of targeted loci into orthologous matrices and haplotype phasing to infer allopolyploid haplotypes across loci, resulting in datasets amenable to both concatenated maximum likelihood and multi-species coalescent phylogenetic analyses. By comparing phylogenies derived from maximum likelihood and multi- species coalescent analyses of unphased and phased datasets, as well as evaluating discordance among gene trees and species trees, we recover support for incomplete lineage sorting within <em>Polypodium</em> s.s., novel relationships among diploid taxa of the <em>Polypodium</em> <em>vulgare</em> complex and its Mesoamerican sister clade, and the placement of several <em>Polypodium</em> species within other genera. Additionally, we were able to infer well-supported phylogenies that identified the hypothesized progenitors of the allotetraploid species, indicating that SORTER is an effective and accurate tool for reconstructing homeolog haplotypes of allopolyploids in fern taxa and other non-model organisms from target capture data.</p>
Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus
<p>Interspecific hybridization and allopolyploidization merge evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is "dominant" over the other subgenome, having a greater number of retained genes and being more highly expressed. Which subgenome becomes dominantly expressed in allopolyploids remains poorly understood. Here we "replayed the evolutionary tape" with six isogenic resynthesized<i> Brassica napus </i>(rapeseed) allopolyploid lines and investigated subgenome dominance patterns over the first ten generations post merger. We found that the same subgenome was consistently more dominantly expressed in all lines and generations and that >70% of biased gene pairs showed the same dominance patterns across all lines and an <i>in silico</i> hybrid of the parents. Gene network analyses indicated an enrichment for network interactions and several biological functions for the <i>Brassica oleracea </i>derived 'BnC' subgenome biased pairs, but no enrichment was identified for <i>Brassica rapa</i> derived 'BnA' subgenome biased pairs. Furthermore, DNA methylation differences between subgenomes mirrored the observed gene expression bias towards the 'BnC' subgenome in all lines and generations. These methylation patterns were consistent with those previously associated with higher expression, but differ from proposed mechanisms from recent conceptual models and with observations in other polyploid systems that exhibit subgenome dominance. Many of these differences in gene expression and methylation were also found when comparing the progenitor genomes, suggesting subgenome dominance is partly related to parental genome differences rather than just a byproduct of allopolyploidization. These findings demonstrate that "replaying the evolutionary tape" in an allopolyploid results in largely repeatable and predictable subgenome expression dominance patterns, partly due to preexisting genetic differences among the parental species.</p>
Phylogenomic analyses reveal an allopolyploid origin of core Didymocarpinae (Gesneriaceae) followed by rapid radiation
<p><span>Allopolyploid plants have long been regarded as possessing genetic advantages under certain circumstances due to the combined effects of their hybrid origins and duplicated genomes. However, the evolutionary consequences of allopolyploidy in lineage diversification remain to be fully understood. Here, we investigate the evolutionary consequences of allopolyploidy using 138 transcriptomic sequences of Gesneriaceae, including 124 newly sequenced, focusing particularly on the largest subtribe Didymocarpinae. We estimated the phylogeny of Gesneriaceae using concatenated and coalescent-based methods based on five different nuclear matrices and 27 plastid genes, focusing on relationships among major clades. To better understand the evolutionary affinities in this family, we applied a range of approaches to characterize the extent and cause of phylogenetic incongruence. We found that extensive conflicts between nuclear and chloroplast genomes and among nuclear genes were caused by both incomplete lineage sorting (ILS) and reticulation, and we found evidence of widespread ancient hybridization and introgression. Using the most highly supported phylogenomic framework, we revealed multiple bursts of gene duplication throughout the evolutionary history of Gesneriaceae. By incorporating molecular dating and analyses of diversification dynamics, our study shows that an ancient allopolyploidization event occurred around the Oligocene-Miocene boundary, which may have driven the rapid radiation of core Didymocarpinae.</span></p>
Evolutionary history and genetic diversity of apomictic allopolyploids in Hieracium s.str. (Asteraceae): morphological versus genomic features
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Target capture methods offer insight into the evolution of rapidly diverged taxa and resolve allopolyploid homeologs in the fern genus Polypodium s.s.
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Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species
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Data from: Complex but clear allopolyploid pattern of subtribe Tussilagininae (Asteraceae: Senecioneae) revealed by robust phylogenomic evidence, with development of a novel homeolog-sorting pipeline
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Data from: Evidence for allopolyploid speciation in Nymphoides (Menyanthaceae)
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Origin of subgenomes in the circumboreal allopolyploid carnivorous plant Drosera anglica (Droseraceae)
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Data from: Ortho2Web: A workflow for disentangling the roles of hybridization and allopolyploidization in reticulation within Campanulaceae
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Phylogenomic analyses reveal an allopolyploid origin of core Didymocarpinae (Gesneriaceae) followed by rapid radiation
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Data from: Persistence of an unusual triple sex chromosome system through allopolyploidization in African clawed frogs (<em>Xenopus</em>, subgenus <em>Silurana</em>)
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Unraveling evolutionary pathways: Allopolyploidization and introgression in polyploid Prunus (Rosaceae)
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Allopolyploid origin and diversification of the Hawaiian endemic mints
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