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56 results for “reticulate evolution”
Data from: Reticulate evolution, ancient chloroplast haplotypes, and rapid radiation of the Australian plant genus Adenanthos (Proteaceae)
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Data from: Reticulate evolution, introgression, and intertribal gene capture in an allohexaploid grass
Recent molecular phylogenetic studies of polyploid plants have successfully clarified complex patterns of reticulate evolution. In this study of Elymus repens, an allohexaploid member of the wheat tribe Triticeae, chloroplast and nuclear DNA data reveal an extreme reticulate pattern, revealing at least five distinct gene lineages coexisting within the species, acquired through a possible combination of allohexaploidy and introgression from both within and beyond the Triticeae. Earlier cytogenetic studies of E. repens suggested that Hordeum (genome H) and Pseudoroegneria (St) were genome donors to E. repens. Chloroplast DNA data presented here (from the rpoA gene and from the region between trnT and trnF) identify three potential maternal genome donors (Pseudoroegneria, Thinopyrum, and Dasypyrum), and information from previous molecular work suggests that, of these, Pseudoroegneria is the most likely maternal donor. Nuclear starch synthase gene data indicate that both Hordeum and Pseudoroegneria have contributed to the nuclear genome of E. repens, in agreement with cytogenetic data. However, these data also show unexpected contributions from Taeniatherum, and from two additional donors of unknown identity. One of the sequences of unknown origin falls within the Triticeae, but is not closely associated with any of the sampled diploid genera. The second falls outside of the clade containing Triticeae and its outgroup Bromus, suggesting the acquisition of genetic material from a surprisingly divergent source. Bias toward the amplification of certain starch synthase variants has complicated attempts to thoroughly sample from within individuals, but the data clearly indicate a complex pattern of reticulate evolution, consistent not only with allohexaploidy, but also with introgression from unexpectedly divergent sources.
Fig. 1 in A phylogenetic investigation of the taxonomically problematic Eucalyptus odorata complex (E. section Adnataria series Subbuxeales): evidence for extensive interspecific gene flow and reticulate evolution
Fig. 1. (Caption on next page)
Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)
<p>Understanding biological diversity and the mechanisms of the Sino-Japanese disjunctions are major challenge<span>s in</span><span> </span><span>eastern Asia biogeography</span><span>. </span><span>The Sino-Japanese flora has been broadly studied as an ideal model</span><span> for plant phylogeography</span><span>. </span><span>Diabelia</span><span> (Caprifoliaceae) is an</span><span> East Asian genus, </span><span>with a disjunctive distribution across </span><span>the </span><span>Sino-</span><span>J</span><span>apanese region.</span><span> However, </span><span>relationships within </span><span>Diabelia</span><span> remain elusive. In this study, </span><span>we reconstructed</span><span> the </span><span>phylogeny of </span><span>Diabelia</span><span> </span><span>and </span><span>inferred historical biogeography and evolutionary patterns</span><span> based on nuclear and </span><span>plastid</span><span> sequence</span><span>s</span><span> from </span><span>target enrichment</span><span> and genome skimming approaches, respectively</span><span>.</span><span> We found that the </span><span>main </span><span>clades</span><span> within </span><span>Diabelia</span><span> were</span><span> </span><span>discordant between nuclear and plastid trees</span><span>. </span><span>Both </span><span>nuclear and plastid </span><span>phylogenetic analys</span><span>e</span><span>s </span><span>supported</span><span> five main clades: </span><span>D. serrata</span><span>, </span><span>D. </span><span>tetrasepala</span><span>, </span><span>D. </span><span>sanguinea</span><span>, </span><span>D. </span><span>spathulata</span><span> </span><span>var. </span><span>stenophylla</span><span> and </span><span>D. </span><span>spathulata</span><span> </span><span>var. </span><span>spathulata</span><span>. Species network analyses revealed that </span><span>Diabelia</span><span> </span><span>tetrasepala</span><span> </span><span>is likely the </span><span>result </span><span>of a</span><span> hybridization event</span><span>. Divergence time estimation</span><span> and </span><span>ancestral area reconstructions</span><span> showed that </span><span>Diabelia</span><span> originated in</span><span> </span><span>Japan during </span><span>the </span><span>early Miocene, with subsequent vicariance </span><span>and dispersal </span><span>events between Japan and Korea, and between Japan and China</span><span>.</span><span> </span><span>Overall</span><span>, </span><span>our results support the division of</span><span> </span><span>Diabelia</span><span> into five main clades and </span><span>the recognition of five species in the genus.</span><span> </span><span>T</span><span>his research </span><span>provides new insights in the species delimitation and</span><span> </span><span>speciation processes of</span><span> </span><span>taxonomically complex lineages such as </span><span>Diabelia</span><span>.</span></p>
Data from: Molecular signatures of reticulate evolution within the complex of European pine taxa
<p>Speciation mechanisms, including the role of interspecific gene flow and introgression in emergence of new species, are the major focus of evolutionary studies. Inference of taxonomic relationship between closely related species maybe challenged by past hybridization events, but at the same time it may provide new knowledge about mechanisms responsible for the maintenance of species integrity despite interspecific gene flow. Here, using nucleotide sequence variation and utilizing a coalescent modelling framework, we tested the role of hybridization and introgression in the evolutionary history of closely related pine taxa from <i>Pinus mugo</i> complex and <i>P. sylvestris</i>. We compared the patterns of polymorphism and divergence between taxa and found great overlap of neutral variation within <i>P. mugo</i> complex. Our phylogeny reconstruction indicated multiple instances of reticulation events in the past, suggesting an important role of interspecific gene flow in the species divergence. The best fitting model revealed <i>P. mugo</i> and <i>P. uncinata</i> as sister species with basal <i>P. uliginosa</i> and asymmetric migration between all investigated species after their divergence. The magnitude of interspecies gene flow differed greatly, and it was consistently stronger from representatives of <i>P. mugo</i> complex to <i>P. sylvestris</i> than in the opposite direction. The results indicate the prominent role of reticulation evolution in those forest trees and provide genetic framework to study species integrity maintained by selection and local adaptation.</p>
Reconstruction of reticulate evolution and divergence timing based on RNA-seq: Hippophae as a case
<p>Phylotranscriptomic analysis has successfully been used to reconstruct phylogenies of higher taxa. However, depicting the patterns of phylogenies in more details and, especially, estimating time of introgression for lower taxa remain challenging. Here, we selected Hippophae (Elaeagnaceae), a small genus restricted to the Qinghai-Tibet Plateau (QTP) and adjacent areas, as an example to optimize approaches to investigate reticulate evolution in lower taxa with RNA-seq. Plastid genes and low copy nuclear genes were extracted from RNA-seq data to reconstruct a reliable species tree of Hippophae and estimate the time of species divergence, respectively. Results show that the phylogeny of five Hippophae species has been consistently solved except for H. salicifolia and a potential hybrid species. The divergence time of 5 species ranged from 17.56 Ma to 6.04 Ma, the era of the Himalayas uplift. The inconsistence between gene trees was integrated with the implicit network analysis approaches, such as investigating statistical difference of anomalous gene trees and asymmetry of average most recent common ancestor (MRCA) ages, and explicit network analysis approaches, such as PhyloNet and SNaQ. At least two separate introgression cases were involved in the history of Hippophae: one took place between two basial clades of this genus, in which an early member or common ancestor of H. rhamnoides and H. thibetana lineages experienced introgression with an early member or common ancestor of H. neurocarpa and H. gyantsensis; the other was between H. gyantsensis and H. neurocarpa. Using a MCMC fitting model, we estimated the secondary divergence time after the first introgression, finding two secondary divergence times: one was about 8.79 (7.05-10.64) Ma and between H. rhamnoides and the MRCA of H. neurocarpa and H. gyantsensis, and the other was near 7.76 (5.89-9.58) Ma and between H. tibetana and the MRCA of H. neurocarpa and H. gyantsensis. Furthermore, introgressed gene candidates, including some potential adaptive genes, were found, indicating that even the introgression in small genus is important and functional for species differentiation. Based on the above results and previous studies, the reticulate evolution of Hippophae was highlighted, providing a potential guidance in using RNA-seq data for reconstructing the complex evolution history of lower taxa.</p>
Data from: Comparative transcriptomics provides insights into reticulate and adaptive evolution of a butterfly radiation
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Data from: Molecular evidence for the compilospecies model of reticulate evolution in Armeria (Plumbaginaceae)
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Data from: Reticulate evolution, introgression, and intertribal gene capture in an allohexaploid grass
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Data from: Testing reticulate evolution of four Vitis species from East Asia using restriction‐site associated DNA sequencing
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Data from: Molecular signatures of reticulate evolution within the complex of European pine taxa
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Reconstruction of reticulate evolution and divergence timing based on RNA-seq: Hippophae as a case
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Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)
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Data from: Reticulate evolution and sea-level fluctuations together drove species diversification of slipper orchids (Paphiopedilum) in Southeast Asia
South-East Asia covers four of the world's biodiversity hotspots, showing high species diversity and endemism. Owing to the successive expansion and contraction of distribution and the fragmentation by geographical barriers, the tropical flora greatly diversified in this region during the Tertiary, but the evolutionary tempo and mode of species diversity remain poorly investigated. Paphiopedilum, the largest genus of slipper orchids comprising nearly 100 species, is mainly distributed in South-East Asia, providing an ideal system for exploring how plant species diversity was shaped in this region. Here, we investigated the evolutionary history of this genus with eight cpDNA regions and four low-copy nuclear genes. Discordance between gene trees and network analysis indicates that reticulate evolution occurred in the genus. Ancestral area reconstruction suggests that vicariance and long-distance dispersal together led to its current distribution. Diversification rate variation was detected and strongly correlated with the species diversity in subg. Paphiopedilum (~80 species). The shift of speciation rate in subg. Paphiopedilum was coincident with sea-level fluctuations in the late Cenozoic, which could have provided ecological opportunities for speciation and created bridges or barriers for gene flow. Moreover, some other factors (e.g. sympatric distribution, incomplete reproductive barriers and clonal propagation) might also be advantageous for the formation and reproduction of hybrid species. In conclusion, our study suggests that the interplay of reticulate evolution and sea-level fluctuations has promoted the diversification of the genus Paphiopedilum and sheds light into the evolution of Orchidaceae and the historical processes of plant species diversification in South-East Asia.
Data from: Reticulate evolution and sea-level fluctuations together drove species diversification of slipper orchids (Paphiopedilum) in Southeast Asia
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Fig. 1 a Dated phylogeny and ancestral area reconstruction for 147 in Against all odds: reconstructing the evolutionary history of Scrophularia (Scrophulariaceae) despite high levels of incongruence and reticulate evolution
Fig. 1 a Dated phylogeny and ancestral area reconstruction for 147 Scrophularia species, on a majority-rule consensus tree obtained from Bayesian analysis of combined plastid trnQ-rps16 intergenic spacer and trnL-trnF region alongside coded indels. Branches indicate levels of support, based on posterior probabilities (PP) and plotted bootstrap support values (BS) from Maximum Likelihood optimization; bold PP ≥ 95 or BS ≥ 85, semi-bold PP ≥ 90 or BS ≥ 75, thin PP <90/BS <75. Seven additional nodes only supported by ML (BS ≥ 50) were added manually but not incorporated into further analyses. Gray bars on the right denote Clades 1–18 and main species groups as discussed in the text. An arrow indicates the position of the Himalayan-Tibetan endemic genus Oreosolen. Single accessions displaying hard incongruence among (2ISP-coded) nuclear and plastid trees are marked in bold; Clades 7 and 5 (excluding S. chlorantha; plus S. cryptophila) as a whole are also hardly incongruent. The occurrence of large indels as defined in Table 2 is indicated next to each accession with the respective length type number;
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