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publicJul 2013View details →

Data from: A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change

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publicMar 2022View details →

Deep-time reticulation and ancient mitochondrial genome capture during the radiation of Jamaican Anolis lizards (Squamata; Iguanidae)

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publicSep 2021View details →

Larval A. bishopi microsatellite data from: Metapopulation genetics of endangered reticulated flatwoods salamanders (Ambystoma bishopi) in a dynamic and fragmented landscape

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publicJan 2021View details →

Data from: Reticulate evolution, ancient chloroplast haplotypes, and rapid radiation of the Australian plant genus Adenanthos (Proteaceae)

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opencc-zeroAug 2020View details →

Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity

Hybridisation has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of plant species undergoing inter-specific gene flow. However, hybridisation in Amazonia's megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridisation among multiple lineages across phylogenetic scales. More specifically, using targeted sequence capture our results uncovered several historical introgression events between Brownea lineages and indicated that gene tree incongruence in Brownea is best explained by reticulation, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridisation using ~19,000 ddRAD loci recovered a high degree of shared variation between two Brownea species that co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and persistent hybridisation. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridisation's rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.

opencc-zeroDec 2015View details →

Data from: Analyzing reticulate relationships using CpDNA and pyrosequenced ITS1 as exemplified by Veronica subgen. Pseudolysimachium (Plantaginaceae)

Veronica subgen. Pseudolysimachium constitutes a group of about 28 species across northern Eurasia, many of them with considerable intraspecific morphological variation. This intraspecific variation may be due to large geographical distribution area, wide ecological amplitude, or widespread hybridization and polyploidization. Several recent studies using molecular data have shown that hybridization as an explanation for generating evolutionary novelties and high intraspecific variation may be more common than previously thought. Here we investigate the importance of hybridization in generating morphological variation and blurring species boundaries in V. subgen. Pseudolysimachium using analyses of cpDNA sequences from 139 individuals from 18 species and ten putative hybrids, and pyrosequenced ITS1 nrDNA sequences from 37 individuals from 16 species and four putative hybrids. In addition, we estimated ploidy levels for 42 individuals of ten species and five putative hybrids using flow cytometry. Analyses of cpDNA did not resolve phylogenetic structure (most of the species were polyphyletic). Our second approach, pyrosequencing of ITS1, generated up to nine different unique sequences per individual and phylogenetic analyses of the dataset resolved some basal nodes but, again, species were often non-monophyletic. The results are most compatible with a scenario of an East Asian origin and repeated spread across Pleistocene Eurasian steppes, known as important plant diversification center, with frequent interspecific hybridization. We compare the applicability of these molecular regions for resolving hybridizing species complexes and specifically address hypotheses of hybrid origins for several species within the subgenus. However, any population genetic, phylogeographic or other analysis of evolutionary questions in one species alone would be futile without considering introgression from related species.

opencc-zeroDec 2015View details →

Data from: Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of 'network thinking' and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.

opencc-zeroDec 2016View details →

Data from: Coestimating reticulate phylogenies and gene trees from multilocus sequence data

The multispecies network coalescent (MSNC) is a stochastic process that captures how gene trees grow within the branches of a phylogenetic network. Coupling the MSNC with a stochastic mutational process that operates along the branches of the gene trees gives rise to a generative model of how multiple loci from within and across species evolve in the presence of both incomplete lineage sorting (ILS) and reticulation (e.g., hybridization). We report on a Bayesian method for sampling the parameters of this generative model, including the species phylogeny, gene trees, divergence times, and population sizes, from DNA sequences of multiple independent loci. We demonstrate the utility of our method by analyzing simulated data and reanalyzing an empirical data set. Our results demonstrate the significance of not only co-estimating species phylogenies and gene trees, but also accounting for reticulation and ILS simultaneously. In particular, we show that when gene flow occurs, our method accurately estimates the evolutionary histories, coalescence times, and divergence times. Tree inference methods, on the other hand, underestimate divergence times and overestimate coalescence times when the evolutionary history is reticulate. While the MSNC corresponds to an abstract model of ``intermixture," we study the performance of the model and method on simulated data generated under a gene flow model. We show that the method accurately infers the most recent time at which gene flow occurs. Finally, we demonstrate the application of the new method to a 106-locus yeast data set.

opencc-zeroDec 2015View details →

Data from: Bayesian inference of reticulate phylogenies under the multispecies network coalescent

The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation.

opencc-zeroDec 2008View details →

Data from: Divergence and reticulation among montane populations of a jumping spider (Habronattus pugillis Griswold)

Populations of the jumping spider Habronattus pugillis Griswold isolated on nearby mountain ranges in southern Arizona are differentiated in many features of the males (color, shape and orientation of setae on face, shape of carapace, markings of palpi and legs, motions during courtship behavior). These features are (mostly) consistent within a range and different between ranges. The concentration of differences to male courtship behavior and body parts exposed to the female during courtship and correlations between form and courtship behavior suggest sexual selection was involved in the differentiation. A phylogenetic analysis of the populations yields a tree that for the most part groups geographic neighbors, but the history of H. pugillis populations may not be adequately described by a tree. Geographic proximity of apparent convergences suggests that populations from at least some of the mountain ranges acquired characteristics through introgression. Lowering of the woodland habitat during the last glacial period probably brought some populations into contact, but it is not clear if the interrange woodlands would have provided corridors for extensive mixing.

opencc-zeroDec 2017View details →

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.

opennotspecifiedOct 2022View details →

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)

opencc-zeroNov 2021View details →

Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)

Understanding biological diversity and the mechanisms of the Sino-Japanese disjunctions are major challenges in eastern Asia biogeography. The Sino-Japanese flora has been broadly studied as an ideal model for plant phylogeography. Diabelia (Caprifoliaceae) is an East Asian genus, with a disjunctive distribution across the Sino-Japanese region. However, relationships within Diabelia remain elusive. In this study, we reconstructed the phylogeny of Diabelia and inferred historical biogeography and evolutionary patterns based on nuclear and plastid sequences from target enrichment and genome skimming approaches, respectively. We found that the main clades within Diabelia were discordant between nuclear and plastid trees. Both nuclear and plastid phylogenetic analyses supported five main clades: D. serrata, D. tetrasepala, D. sanguinea, D. spathulata var. stenophylla and D. spathulata var. spathulata. Species network analyses revealed that Diabelia tetrasepala is likely the result of a hybridization event. Divergence time estimation and ancestral area reconstructions showed that Diabelia originated in Japan during the early Miocene, with subsequent vicariance and dispersal events between Japan and Korea, and between Japan and China. Overall, our results support the division of Diabelia into five main clades and the recognition of five species in the genus. This research provides new insights in the species delimitation and speciation processes of taxonomically complex lineages such as Diabelia.

opencc-zeroNov 2021View details →

Data from: Molecular signatures of reticulate evolution within the complex of European pine taxa

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 Pinus mugo complex and P. sylvestris. We compared the patterns of polymorphism and divergence between taxa and found great overlap of neutral variation within P. mugo 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 P. mugo and P. uncinata as sister species with basal P. uliginosa 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 P. mugo complex to P. sylvestris 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.

opencc-zeroMay 2022View details →

Reconstruction of reticulate evolution and divergence timing based on RNA-seq: Hippophae as a case

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.

opennotspecifiedMar 2019View details →

FIGURE 3 in A new reticulated beetle (Coleoptera: Cupedidae) from Mexico with a catalogue of Cupedidae species of the world

FIGURE 3. Pronotum of Paracupes spp.: A) P. mexicanus sp. nov.; B) P. brasiliensis; C) P. ascius.

opennotspecifiedMar 2019View details →

FIGURE 6 in A new reticulated beetle (Coleoptera: Cupedidae) from Mexico with a catalogue of Cupedidae species of the world

FIGURE 6. Dorsal habitus: A) P. brasiliensis; B) P. ascius, photograph by Geoffrey Easton Morse.

opencc-zeroAug 2021View details →

Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards

Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of South American lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrial DNA (mtDNA) and genome-wide restriction site-associated DNA sequencing (RADseq; nDNA hereafter), we inferred a time-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordance between mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data also reveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogenetic discordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, and contracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of the most studied lizard groups in the New World.

opencc-by-4.0Dec 2022View details →

Text-fig. 39. Scanning electron microscope (SEM) images of "Pollen clump with tricolpate pollen sp. 3"; Catefica locality, Portugal. a) Pollen clump, probably an anther fragment, containing one kind of pollen; b, d, e) Pollen grains from stamen fragment in polar (b, d) and equatorial (e) views showing the long colpi with coarsely verrucate aperture membranes; note the semitectate-reticulate tectum in the mesocolpium regions and foveolate-punctate tectum in the polar regions and along the aperture margins; c) Detail of pollen wall showing smooth muri and short, densely-spaced columellae. Specimen, Catefica 49-S107785 (a–e). Scale bars = 600 Μm (a), 6 Μm (b, d, e), 1.5 Μm (c). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 39. Scanning electron microscope (SEM) images of "Pollen clump with tricolpate pollen sp. 3"; Catefica locality, Portugal. a) Pollen clump, probably an anther fragment, containing one kind of pollen; b, d, e) Pollen grains from stamen fragment in polar (b, d) and equatorial (e) views showing the long colpi with coarsely verrucate aperture membranes; note the semitectate-reticulate tectum in the mesocolpium regions and foveolate-punctate tectum in the polar regions and along the aperture margins; c) Detail of pollen wall showing smooth muri and short, densely-spaced columellae. Specimen, Catefica 49-S107785 (a–e). Scale bars = 600 Μm (a), 6 Μm (b, d, e), 1.5 Μm (c).