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Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis.

ABSTRACT: 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.

SUBMITTER: Wen D

PROVIDER: S-EPMC5146328 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Project description:Gametic isolation is thought to play an important role in the evolution of reproductive isolation in broadcast-spawning marine invertebrates. However, it is unclear whether gametic isolation commonly evolves early in the speciation process or only accumulates after other reproductive barriers are already in place. It is also unknown whether gametic isolation is an effective barrier to introgression following speciation. Here, we used whole-genome sequencing data and multiple complementary phylogenomic approaches to test whether the well-documented gametic incompatibilities among the strongylocentrotid sea urchins have limited introgression. We quantified phylogenetic discordance, inferred reticulate phylogenetic networks, and applied the Δ statistic using gene tree topologies reconstructed from multiple sequence alignments of protein-coding single-copy orthologs. In addition, we conducted ABBA-BABA tests on genome-wide single nucleotide variants and reconstructed a phylogeny of mitochondrial genomes. Our results revealed strong mito-nuclear discordance and considerable nonrandom gene tree discordance that cannot be explained by incomplete lineage sorting alone. Eight of the nine species examined demonstrated a history of introgression with at least one other species or ancestral lineage, indicating that introgression was common during the diversification of the strongylocentrotid urchins. There was strong support for introgression between four extant species pairs (Strongylocentrotus pallidus ⇔ S. droebachiensis, S. intermedius ⇔ S. pallidus, S. purpuratus ⇔ S. fragilis, and Mesocentrotus franciscanus ⇔ Pseudocentrotus depressus) and additional evidence for introgression on internal branches of the phylogeny. Our results suggest that the existing gametic incompatibilities among the strongylocentrotid urchin species have not been a complete barrier to hybridization and introgression following speciation. Their continued divergence in the face of widespread introgression indicates that other reproductive isolating barriers likely exist and may have been more critical in establishing reproductive isolation early in speciation.

Project description:Background and aimsThe genetic and morphological consequences of natural selection and selective breeding are explored in the genus Abelia . The genus consists of ornamental shrubs endemic to China, which have been bred to create attractive and diverse cultivars.MethodsDNA fingerprinting (AFLP) and DNA sequence data are used to investigate the genetic diversity among 46 accessions of Abelia (22 natural taxa and 24 horticultural breeds). In the cultivated varieties these data are used to explore taxon boundaries, hybridisation and backcrossing. The genetic analysis dataset is also used to investigate morphological variation within natural species complexes and subsequently to inform a taxonomic treatment.Key resultsAbelia comprises five species: A. forrestii , A. schumannii , A. macrotera , A. uniflora and A. chinensis and has a total of 11 varieties. Abelia uniflora and A. macrotera do not occur in sympatry and are disjunctly distributed to the east and west of the A. chinensis distribution range. Abelia chinensis is widespread in eastern China and creates hybrids and introgressive taxa, including A. uniflora , along the contact zones with the previous taxa. Abelia `Maurice Foster' is a horticultural variety collected from wild stocks in Sichuan (China). Bayesian clustering methods (inferred in STRUCTURE based on AFLP data) indicate admixture between A. macrotera and A. schumannii in this variety. Hybridization probably occurred in the wild where these progenitor taxa co-occur and naturally form hybrids. AFLP results also reveal that a few diagnostic morphological characters such as sepal number or inflorescence structure were transferred between natural species and this is mirrored by taxa such as in Abelia `Saxon Gold' and A. forrestii .ConclusionsStudying both natural and cultivated species from the same group has helped understanding both differentiation mechanisms and how to improve cultivated plants in the future by studying which morphological characters are transferred between species and which taxa may already have arisen through hybridisation.

Project description:BackgroundRooted phylogenetic networks are used to display complex evolutionary history involving so-called reticulation events, such as genetic recombination. Various methods have been developed to construct such networks, using for example a multiple sequence alignment or multiple phylogenetic trees as input data. Coronaviruses are known to recombine frequently, but rooted phylogenetic networks have not yet been used extensively to describe their evolutionary history. Here, we created a workflow to compare the evolutionary history of SARS-CoV-2 with other SARS-like viruses using several rooted phylogenetic network inference algorithms. This workflow includes filtering noise from sets of phylogenetic trees by contracting edges based on branch length and bootstrap support, followed by resolution of multifurcations. We explored the running times of the network inference algorithms, the impact of filtering on the properties of the produced networks, and attempted to derive biological insights regarding the evolution of SARS-CoV-2 from them.ResultsThe network inference algorithms are capable of constructing rooted phylogenetic networks for coronavirus data, although running-time limitations require restricting such datasets to a relatively small number of taxa. Filtering generally reduces the number of reticulations in the produced networks and increases their temporal consistency. Taxon bat-SL-CoVZC45 emerges as a major and structural source of discordance in the dataset. The tested algorithms often indicate that SARS-CoV-2/RaTG13 is a tree-like clade, with possibly some reticulate activity further back in their history. A smaller number of constructed networks posit SARS-CoV-2 as a possible recombinant, although this might be a methodological artefact arising from the interaction of bat-SL-CoVZC45 discordance and the optimization criteria used.ConclusionOur results demonstrate that as part of a wider workflow and with careful attention paid to running time, rooted phylogenetic network algorithms are capable of producing plausible networks from coronavirus data. These networks partly corroborate existing theories about SARS-CoV-2, and partly produce new avenues for exploration regarding the location and significance of reticulate activity within the wider group of SARS-like viruses. Our workflow may serve as a model for pipelines in which phylogenetic network algorithms can be used to analyse different datasets and test different hypotheses.

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Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis.

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