scholarly journals Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts

2019 ◽  
Author(s):  
Joshua I Brian ◽  
Simon K Davy ◽  
Shaun P Wilkinson
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Reticulate Evolution ◽  
Next Generation Sequencing Data ◽  
Putative Hybrid ◽  
Its2 Region ◽  
Sequencing Data ◽  
Lineage Sorting ◽  
Evolutionary Potential ◽  
Unbiased Test

Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondria; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of Next Generation Sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.

scholarly journals Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7178 ◽  
Author(s):  
Joshua I. Brian ◽  
Simon K. Davy ◽  
Shaun P. Wilkinson
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Reticulate Evolution ◽  
Next Generation Sequencing Data ◽  
Putative Hybrid ◽  
Its2 Region ◽  
Sequencing Data ◽  
Lineage Sorting ◽  
Evolutionary Potential ◽  
Unbiased Test

Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondrion; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of next generation sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting or the presence of co-dominance, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.

scholarly journals Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts

2019 ◽  
Author(s):  
Joshua I Brian ◽  
Simon K Davy ◽  
Shaun P Wilkinson
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Reticulate Evolution ◽  
Next Generation Sequencing Data ◽  
Putative Hybrid ◽  
Its2 Region ◽  
Sequencing Data ◽  
Lineage Sorting ◽  
Evolutionary Potential ◽  
Unbiased Test

Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondria; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of Next Generation Sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.

scholarly journals ALSgeneScanner: a pipeline for the analysis and interpretation of DNA NGS data of ALS patients

2018 ◽  
Author(s):  
Alfredo Iacoangeli ◽  
Ahmad Al Khleifat ◽  
William Sproviero ◽  
Aleksey Shatunov ◽  
Ashley R Jones ◽  
...  
Keyword(s):  
Motor Neurons ◽  
Health Care Professionals ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Whole Exome ◽  
Exome Sequence Data ◽  
Als Patients ◽  
Ngs Data

AbstractAmyotrophic lateral sclerosis (ALS, MND) is a neurodegenerative disease of upper and lower motor neurons resulting in death from neuromuscular respiratory failure, typically within two years of first symptoms. Genetic factors are an important cause of ALS, with variants in more than 25 genes having strong evidence, and weaker evidence available for variants in more than 120 genes. With the increasing availability of Next-Generation sequencing data, non-specialists, including health care professionals and patients, are obtaining their genomic information without a corresponding ability to analyse and interpret it. Furthermore, the relevance of novel or existing variants in ALS genes is not always apparent. Here we present ALSgeneScanner, a tool that is easy to install and use, able to provide an automatic, detailed, annotated report, on a list of ALS genes from whole genome sequence data in a few hours and whole exome sequence data in about one hour on a readily available mid-range computer. This will be of value to non-specialists and aid in the interpretation of the relevance of novel and existing variants identified in DNA sequencing data.

Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment

Zootaxa ◽  
2020 ◽  
Vol 4750 (3) ◽  
pp. 328-348 ◽  
Author(s):  
DAVID A. GRAY ◽  
DAVID B. WEISSMAN ◽  
JEFFREY A. COLE ◽  
EMILY MORIARTY LEMMON
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
The United States ◽  
Field Cricket ◽  
Future Research ◽  
Gene Trees ◽  
Lineage Sorting ◽  
The Bahamas ◽  
Field Crickets ◽  
Anchored Hybrid Enrichment

We present the first comprehensive molecular phylogeny of Gryllus field cricket species found in the United States and Canada, select additional named Gryllus species found in Mexico and the Bahamas, plus the European field cricket G. campestris Linnaeus and the Afro-Eurasian cricket G. bimaculatus De Geer. Acheta, Teleogryllus, and Nigrogryllus were used as outgroups. Anchored hybrid enrichment was used to generate 492,531 base pairs of DNA sequence from 563 loci. RAxML analysis of concatenated sequence data and Astral analysis of gene trees gave broadly congruent results, especially for older branches and overall tree structure. The North American Gryllus are monophyletic with respect to the two Old World taxa; certain sub-groups show rapid recent divergence. This is the first Anchored Hybrid Enrichment study of an insect group done for closely related species within a single genus, and the results illustrate the challenges of reconstructing the evolutionary history of young rapidly diverged taxa when both incomplete lineage sorting and probable hybridization are at play. Because Gryllus field crickets have been used extensively as a model system in evolutionary ecology, behavior, neuro-physiology, speciation, and life-history and life-cycle evolution, these results will help inform, interpret, and guide future research in these areas. 

scholarly journals A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

2019 ◽  
Vol 37 (4) ◽  
pp. 1211-1223 ◽  
Author(s):  
Tomáš Flouri ◽  
Xiyun Jiao ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Mosquito Species ◽  
Phylogenomic Analysis ◽  
Data Sets ◽  
Lineage Sorting ◽  
Coalescent Model ◽  
Multispecies Coalescent

Abstract Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here, we implement the multispecies-coalescent-with-introgression model, an extension of the multispecies-coalescent model to incorporate introgression, in our Bayesian Markov chain Monte Carlo program Bpp. The multispecies-coalescent-with-introgression model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Reanalysis of data sets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

Phylogeny, biogeography and foliar manganese accumulation of Gossia (Myrtaceae)

2018 ◽  
Author(s):  
Todd McLay ◽  
Gareth D. Holmes ◽  
Paul I. Forster ◽  
Susan E. Hoebee ◽  
Denise R. Fernando
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Position ◽  
Strongly Correlated ◽  
Lineage Sorting ◽  
Dna Sequence Data ◽  
Australian Species ◽  
Wide Range ◽  
Single Clade ◽  
The Relationship

The rainforest genus Gossia N.Snow & Guymer (Myrtaceae) occurs in Australia, Melanesia and Malesia, and is capable of hyperaccumulating the heavy metal manganese (Mn). Here, we used nuclear ribosomal and plastid spacer DNA-sequence data to reconstruct the phylogeny of 19 Australian species of Gossia and eight New Caledonian taxa. Our results indicated that the relationship between Gossia and Austromyrtus (Nied.) Burret is not fully resolved, and most Australian species were supported as monophyletic. Non-monophyly might be related to incomplete lineage sorting or inaccurate taxonomic classification. Bark type appears to be a morphological synapomorphy separating two groups of species, with more recently derived lineages having smooth and mottled ‘python’ bark. New Caledonian species were well resolved in a single clade, but were not the first diverging Gossia lineage, calling into doubt the results of a recent study that found Zealandia as the ancestral area of tribe Myrteae. Within Australia, the evolution of multiple clades has probably been driven by well-known biogeographic barriers. Some species with more widespread distributions have been able to cross these barriers by having a wide range of soil-substrate tolerances. Novel Mn-hyperaccumulating species were identified, and, although Mn hyperaccumulation was not strongly correlated with phylogenetic position, there appeared to be some difference in accumulation levels among clades. Our study is the first detailed phylogenetic investigation of Gossia and will serve as a reference for future studies seeking to understand the origin and extent of hyperaccumulation within the Myrteae and Myrtaceae more broadly.

scholarly journals M. tuberculosis microvariation is common and is associated with transmission: analysis of three years prospective universal sequencing in England

2019 ◽  
Author(s):  
David Wyllie ◽  
Trien Do ◽  
Richard Myers ◽  
Vlad Nikolayevskyy ◽  
Derrick Crook ◽  
...  
Keyword(s):  
Public Health ◽  
Mixed Infection ◽  
English Language ◽  
Sequence Data ◽  
Added Value ◽  
Next Generation Sequencing Data ◽  
Nucleotide Position ◽  
Sequencing Data ◽  
Increased Risk ◽  
Low Incidence

AbstractBackgroundThe prevalence, association with disease status, and public health impact of infection with mixtures of M. tuberculosis strains is unclear, in part due to limitations of existing methods for detecting mixed infections.MethodsWe developed an algorithm to identify mixtures of M. tuberculosis strains using next generation sequencing data, assessing performance using simulated sequences. We identified mixed M. tuberculosis strains when there was at least one mixed nucleotide position, and where both the mixture’s components were present in similar isolates from other individuals. We determined risk factors for mixed infection among isolations of M. tuberculosis in England using logistic regression. We used survival analyses to assess the association between mixed infection and putative transmission.Findings6,560 isolations of TB were successfully sequenced in England 2016-2018. Of 3,691 (56%) specimens for which similar sequences had been isolated from at least two other individuals, 341 (9.2%) were mixed. Infection with lineages other than Lineage 4 were associated with mixed infection. Among the 1,823 individuals with pulmonary infection with Lineage 4 M. tuberculosis, mixed infection was associated with significantly increased risk of subsequent isolation of closely related organisms from a different individual (HR 1.43, 95% CI 1.05,1.94), indicative of transmission.InterpretationMixtures of transmissible strains occur in at least 5% of tuberculosis infections in England; when present in pulmonary disease, such mixtures are associated with an increased risk of tuberculosis transmission.FundingPublic Health England; NIHR Health Protection Research Unit Oxford; European Union.Research in ContextEvidence Before This StudyWe searched Pubmed using the search terms ‘tuberculosis’ and ‘mixed’ or ‘mixture’ for English Language articles published up to 1 April 2019. Studies, most performed without the benefit of genomic sequencing, report mixed TB infection from a range of medium and high prevalence areas and show it to be associated with delayed treatment response. Modelling suggests detection and treatment of mixed TB infection is an important goal for TB eradication campaigns. Although routine DNA sequencing of M. tuberculosis isolates is becoming widespread, efficient methods for detecting mixed infection from such data are underdeveloped, and the true prevalence of mixed infection and its association with transmission is unclear.Added Value of This StudyThis study investigated a large series of TB isolations obtained as part of a routine Mycobacterial sequencing program by two reference laboratories, in a low incidence area, England. We developed an efficient generalisable approach to identify transmitted mixed M. tuberculosis infection; our approach is capable of sensitive and specific detection of a single mixed nucleotide position. We identified mixed infection of similar strains (‘microvariation’) in about 9.2% of the M. tuberculosis samples which we were able to assess, and found evidence of increased transmission from individuals with mixed infection.Implications of All the Available EvidenceTB microvariation is a risk factor for TB transmission, even in the low incidence area studied. Although an efficient and highly specific technique identifying microvariation exists, it relies on comparison with similar sequences isolated from other patients. Sharing of sequence data from the many TB sequencing programs being deployed globally will increase the sensitivity of microvariation detection, and may assist targeted public health interventions.

scholarly journals A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis

2019 ◽  
Author(s):  
Thomas Flouris ◽  
Xiyun Jiao ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Mosquito Species ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Lineage Sorting ◽  
Multispecies Coalescent ◽  
Important Means

AbstractRecent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here we implement the multispecies-coalescent-with-introgression (MSci) model, an extension of the multispecies-coalescent (MSC) model to incorporate introgression, in our Bayesian Markov chain Monte Carlo (MCMC) program BPP. The MSci model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Re-analysis of datasets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

scholarly journals Exogene: A performant workflow for detecting viral integrations from paired-end next-generation sequencing data

2021 ◽  
Author(s):  
Jean-Pierre Kocher ◽  
Zachary Stephens ◽  
Daniel O'Brien ◽  
Mrunal Dehankar ◽  
Lewis Roberts ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Data ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Long Read ◽  
Breakpoint Detection ◽  
Targeted Capture ◽  
Genome Heterogeneity ◽  
Generation Sequencing

The integration of viruses into the human genome is known to be associated with tumorigenesis in many cancers, but the accurate detection of integration breakpoints from short read sequencing data is made difficult by human-viral homologies, viral genome heterogeneity, coverage limitations, and other factors. To address this, we present Exogene, a sensitive and efficient workflow for detecting viral integrations from paired-end next generation sequencing data. Exogene's read filtering and breakpoint detection strategies yield integration coordinates that are highly concordant with those found in long read validation sets. We demonstrate this concordance across 6 TCGA Hepatocellular carcinoma (HCC) tumor samples, identifying integrations of hepatitis B virus that are validated by long reads. Additionally, we applied Exogene to targeted capture data from 426 previously studied HCC samples, achieving 98.9% concordance with existing methods and identifying 238 high-confidence integrations that were not previously reported. Exogene is applicable to multiple types of paired-end sequence data, including genome, exome, RNA-Seq or targeted capture.

scholarly journals Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone

2019 ◽  
Vol 68 (6) ◽  
pp. 937-955 ◽  
Author(s):  
Alison Cloutier ◽  
Timothy B Sackton ◽  
Phil Grayson ◽  
Michele Clamp ◽  
Allan J Baker ◽  
...  
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Estimation Error ◽  
Gene Tree ◽  
Species Tree ◽  
Tree Topology ◽  
Whole Genome ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Genome Analyses

Abstract Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totaling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4274 CR1 retroelements identified from multispecies whole-genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other nonostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations and topology tests indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.

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