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4,838 results for “lineage”
The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high-levels of lineage-specific diversity driven by recombination
<p><em>Aspergillus fumigatus </em>is a deadly agent of human fungal disease, where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on <em>de novo</em> assemblies offer a promising alternative to reference-based genomics, with the potential to address the full genetic repertoire of a species. Here, we use a combination of population genomics, phylogenomics, and pan-genomics to assess population structure and recombination frequency, phylogenetically structured gene presence-absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes in <em>A. fumigatus</em>. We provide evidence for three distinct populations of <em>A. fumigatus</em>, structured by both gene variation (SNPs and indels) and distinct gene presence-absence variation with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism, hinting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. Despite low levels of outcrossing, <em>A. fumigatus</em> demonstrated a large pan-genome including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference based approach for evaluating intraspecific variation, and the power of combined genomic approaches to elucidate population structure, genetic diversity, and the putative ecological drivers of clinically relevant fungi.</p> <p>Accompanying manuscript is available as preprint at <a href="https://dx.doi.org/10.1101/2021.12.12.472145">https://dx.doi.org/10.1101/2021.12.12.472145</a> </p> <p>Lotus A. Lofgren, Brandon S. Ross, Robert A. Cramer, Jason E. Stajich. Combined Pan-, Population-, and Phylo-Genomic Analysis of <em>Aspergillus fumigatus</em> Reveals Population Structure and Lineage-Specific Diversity bioRxiv 2021.12.12.472145; doi: https://doi.org/10.1101/2021.12.12.472145</p>
SMDP: SARS-CoV-2 Mutation Distribution Profiler for rapid estimation of mutational histories of unusual lineages
<p>Supplementary information relating to the manuscript titled "SMDP: SARS-CoV-2 Mutation Distribution Profiler for rapid estimation of mutational histories of unusual lineages" that has been published on the preprint server arXiv.</p> <ul> <li>PersistentInfectionScore.nb: Mathematica code used to process the data and generate Figure 2</li> <li>PersistentInfectionScore.pdf: pdf version of the above file</li> <li>Supplementary_tables_Harari_et_al_2022.xlsx: raw data from (<a href="https://www.nature.com/articles/s41591-022-01882-4#Sec19">Harari et al. 2022</a>) that was used to generate mutation distributions</li> </ul>
Phlorest phylogeny derived from Dunn et al. 2011 'Evolved structure of language shows lineage-specific trends in word-order universals'
<p>Cite the source of the dataset as:</p> <blockquote> <p>Dunn M, Greenhill SJ, Levinson SC & Gray RD. 2011. Evolved structure of language shows lineage-specific trends in word-order universals. Nature, 473(7345), 79-82.</p> </blockquote>
Exploring the Pocillopora cryptic diversity: a new genetic lineage in the western Indian Ocean or remnants from an ancient one?
<p>Cryptic species and lineages have been widely reported during the last decades, particularly in the marine realm. Misidentifications and ignoring species complexes imply many consequences, notably biasing biodiversity and connectivity assessments, which in turn mislead our understanding of ecosystems and impact the effective design and management of conservation plans. Focusing on the Indo-Pacific coral genus <em>Pocillopora</em>, playing key roles in reef ecosystems as one of the main bio-constructors, we report the first <em>Pocillopora</em> PSH16 (ORF53; <em>sensu</em> Gélin et al. 2017, Mol Phylogenet Evol 109:430–446) colonies (<em>N</em> = 19) in the western Indian Ocean (Nosy Tanikely, Madagascar), 6,000 km further from its current distribution. Colonies were identified according to their mitochondrial Open Reading Frame (ORF) haplotype and Bayesian assignment tests based on 13-microsatellite genotypes. Additionally, we performed genetic structure and diversity analyses with sympatric colonies from other <em>Pocillopora</em> species and <em>Pocillopora</em> PSH16 colonies from the tropical southwestern Pacific, revealing (1) a weak clonal richness, (2) a weak genetic diversity and (3) a relative isolation for the newly reported PSH16 colonies. These colonies thus represent either a new, distinct and uncommon, genetic lineage, or isolated remnants of a wider one. In any case, unless specific management measures are implemented, their long-term maintenance seems compromised due to restricted gene flow within a restricted pool of genes.</p> <p> </p> <p>This dataset contains the microsatellite genotypes analysed (98 <em>Pocillopora</em> colonies × 13 loci + ORF). Missing data are encoded as "?". The sampling marine province and the population are indicated for each individual.</p>
Lineage and role in integrative taxonomy of a heterotrophic orchid complex
<p>Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological ‘role’ shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the <em>Corallorhiza striata</em> complex, analyzing genomic, morphological, phenological, reproductive-mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data–ISSRseq–demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the ‘extended’ data, albeit with weaker signal. However, none of the ‘extended’ datasets fully satisfy the condition of a significant ‘role’ shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of ‘lineage+role’ to date and illustrates the advantages of such an approach.</p>
Data for "A promiscuous mechanism to phase separate eukaryotic carbon fixation in the green lineage"
<p>This repository contains all raw data associated with the manuscript:</p> <p>"<em><strong>A promiscuous mechanism to phase separate eukaryotic carbon fixation in the green lineage</strong></em>"</p> <p> </p> <p>The files are organised according to their appearance as figures in the manuscript.</p> <p>Within each of the zipped figure folders is a <strong>_readme.txt</strong> file that contains information about the raw data provided for each figure.</p>
Map of the archaeological sites mentionned in the paper "Abstraction in Archaeological Stratigraphy: a Pyrenean Lineage of Innovation (late 19th–early 21th century)"
<p>Projection: WGS 84. QGIS 3.14.16</p> <p>Sources:</p> <ul> <li>DEM: GEBCO (<a href="https://doi.org/10.5285/A29C5465-B138-234D-E053-6C86ABC040B9">https://doi.org/10.5285/A29C5465-B138-234D-E053-6C86ABC040B9</a>)</li> <li>Borders:<em> Límites municipales, provinciales y autonómicosRecintos municipales y líneas límite (municipales, provinciales y autonómicos)</em>. BDLJE CC-BY 4.0.</li> </ul>
Comparative metabolomics of fruits and leaves in a hyperdiverse lineage suggests fruits are a key incubator of phytochemical diversification
<p>Data files, chromatograms, and metadata for the Frontiers in Plant Science article "Comparative metabolomics of fruits and leaves in a hyperdiverse lineage suggests fruits are a key incubator of phytochemical diversification" . </p> <p>doi: 10.3389/fpls.2021.693739</p>
Dataset for "Mapping of centriolar proteins onto the post-embryonic lineage of C. elegans"
<p>This is the dataset with all spreadsheets, confocal and wide field microscopy images and related scripts, related to the publication " "Mapping of centriolar proteins onto the post-embryonic lineage of <em>C. elegans</em>". Refer to the Read me file for further information.</p>
Variant calls for 'Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration'
<p>A VCF of SNP calls used for input to GWAS in https://elifesciences.org/articles/26255</p>
Identification of a lineage-specific protein network at the trypanosome nuclear envelope
<p>The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization, nucleocytoplasmic transport, ribosomal maturation and mRNA processing/quality control. The molecular basis for many of these functions have diverged between different eukaryotic lineages. <em>Trypanosoma brucei</em>, a member of the early branching eukaryotic lineage Discoba, highlight many of these, including a distinct lamina and kinetochore composition. Here we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with <em>S. cerevisiae </em>Pom152 and <em>H. sapiens </em>Nup210, and additional peripheral components of the NPC. While many of the LAPs are specific to Trypanosomatids, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the NE proteome of trypanosomes, highlighting the diversity of nuclear biology across the eukaryotes and increasing our understanding of eukaryotic and NPC evolution.</p>
Fig. 13 in On the Bennelongia nimala and B. triangulata lineages (Crustacea, Ostracoda) in Western Australia, with the description of six new species
Fig. 13. Bennelongia triangulata sp. nov. (all ♂, A–D from CB75a, Cattle Camp Pan, Gascoyne, WA; E–G holotype (WAMC55564): cane grass pan on Wooramel Station, Murchison/Gascoyne, WA). A. Outline of hemipenis (WAMC55584). B. Lpp (WAMC55584). C. Lpp (WAMC55575). D. Rpp (WAMC55584). E. Outline of hemipenis. F. Lpp. F'. Lpp, detail of distal part of first segment. G. Rpp. Scale = 156 µm for A, E; 73 µm for B–D, F–G.
Fig. 11 in On the Bennelongia nimala and B. triangulata lineages (Crustacea, Ostracoda) in Western Australia, with the description of six new species
Fig. 11. Bennelongia triangulata sp. nov. (all ♀, A–G & K–M from type locality: canegrass pan on Wooramel Station, Murchison/Gascoyne, WA; H–J from CB54, Boolathana Station, Carnarvon Basin, WA). A. LVi (allotype, WAMC55565). B. CpRL (OC3368). C. RVi (WAMC55565). D. CpD, detail anterior margin (WAMC55569). E. CpD (WAMC55569). F. CpV (WAMC55570). G. CpV, detail anterior margin (WAMC55570). H. LVi (OC3370). I. LVi, detail posterior margin (OC3370). J. RVi (OC3370). K. RVi, detail anterior margin (WAMC55565). L. CpRL, detail anterior margin (OC3368). M. RVi, tilted, detail anterior margin (WAMC55565). Scales = 1 mm for A–C, E–F, H, J; 200 µm for D, G, I, K–M.
Fig. 8 in On the Bennelongia nimala and B. triangulata lineages (Crustacea, Ostracoda) in Western Australia, with the description of six new species
Fig. 8. Bennelongia pinderi sp. nov. (all ♀, all from type locality: unnamed claypan in Murchison/ Gascoyne, WA). A. LVi (holotype, WAMC55620). B. CpRL (WAMC55622). C. RVi (WAMC55620). D. CpD (WAMC55621). E. CpV (OC3378). F. RVi, detail anterior margin (WAMC55620). G. RVi, tilted, detail anterior margin (WAMC55620). Scale = 1 mm for A–E; 200 µm for F–G.
Fig. 4 in On the Bennelongia nimala and B. triangulata lineages (Crustacea, Ostracoda) in Western Australia, with the description of six new species
Fig. 4. Bennelongia nimala De Deckker, 1981 (all ♀, all from Kakadu National Park, NT). A. LVi (WAMC55593). B. RVi (WAMC55593). C. RVe (WAMC55589). D. LVe (WAMC55589). E. RVi, detail of central muscle scars (WAMC55593). F. LVe, detail of surface ornamentation (WAMC55589). G. CpD (OC3373). H. LVi, detail of caudal side (WAMC55593). I. LVi, detail of anterior side (WAMC55593). J. CpD (juvenile A-3, specimen lost). K. CpRL (OC3373). L. RVi, detail of anterior margin (WAMC55593). M. CpRL, detail of anterior margin, showing external view of lapel (OC3373). N. RVi, tilted, detail of anterior margin and of lapel (WAMC55593). Scale = 1 mm for A–D, G, K; 500 µm for J; 200 µm for E–F, H–I, L–N.
Fig. 5 in On the Bennelongia nimala and B. triangulata lineages (Crustacea, Ostracoda) in Western Australia, with the description of six new species
Fig. 5. Bennelongia tirigie sp. nov. (all from type locality: Tirigie Claypan, Murchison/Gascoyne, WA). A. LVi (allotype ♀, WAMC55596). B. CpRL (♀, WAMC 55600). C. RVi (♀, WAMC55596). D. LVi (holotype ♂, WAMC55595). E. CpRL (♂, WAMC55597). F. RVi (♂, WAMC55595). G. CpD (♀, WAMC55599). H. CpV (♀, WAMC55598). I. CpD (♂, WAMC55597). J. CpV (♂, WAMC55597). K. RVi, detail anterior margin (♀, WAMC55596). L. RVi, tilted, detail anterior margin (♀, WAMC55596). M. RVi, detail anterior margin (♂, WAMC55595). N. RVi, tilted, detail anterior margin (♂, WAMC55595). Scale = 1 mm for A–J; 200 µm for K–N.
Fig. 1 in On the Bennelongia nimala and B. triangulata lineages (Crustacea, Ostracoda) in Western Australia, with the description of six new species
Fig. 1. Map of Western Australia with localities of Bennelongia species described in the present paper.
Fig. 2 in On the Bennelongia nimala and B. triangulata lineages (Crustacea, Ostracoda) in Western Australia, with the description of six new species
Fig. 2. Phylogenetic tree constructed with Bayesian Inference (BI) and Maximum Likelihood (ML) methods from COI sequences belonging to a total of 54 ostracods from the Bennelongia nimala and B. triangulata lineages, respectively, with the marine ostracod Macroscapha walterae from Genbank (accession number GU566887) as outgroup. Numbers above and below nodes illustrate statistical support for this particular node. Numbers above nodes are % bootstrap values of ML analyses with 1000 replicates, numbers below nodes in italics represent Bayesian posterior probabilities (ranging from 0 to 1). Both methods, BI and ML, resulted in the same tree topology. Different phylogenetic clades are indicated by different colours.
Fig. 6 in On the Bennelongia nimala and B. triangulata lineages (Crustacea, Ostracoda) in Western Australia, with the description of six new species
Fig. 6. Bennelongia tirigie sp. nov. (A–D, WAMC55595, holotype) and B. koendersae sp. nov. (E– H, WAMC55615, paratype), all ♂. A–B. Outlines of hemipenes. C. Lpp. D. Rpp. E–F. Outlines of hemipenes. G. Lpp. H. Rpp. Scale = 73 µm for A, D–E; 31 µm for B–C, F–H.
Fig. 3 in On the Bennelongia nimala and B. triangulata lineages (Crustacea, Ostracoda) in Western Australia, with the description of six new species
Fig. 3. Parsimonius networks, based on COI sequences of the Bennelongia nimala and B. triangulata lineages. Squares represent ancestral sequences (or haplotypes), small circles missing haplotypes. The size of squares and large ovals is proportional to the number of individuals with the same sequence in the analysed population. The networks were constructed with up to 14 mutations steps connecting different sequences or haplotypes. Different phylogenetic clades are indicated by different colours (see Fig. 2).
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