The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life’s species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description. This article is part of the themed issue ‘From DNA barcodes to biomes’

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

FIGURE 13. Hydropsyche resmineda Malicky 1977, Moroccan form. 13A in Larval Taxonomy and Distribution of Genus Hydropsyche (Trichoptera: Hydropsychidae) in Northwestern Algeria

FIGURE 13. Hydropsyche resmineda Malicky 1977, Moroccan form. 13A, head and thorax, dorsal; 13B, cephalic capsule, dorsal; 13C, cephalic capsule, ventral; 13D, posterior prosternites, ventral. [scale bar = 1 mm]

FIGURE 7 in Larval Taxonomy and Distribution of Genus Hydropsyche (Trichoptera: Hydropsychidae) in Northwestern Algeria

FIGURE 7. Hydropsyche iberomaroccana Navás 1932, morphotype 2. 7A, head and thorax, dorsal; 7B, cephalic capsule, dorsal; 7C, cephalic capsule, ventral, 7D, posterior prosternites, ventral. [scale bar = 1 mm]

FIGURE 2. Hydropsyche siltalai D in Larval Taxonomy and Distribution of Genus Hydropsyche (Trichoptera: Hydropsychidae) in Northwestern Algeria

FIGURE 2. Hydropsyche siltalai D̂hler 1963, morphotype 1. 2A, head and thorax, dorsal; 2B, cephalic capsule, dorsal; 2C, cephalic capsule; ventral; 2D, posterior prosternites, ventral. [scale bar = 1 mm]

FIGURE 11. Hydropsyche lobata McLachlan 1884, morphotype 2. 11A in Larval Taxonomy and Distribution of Genus Hydropsyche (Trichoptera: Hydropsychidae) in Northwestern Algeria

FIGURE 11. Hydropsyche lobata McLachlan 1884, morphotype 2. 11A, head and thorax dorsal; 11B, cephalic capsule, dorsal; 11C, cephalic capsule, ventral; 11D, posterior prosternites ventral. [scale bar = 1 mm]

Larval Taxonomy and Distribution of Genus Hydropsyche (Trichoptera: Hydropsychidae) in Northwestern Algeria

Bemmoussat-Dekkak, Soumya, Abdellaoui-Hassaine, Karima, Sartori, Michel, Morse, John C., Zamora-Muñoz, Carmen (2021): Larval Taxonomy and Distribution of Genus Hydropsyche (Trichoptera: Hydropsychidae) in Northwestern Algeria. Zootaxa 4915 (4): 481-505, DOI: https://doi.org/10.11646/zootaxa.4915.4.

The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life.

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between 'Barcode Index Numbers' (BINs) and 'species' that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.This article is part of the themed issue 'From DNA barcodes to biomes'

Impact of late presentation of HIV infection on short-, mid- and long-term mortality and causes of death in a multicenter national cohort : 2004-2013

To analyze the impact of late presentation (LP) on overall mortality and causes of death and describe LP trends and risk factors (2004-2013). Cox models and logistic regression were used to analyze data from a nation-wide cohort in Spain. LP is defined as being diagnosed when CD4 < 350 cells/ml or AIDS. Of 7165 new HIV diagnoses, 46.9% (CI:45.7-48.0) were LP, 240 patients died.First-year mortality was the highest (aHR = 10.3[CI:5.5-19.3]); between 1 and 4 years post-diagnosis, aHR = 1.9(1.2-3.0); an