Una nueva especie del género Yuriria Jordan & Evermann, 1896 (Actinopterygii, Cyprinidae) de la cuenca del río Ameca en la Mesa Central Mexicana

A new cyprinid species is described based on morfometric, meristic and genetic characters. The new species identified, Yuriria amatlana sp. nov., inhabits the high Ameca Basin in the central plateau of Mexico. This Mexican minnow differs from Yuriria alta and Yuriria chapalae in terms of the following characters: (50-52) 53-54 pored lateralline scales; 10 upper transverse-line scales, 5-6 lower transverse-line scales and 8-10 gill rakers. Body coloration is light yellowish-brown. Compared to Yuriria alta and Yuriria chapalae, the new species has a less conspicuous dark grey band running from the start of the dorsal fin to the head. Cytochrome b gene sequences differ from those of Yuriria alta and Yuriria chapalae in terms of 29 fixed nucleotide positions (molecular autopomorphies). Calculated genetic divergences for the cytochrome b gene were: `DHKY = 3.8 (3.2-4.4%) between Yuriria amatlana sp. nov. and Y. alta; `DHKY = 5 (4.8-5.2%) between Y. amatlana sp. nov and Y. chapalae; and `DHKY = 2.6 (2.1-3.3%) between Y. chapalae and Y. alta.Se describe una nueva especie, Yuriria amatlana sp. nov., en base a caracteres morfométricos, merísticos y genéticos. La nueva especie proviene de la parte alta de la cuenca del río Ameca en la Meseta Central de México. Esta especie se diferencia de Yuriria alta y Yuriria chapalae por una combinación de los siguientes caracteres: (50-52) 53-54 escamas en una serie longitudinal, 10 escamas en una serie transversal por encima de la línea lateral y 5-6 escamas por debajo de la línea lateral y 8-10 branquiespinas. El color del cuerpo es amarillo-marrón claro. La nueva especie tiene una banda gris oscura menos marcada en el cuerpo desde el comienzo de la aleta dorsal hacia la cabeza con respecto a Yuriria alta y Yuriria chapalae. La nueva especie se diferencia de Yuriria alta y Yuriria chapalae en 29 posiciones nucleotídicas fijadas (autopomorfias moleculares) para el citocromo b. La divergencia genética entre Yuriria alta y Yuriria amatlana sp. nov. para el citocromo b fue de `DHKY = 3.8 (3.2-4.4%); entre Y. amatlana sp. nov. y Y. chapalae fue `DHKY = 5 (4.8-5.2%) y entre Y. chapalae y Y. alta fue `DHKY = 2.6 (2.1-3.3%)

Calidad del bosque de ribera del río El Tunal, Durango, México; mediante la aplicación del índice QBR

The assessment of the ecological condition of the river banks is an important element in the rivers study around the world.The objective of this work was to evaluate the ecological condition of the riparian forest in a transect of 21 km of ElTunal river in Mexico with the QBR index. In the transect of study six sites were evaluated which were selected by therepresentation, possibilities of access and the heterogeneity of the vegetation. In general, the results have shown a riverwith important signs of deterioration; two sites results in an intermediate quality, two sites results in bad quality and tworesults in poor quality.La evaluación de la condición ecológica de las riberas es un elemento importante en el estudio de los ríos alrededor delmundo. El objetivo del presente trabajo fue evaluar la calidad del bosque de ribera, desde un punto de vista estructural yfuncional, en un tramo de 21 kilómetros del río El Tunal en Durango, México, mediante la aplicación del índice QBR. Enel tramo estudiado se evaluaron seis sitios seleccionados por su representatividad, accesibilidad y heterogeneidad de suvegetación. En general, los resultados muestran un río con indicios importantes de deterioro; se encontraron dos sitios concalidad intermedia, dos sitios presentaron calidad mala y los dos restantes presentaron calidad pésima

Complex evolutionary history of the Mexican stoneroller Campostoma ornatum Girard, 1856 (Actinopterygii: Cyprinidae)

<p>Abstract</p> <p>Background</p> <p>Studies of the phylogeography of Mexican species are steadily revealing genetic patterns shared by different species, which will help to unravel the complex biogeographic history of the region. <it>Campostoma ornatum </it>is a freshwater fish endemic to montane and semiarid regions in northwest Mexico and southern Arizona. Its wide range of distribution and the previously observed morphological differentiation between populations in different watersheds make this species a useful model to investigate the biogeographic role of the Sierra Madre Occidental and to disentangle the actions of Pliocene tecto-volcanic processes <it>vs </it>Quaternary climatic change. Our phylogeographic study was based on DNA sequences from one mitochondrial gene (<it>cytb</it>, 1110 bp, n = 285) and two nuclear gene regions (S7 and RAG1, 1822 bp in total, n = 56 and 43, respectively) obtained from 18 to 29 localities, in addition to a morphological survey covering the entire distribution area. Such a dataset allowed us to assess whether any of the populations/lineages sampled deserve to be categorised as an evolutionarily significant unit.</p> <p>Results</p> <p>We found two morphologically and genetically well-differentiated groups within <it>C. ornatum</it>. One is located in the northern river drainages (Yaqui, Mayo, Fuerte, Sonora, Casas Grandes, Santa Clara and Conchos) and another one is found in the southern drainages (Nazas, Aguanaval and Piaxtla). The split between these two lineages took place about 3.9 Mya (CI = 2.1-5.9). Within the northern lineage, there was strong and significant inter-basin genetic differentiation and also several secondary dispersal episodes whit gene homogenization between drainages. Interestingly, three divergent mitochondrial lineages were found in sympatry in two northern localities from the Yaqui river basin.</p> <p>Conclusions</p> <p>Our results indicate that there was isolation between the northern and southern phylogroups since the Pliocene, which was related to the formation of the ancient Nazas River paleosystem, where the southern group originated. Within groups, a complex reticulate biogeographic history for <it>C. ornatum </it>populations emerges, following the taxon pulse theory and mainly related with Pliocene tecto-volcanic processes. In the northern group, several events of vicariance promoted by river or drainage isolation episodes were found, but within both groups, the phylogeographic patterns suggest the occurrence of several events of river capture and fauna interchange. The Yaqui River supports the most diverse populations of <it>C. ornatum</it>, with several events of dispersal and isolation within the basin. Based on our genetic results, we defined three ESUs within <it>C. ornatum </it>as a first attempt to promote the conservation of the evolutionary processes determining the genetic diversity of this species. They will likely be revealed as a valuable tool for freshwater conservation policies in northwest Mexico, where many environmental problems concerning the use of water have rapidly arisen in recent decades.</p

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

Una nueva especie del género Yuriria Jordan & Evermann, 1896 (Actinopterygii, Cyprinidae) de la cuenca del río Ameca en la Mesa Central Mexicana

13 pages, 4 figures, 7 tables.[EN] A new cyprinid species is described based on morfometric, meristic and genetic characters. The new species identified, Yuriria amatlana sp. nov., inhabits the high Ameca Basin in the central plateau of Mexico. This Mexican minnow differs from Yuriria alta and Yuriria chapalae in terms of the following characters: (50-52) 53-54 pored lateralline scales; 10 upper transverse-line scales, 5-6 lower transverse-line scales and 8-10 gill rakers. Body coloration is light yellowish-brown. Compared to Yuriria alta and Yuriria chapalae, the new species has a less conspicuous dark grey band running from the start of the dorsal fin to the head. Cytochrome b gene sequences differ from those of Yuriria alta and Yuriria chapalae in terms of 29 fixed nucleotide positions (molecular autopomorphies). Calculated genetic divergences for the cytochrome b gene were: `DHKY = 3.8 (3.2-4.4%) between Yuriria amatlana sp. nov. and Y. alta; `DHKY = 5 (4.8-5.2%) between Y. amatlana sp. nov and Y. chapalae; and `DHKY = 2.6 (2.1-3.3%) between Y. chapalae and Y. alta.[ES] Se describe una nueva especie, Yuriria amatlana sp. nov., en base a caracteres morfométricos, merísticos y genéticos. La nueva especie proviene de la parte alta de la cuenca del río Ameca en la Meseta Central de México. Esta especie se diferencia de Yuriria alta y Yuriria chapalae por una combinación de los siguientes caracteres: (50-52) 53-54 escamas en una serie longitudinal, 10 escamas en una serie transversal por encima de la línea lateral y 5-6 escamas por debajo de la línea lateral y 8-10 branquiespinas. El color del cuerpo es amarillo-marrón claro. La nueva especie tiene una banda gris oscura menos marcada en el cuerpo desde el comienzo de la aleta dorsal hacia la cabeza con respecto a Yuriria alta y Yuriria chapalae. La nueva especie se diferencia de Yuriria alta y Yuriria chapalae en 29 posiciones nucleotídicas fijadas (autopomorfias moleculares) para el citocromo b. La divergencia genética entre Yuriria alta y Yuriria amatlana sp. nov. para el citocromo b fue de `DHKY = 3.8 (3.2-4.4%); entre Y. amatlana sp. nov. y Y. chapalae fue `DHKY = 5 (4.8-5.2%) y entre Y. chapalae y Y. alta fue `DHKY = 2.6 (2.1-3.3%).OD was funded by the Chester Zoo Garden, England. We are indebted to Ivan Dibble for his support from the Hobbyist Aqualab Conservation Project (HALCP) that receives funds from European and North American aquarist associations. OD was awarded a scholarship by the Consejo Nacional de Ciencia y Tecnología.Peer reviewe

Novel genes and sex differences in COVID-19 severity.

Here we describe the results of a genome-wide study conducted in 11 939 COVID-19 positive cases with an extensive clinical information that were recruited from 34 hospitals across Spain (SCOURGE consortium). In sex-disaggregated genome-wide association studies for COVID-19 hospitalization, genome-wide significance (p &lt; 5x10-8) was crossed for variants in 3p21.31 and 21q22.11 loci only among males (p =&nbsp;1.3x10-22 and p =&nbsp;8.1x10-12, respectively), and for variants in 9q21.32 near TLE1 only among females (p =&nbsp;4.4x10-8). In a second phase, results were combined with an independent Spanish cohort (1598 COVID-19 cases and 1068 population controls), revealing in the overall analysis two novel risk loci in 9p13.3 and 19q13.12, with fine-mapping prioritized variants functionally associated with AQP3 (p =&nbsp;2.7x10-8) and ARHGAP33 (p =&nbsp;1.3x10-8), respectively. The meta-analysis of both phases with four European studies stratified by sex from the Host Genetics Initiative confirmed the association of the 3p21.31 and 21q22.11 loci predominantly in males and replicated a recently reported variant in 11p13 (ELF5, p = 4.1x10-8). Six of the COVID-19 HGI discovered loci were replicated and an HGI-based genetic risk score predicted the severity strata in SCOURGE. We also found more SNP-heritability and larger heritability differences by age (&lt;60 or ≥ 60&nbsp;years) among males than among females. Parallel genome-wide screening of inbreeding depression in SCOURGE also showed an effect of homozygosity in COVID-19 hospitalization and severity and this effect was stronger among older males. In summary, new candidate genes for COVID-19 severity and evidence supporting genetic disparities among sexes are provided

GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19

Data availability: Downloadable summary data are available through the GenOMICC data site (https://genomicc.org/data). Summary statistics are available, but without the 23andMe summary statistics, except for the 10,000 most significant hits, for which full summary statistics are available. The full GWAS summary statistics for the 23andMe discovery dataset will be made available through 23andMe to qualified researchers under an agreement with 23andMe that protects the privacy of the 23andMe participants. For further information and to apply for access to the data, see the 23andMe website (https://research.23andMe.com/dataset-access/). All individual-level genotype and whole-genome sequencing data (for both academic and commercial uses) can be accessed through the UKRI/HDR UK Outbreak Data Analysis Platform (https://odap.ac.uk). A restricted dataset for a subset of GenOMICC participants is also available through the Genomics England data service. Monocyte RNA-seq data are available under the title ‘Monocyte gene expression data’ within the Oxford University Research Archives (https://doi.org/10.5287/ora-ko7q2nq66). Sequencing data will be made freely available to organizations and researchers to conduct research in accordance with the UK Policy Framework for Health and Social Care Research through a data access agreement. Sequencing data have been deposited at the European Genome–Phenome Archive (EGA), which is hosted by the EBI and the CRG, under accession number EGAS00001007111.Extended data figures and tables are available online at https://www.nature.com/articles/s41586-023-06034-3#Sec21 .Supplementary information is available online at https://www.nature.com/articles/s41586-023-06034-3#Sec22 .Code availability: Code to calculate the imputation of P values on the basis of SNPs in linkage disequilibrium is available at GitHub (https://github.com/baillielab/GenOMICC_GWAS).Acknowledgements: We thank the members of the Banco Nacional de ADN and the GRA@CE cohort group; and the research participants and employees of 23andMe for making this work possible. A full list of contributors who have provided data that were collated in the HGI project, including previous iterations, is available online (https://www.covid19hg.org/acknowledgements).Change history: 11 July 2023: A Correction to this paper has been published at: https://doi.org/10.1038/s41586-023-06383-z. -- In the version of this article initially published, the name of Ana Margarita Baldión-Elorza, of the SCOURGE Consortium, appeared incorrectly (as Ana María Baldion) and has now been amended in the HTML and PDF versions of the article.Copyright © The Author(s) 2023, Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown1 to be highly efficient for discovery of genetic associations2. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group3. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte–macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).GenOMICC was funded by Sepsis Research (the Fiona Elizabeth Agnew Trust), the Intensive Care Society, a Wellcome Trust Senior Research Fellowship (to J.K.B., 223164/Z/21/Z), the Department of Health and Social Care (DHSC), Illumina, LifeArc, the Medical Research Council, UKRI, a BBSRC Institute Program Support Grant to the Roslin Institute (BBS/E/D/20002172, BBS/E/D/10002070 and BBS/E/D/30002275) and UKRI grants MC_PC_20004, MC_PC_19025, MC_PC_1905 and MRNO2995X/1. A.D.B. acknowledges funding from the Wellcome PhD training fellowship for clinicians (204979/Z/16/Z), the Edinburgh Clinical Academic Track (ECAT) programme. This research is supported in part by the Data and Connectivity National Core Study, led by Health Data Research UK in partnership with the Office for National Statistics and funded by UK Research and Innovation (grant MC_PC_20029). Laboratory work was funded by a Wellcome Intermediate Clinical Fellowship to B.F. (201488/Z/16/Z). We acknowledge the staff at NHS Digital, Public Health England and the Intensive Care National Audit and Research Centre who provided clinical data on the participants; and the National Institute for Healthcare Research Clinical Research Network (NIHR CRN) and the Chief Scientist’s Office (Scotland), who facilitate recruitment into research studies in NHS hospitals, and to the global ISARIC and InFACT consortia. GenOMICC genotype controls were obtained using UK Biobank Resource under project 788 funded by Roslin Institute Strategic Programme Grants from the BBSRC (BBS/E/D/10002070 and BBS/E/D/30002275) and Health Data Research UK (HDR-9004 and HDR-9003). UK Biobank data were used in the GSMR analyses presented here under project 66982. The UK Biobank was established by the Wellcome Trust medical charity, Medical Research Council, Department of Health, Scottish Government and the Northwest Regional Development Agency. It has also had funding from the Welsh Assembly Government, British Heart Foundation and Diabetes UK. The work of L.K. was supported by an RCUK Innovation Fellowship from the National Productivity Investment Fund (MR/R026408/1). J.Y. is supported by the Westlake Education Foundation. SCOURGE is funded by the Instituto de Salud Carlos III (COV20_00622 to A.C., PI20/00876 to C.F.), European Union (ERDF) ‘A way of making Europe’, Fundación Amancio Ortega, Banco de Santander (to A.C.), Cabildo Insular de Tenerife (CGIEU0000219140 ‘Apuestas científicas del ITER para colaborar en la lucha contra la COVID-19’ to C.F.) and Fundación Canaria Instituto de Investigación Sanitaria de Canarias (PIFIISC20/57 to C.F.). We also acknowledge the contribution of the Centro National de Genotipado (CEGEN) and Centro de Supercomputación de Galicia (CESGA) for funding this project by providing supercomputing infrastructures. A.D.L. is a recipient of fellowships from the National Council for Scientific and Technological Development (CNPq)-Brazil (309173/2019-1 and 201527/2020-0)

Novel genes and sex differences in COVID-19 severity.

Here we describe the results of a genome-wide study conducted in 11 939 COVID-19 positive cases with an extensive clinical information that were recruited from 34 hospitals across Spain (SCOURGE consortium). In sex-disaggregated genome-wide association studies for COVID-19 hospitalization, genome-wide significance (p < 5x10-8) was crossed for variants in 3p21.31 and 21q22.11 loci only among males (p = 1.3x10-22 and p = 8.1x10-12, respectively), and for variants in 9q21.32 near TLE1 only among females (p = 4.4x10-8). In a second phase, results were combined with an independent Spanish cohort (1598 COVID-19 cases and 1068 population controls), revealing in the overall analysis two novel risk loci in 9p13.3 and 19q13.12, with fine-mapping prioritized variants functionally associated with AQP3 (p = 2.7x10-8) and ARHGAP33 (p = 1.3x10-8), respectively. The meta-analysis of both phases with four European studies stratified by sex from the Host Genetics Initiative confirmed the association of the 3p21.31 and 21q22.11 loci predominantly in males and replicated a recently reported variant in 11p13 (ELF5, p = 4.1x10-8). Six of the COVID-19 HGI discovered loci were replicated and an HGI-based genetic risk score predicted the severity strata in SCOURGE. We also found more SNP-heritability and larger heritability differences by age (<60 or ≥ 60 years) among males than among females. Parallel genome-wide screening of inbreeding depression in SCOURGE also showed an effect of homozygosity in COVID-19 hospitalization and severity and this effect was stronger among older males. In summary, new candidate genes for COVID-19 severity and evidence supporting genetic disparities among sexes are provided