Evolutionary ecology of hares (Lepus spp.) from northwest Africa: the existence of cryptic species and description of a new species (Lepus saharae sp. nov.)

Objective: We examine the different pressures that lead to the occurrence of new species and thus to their phylogenies. From an evolutionary ecology perspective, we examine the phylogenetic relationships of different lineages, as well as the evolutionary pressures that lead to them and, in some cases, mask them. Organisms and locales: Hares (Lepus spp.) in northwest Africa that are morphologically similar, which, superficially, makes it appear that there is only one species. Methods: We describe different populations of hares in northwest Africa. We describe the morphology of a new species and provide photographs of specimens from across the study area. We analyse five mitochondrial DNA fragments. Results: Mitochondrial DNA analysis revealed the presence of three Lepus species which are different from both Lepus capensis and L. victoriae and which have contiguous, partially overlapping geographical ranges. One of the species, found in the western Sahara (Morocco), is new (Lepus saharae sp. nov.). The other two species (Lepus mediterraneus Wagner, 1841 and Lepus schlumbergeri Remy-St. Loup, 1894) inhabit the northern and central regions of Morocco. The distributions of at least two of the three species extend to countries other than Morocco. Various eco-evolutionary pressures have masked this diversity until now. Certainly, the species have had to adapt to different habitats that include mountains and desert; and isolation of populations by distance, or because of climatic or geographical barriers has led – or at least facilitated – them to appear different. Yet some evolutionary pressures have made them converge morphologically, making it appear that there is only one species

Contacts in the last 90,000 years over the Strait of Gibraltar evidenced by genetic analysis of wild boar (Sus scrofa)

[EN] Contacts across the Strait of Gibraltar in the Pleistocene have been studied in different research papers, which have demonstrated that this apparent barrier has been permeable to human and fauna movements in both directions. Our study, based on the genetic analysis of wild boar (Sus scrofa), suggests that there has been contact between Africa and Europe through the Strait of Gibraltar in the Late Pleistocene (at least in the last 90,000 years), as shown by the partial analysis of mitochondrial DNA. Cytochrome b and the control region from North African wild boar indicate a close relationship with European wild boar, and even some specimens belong to a common haplotype in Europe. The analyses suggest the transformation of the wild boar phylogeography in North Africa by the emergence of a natural communication route in times when sea levels fell due to climatic changes, and possibly through human action, since contacts coincide with both the Last Glacial period and the increasing human dispersion via the strait.This study was supported by The Emirates Centre for Wildlife Propagation (Morocco). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Soria-Boix, C.; Donat-Torres, MP.; Urios, V. (2017). Contacts in the last 90,000 years over the Strait of Gibraltar evidenced by genetic analysis of wild boar (Sus scrofa). PLoS ONE. 12(7). doi:10.1371/journal.pone.0181929S12

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

Zoogeografía y ecología evolutiva del jabalí (Sus scrofa) y las liebres (Lepus spp.) en el noroeste de África

Debido a las singulares características del noroeste de África, esta zona constituye un lugar de estudio interesante para entender cómo los cambios que se producen en el entorno pueden afectar a la distribución de las especies y a su historia evolutiva. Para ello es importante integrar varias herramientas para el estudio de la diversidad faunística. El estudio de las especies desde el punto de vista de la ecología evolutiva y la zoogeografía, junto a la realización de análisis moleculares, sirve tanto para entender por qué las especies han llegado a ser como son en la actualidad, como para entender los procesos evolutivos de cada especie. Esto se puede aplicar, por ejemplo, a la hora de tomar medidas correctas para proteger a una especie que se encuentre amenazada. Para esta tesis los animales seleccionados fueron el jabalí (Sus scrofa) y las liebres (Lepus spp.). Para los análisis del jabalí usamos ADN mitocondrial (citocromo b y región control). Los árboles filogenéticos bayesianos y los networks mostraron una estrecha relación entre los ejemplares de ambos continentes, e incluso a algunos ejemplares africanos compartiendo un haplotipo que es común en ejemplares de Europa. De los árboles filogenéticos también se obtuvieron los tiempos de divergencia, que dieron más datos de cuándo debieron de ocurrir aproximadamente estos acontecimientos. Respecto a las liebres, en el noroeste de África actualmente se considera que está presente la liebre del cabo (Lepus capensis); al sur del área de estudio está presente la liebre de la sabana africana (Lepus victoriae). En este trabajo nos adentramos en el análisis de la ecología evolutiva de las liebres con ayuda de análisis moleculares. Estudiamos la posible presencia de otras especies distintas a las mencionadas, y de especies crípticas en el área de estudio, teniendo en cuenta las presiones evolutivas que han podido ocasiones que la diversidad existente haya pasado desapercibida hasta la actualidad

Evolutionary ecology of hares (Lepus spp.) from northwestern Africa; The problem of cryptic species and the description of a new species (Lepus saharae sp. nov.)

[EN] Objective: We examine the different pressures that lead to the occurrence of new species and thus to their phylogenies. From an evolutionary ecology perspective, we examine the phylogenetic relationships of different lineages, as well as the evolutionary pressures that lead to them and, in some cases, mask them. Organisms and locales: Hares (Lepus spp.) in northwest Africa that are morphologically similar, which, superficially, makes it appear that there is only one species. Methods: We describe different populations of hares in northwest Africa. We describe the morphology of a new species and provide photographs of specimens from across the study area. We analyse five mitochondrial DNA fragments. Results: Mitochondrial DNA analysis revealed the presence of three Lepus species which are different from both Lepus capensis and L. victoriae and which have contiguous, partially overlapping geographical ranges. One of the species, found in the western Sahara (Morocco), is new (Lepus saharae sp. nov.). The other two species (Lepus mediterraneus Wagner, 1841 and Lepus schlumbergeri Remy-St. Loup, 1894) inhabit the northern and central regions of Morocco. The distributions of at least two of the three species extend to countries other than Morocco. Various eco-evolutionary pressures have masked this diversity until now. Certainly, the species have had to adapt to different habitats that include mountains and desert; and isolation of populations by distance, or because of climatic or geographical barriers has led - or at least facilitated - them to appear different. Yet some evolutionary pressures have made them converge morphologically, making it appear that there is only one species.Soria-Boix, C.; Donat-Torres, MP.; Rguibi Idrissi, H.; Urios, V. (2019). Evolutionary ecology of hares (Lepus spp.) from northwestern Africa; The problem of cryptic species and the description of a new species (Lepus saharae sp. nov.). Evolutionary Ecology Research (Online). 20(5):537-555. http://hdl.handle.net/10251/167876S53755520

Median-joining networks based on mtDNA.

<p>(A) The cytochrome b network was constructed with 308 wild boar sequences (1,030 bp). (B) The control region network was constructed with 328 wild boar sequences (534 bp).</p

Contemporary use of cefazolin for MSSA infective endocarditis: analysis of a national prospective cohort

Objectives: This study aimed to assess the real use of cefazolin for methicillin-susceptible Staphylococcus aureus (MSSA) infective endocarditis (IE) in the Spanish National Endocarditis Database (GAMES) and to compare it with antistaphylococcal penicillin (ASP). Methods: Prospective cohort study with retrospective analysis of a cohort of MSSA IE treated with cloxacillin and/or cefazolin. Outcomes assessed were relapse; intra-hospital, overall, and endocarditis-related mortality; and adverse events. Risk of renal toxicity with each treatment was evaluated separately. Results: We included 631 IE episodes caused by MSSA treated with cloxacillin and/or cefazolin. Antibiotic treatment was cloxacillin, cefazolin, or both in 537 (85%), 57 (9%), and 37 (6%) episodes, respectively. Patients treated with cefazolin had significantly higher rates of comorbidities (median Charlson Index 7, P <0.01) and previous renal failure (57.9%, P <0.01). Patients treated with cloxacillin presented higher rates of septic shock (25%, P = 0.033) and new-onset or worsening renal failure (47.3%, P = 0.024) with significantly higher rates of in-hospital mortality (38.5%, P = 0.017). One-year IE-related mortality and rate of relapses were similar between treatment groups. None of the treatments were identified as risk or protective factors. Conclusion: Our results suggest that cefazolin is a valuable option for the treatment of MSSA IE, without differences in 1-year mortality or relapses compared with cloxacillin, and might be considered equally effective

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

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