Contrasting Patterns of Differentiation Inferred from Traditional Genetic Markers in the Process of Speciation

Populations of Drosophila serido from various geographic origins were characterized using four markers: morphology of male genitals, inversions in polytene chromosomes, morphology and heterochromatin of metaphase chromosomes, and reproductive isolation. In all cases the species shows itself to be polytypic, but the geographic distribution patterns vary according to the marker utilized. The validity of the use of these parameters for taxonomic purposes and/or for understanding the mechanisms involved in the differentiation among populations is discussed

Chromosomal phylogeny of the Drosophila fasciola species subgroup revisited (Diptera, Drosophilidae)

The analysis of polytene chromosomes in 26 strains of seven species in the Drosophila fasciola subgroup, from several locations in Brazil, in addition to strains of two species belonging to the Drosophila mulleri subgroup (D. aldrichi and D. mulleri), enabled us to determine that the 3c inversion found in the latter species differ in one of its break points from that present in the species of the fasciola subgroup. Therefore, a change in the mulleri complex denomination from inversion 3c to inversion 3u is proposed. Accordingly, the fasciola subgroup is no longer a lesser phylogenetic part within the mulleri subgroup. Rather, it is directly related to the likely ancestor of the repleta group, called Primitive I. This information removes the main obstacle to considering the Drosophila fasciola subgroup as an ancestral group within the Drosophila repleta species group, according to the hypothesis of Throckmorton. Our data also support the conclusion that D. onca and D. carolinae are closely related species based on one new inversion in chromosome 4 (4f²), in both species. D. fascioloides and D. ellisoni also form a pair of sister species based on the presence of fusions of chromosomes 2-4 and 3-5. D. rosinae is related only to the likely ancestor of the fasciola subgroup, where the 3c inversion was fixed

Intra- and interspecific divergence in the nuclear sequences of the clock gene period in species of the Drosophila buzzatii cluster

We have measured nucleotide variation in the CLOCK/CYCLE heterodimer inhibition domain (CCID) of the clock X-linked gene period in seven species belonging to the Drosophila buzzatii cluster, namely D. buzzatii, Drosophila koepferae, Drosophila antonietae, Drosophila serido, Drosophila gouveai, Drosophila seriema and Drosophila borborema. We detected that the purifying selection is the main force driving the sequence evolution in period, in agreement with the important role of CCID in clock machinery. Our survey revealed that period provides valuable phylogenetic information that allowed to resolve phylogenetic relationships among D. gouveai, D. borborema and D. seriema, which composed a polytomic clade in preliminary studies. The analysis of patterns of intraspecific variation revealed two different lineages of period in D. koepferae, probably reflecting introgressive hybridization from D. buzzatii, in concordance with previous molecular data.CAPESCNPqFINEPUniversidade de São Paulo USPFAPESP[03/05031-0]FAPESP[04/08565-8]FAPESP[05/51780-0]ANPCyTUniversidad de Buenos Aires, ArgentinaCONICE

Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

BackgroundWe previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in similar to 80% of cases.MethodsWe report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded.ResultsNo gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P=1.1x10(-4)) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR=3.70[95%CI 1.3-8.2], P=2.1x10(-4)). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR=19.65[95%CI 2.1-2635.4], P=3.4x10(-3)), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR=4.40[9%CI 2.3-8.4], P=7.7x10(-8)). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD]=43.3 [20.3] years) than the other patients (56.0 [17.3] years; P=1.68x10(-5)).ConclusionsRare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old

Correction: Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

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