Mendes, S. L. | bioRxiv Science

bioRxiv2025

Dating and quantifying past gene flow due to hybridization events in Iberian chubs

Hybridization - the successful reproductive cross between individuals from different species - is increasingly recognized as a relatively common phenomenon in nature, mostly due to the increasing availability of genomic data for many organisms and the development of sophisticated methods to detect past gene flow. As a result, evidence of past gene flow has been detected in the genomes of many species, allowing us to investigate the evolutionary forces that act upon hybrid genomes. Biological systems where multiple instances of hybridization have been detected at different time scales are especially useful for this, as they allow investigating the effects of selection and recombination at different time scales post-hybridization. The Iberian chubs (Squalius spp.) present an ideal study system for this. In this group of primary fish inhabiting the rivers of the Iberian Peninsula, multiple instances of past hybridization at different geographical and time scales were reported between different species. However, before we investigate the effects of selection and recombination, it is crucial that we date the hybridization events and quantify the contribution from each parental species. In this study, we infer the demographic history of two Iberian chub hybrid lineages, one resulting from a proposed ancient hybridization event (S. pyrenaicus) and another potentially much more recent (Sao Martinho). We generated whole genome resequencing data for 52 individuals from the two hybrid lineages and their putative parental populations. Our demographic modelling results confirm the hypothesis of ancient hybridization between S. carolitertii and S. tartessicus around 600,000-800,000 years ago, giving rise to the S. pyrenaicus lineage. We also confirm that S. carolitertii is the major parental, with S. tartessicus only contributing <10% to the S. pyrenaicus genome. Furthermore, we confirm the more recent hybridization between S. caetobrigus and S. pyrenaicus (around 4500 years ago) in the Sao Martinho population. We observe similar contributions from both parental species (around 50%) to the genome of the individuals of this population. Overall, our results give us a deeper understanding of how and when these past gene flow events happened and the contributions of each parental species to the genomes of the individuals of the hybrid lineages.

evolutionary biology↗

bioRxiv2020

Detection of Plasmodium vivax in a liver sample of a howler-monkey: one evidence more in favour of the identity between Plasmodium simium and P. vivax

IntroductionThe residual malaria of Atlantic Forest systems in Brazil occurs as an endemic disease with low frequency of cases. The chronological and spatial distance among the cases indicate an absence of fitness to the classical malaria cycle. This peculiar condition raised the suspicion of a reservoir, possibly the non-human primates. Simian and human malaria occur at the same places in that region, and there is already evidence of molecular identity between the simian parasites, Plasmodium simium and Plasmodium brasilianum, and the human parasites, Plasmodium vivax and Plasmodium malariae, respectively. Two different SNPs identified in the COX1 region of the Plasmodium vivax/simium of the Atlantic Forest reinforced its characterization as a zoonotic parasite. This finding supported the development of a PCR-RFLP protocol to identify such polymorphisms, and to monitor zoonotic malaria transmission. MethodsIn the present work, we tested the above-mentioned PCR-RFLP protocol in unprecedented mosquitoes and simian samples collected in Espirito Santo State, Brazil (ES). ResultsThe parasite found in the simian sample was P. vivax, contrary to what the protocol should indicate. In the mosquito samples, the protocol disclosed both forms of the parasite. ConclusionThis result suggests that the previously published pair of SNPs, and, consequently, the PCR-RFLP protocol, are not able to distinguish the dynamics of Plasmodium spp. circulation in the Atlantic Forest endemic area of ES.

molecular biology↗