Biology subjects

Freitas, L.

Publications and source records attributed to Freitas, L..

5 recordsLinked to original sources

bioRxiv2024

Bayesian Selection of Relaxed-clock Models:Distinguishing Between Independent and Autocorrelated Rates

In Bayesian molecular-clock dating of species divergences, rate models are used to construct the prior on the molecular evolutionary rates for branches in the phylogeny, with independent and autocorrelated rate models being commonly used. The two classes of models, however, can result in markedly different divergence time estimates for the same dataset, and thus selecting the best rate model appears important for obtaining reliable inferences of divergence times. However, the properties of Bayesian rate model selection are not well understood, in particular when the number of sequence partitions analysed increases and when age calibrations (such as fossil calibrations) are misspecified. Furthermore, Bayesian rate model selection is computationally expensive as it requires calculation of marginal likelihoods by MCMC sampling, and therefore methods that can speed up the model selection procedure without compromising its accuracy are desirable. In this study, we use a combination of computer simulations and real data analysis to investigate the statistical behaviour of Bayesian rate model selection and we also explore approximations of the likelihood to improve computational efficiency in large phylogenomic datasets. Our simulations demonstrate that the posterior probability for the correct rate model converges to one as more molecular sequence partitions are analysed and when no calibrations are used, as expected due to asymptotic Bayesian model selection theory. Furthermore, we also show the model selection procedure is robust to slight misspecification of calibrations, and reliable inference of the correct rate model is possible in this case. However, we show that when calibrations are seriously misspecified, calculated model probabilities are completely wrong and may converge to one for the wrong rate model. Finally, we demonstrate that approximating the phylogenetic likelihood under an arcsine branch-length transform can dramatically reduce the computational cost of rate model selection without compromising accuracy. We test the approximate procedure on two large phylogenies of primates (372 species) and flowering plants (644 species), replicating results obtained on smaller datasets using exact likelihood. Our findings and methodology can assist users in selecting the optimal rate model for estimating times and rates along the Tree of Life.

evolutionary biology↗

bioRxiv2024

Long term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring of mosquitoes and metatranscriptomics

Arbovirus surveillance of wild-caught mosquitoes is an affordable and sensitive means of monitoring virus transmission dynamics at various spatial-temporal scales, and emergence and re-emergence during epidemic and interepidemic periods. A variety of molecular diagnostics for arbovirus screening of mosquitoes (known as xeno-monitoring) are available, but most provide limited information about virus diversity. PCR-based screening coupled with metatranscriptomics is an increasingly affordable and sensitive pipeline for integrating complete viral genome sequencing into surveillance programs. This enables large-scale, high-throughput arbovirus screening from diverse samples. We collected mosquitoes in CO2-baited light traps from five urban parks in Brisbane from March 2021 to May 2022. Mosquito pools of [≤]200 specimens were screened for alphaviruses and flaviviruses using virus genus-specific primers and reverse transcription quantitative PCR (qRT-PCR). A subset of virus-positive samples was then processed using a mosquito-specific ribosomal RNA depletion method and then sequenced on the Illumina NextSeq. Overall, 54,670 mosquitoes, representing 26 species were screened in 382 pools. Thirty detections of arboviruses were made in 28 pools. Twenty of these positive pools were further characterised using meta-transcriptomics generating 18 full-length genomes. These full-length sequences belonged to four medically relevant arboviruses: Barmah Forest, Ross River, Sindbis-like and Stratford viruses. Phylogenetic and evolutionary analyses revealed the evolutionary progression of arbovirus lineages over the last 100 years, highlighting long-distance dispersal across the Australian continent and continuous circulation characterised by constant turnover of virus lineages.

genomics↗

bioRxiv2023

Adaptive evolution of hearing genes suggests multiple evolutionary paths for dolphin echolocation in different environments.

BackgroundEcholocation was a key development in toothed whale evolution, enabling their adaptation and diversification across various environments. Previous bioacoustic and morphological studies suggest that environmental pressures have influenced the evolution of echolocation in toothed whales. This hypothesis demands further investigation, especially regarding the molecular mechanisms involved in the adaptive radiation of toothed whales across multiple habitats. Here we show that the coding sequences of four hearing genes involved in echolocation (CDH23, SLC26A5, TMC1, and CLDN14) have different signatures of molecular evolution among riverine, coastal, and oceanic dolphins, suggesting that the evolutionary constraints of these habitats shaped the underlying genetic diversity of the toothed whale sonar. ResultsOur comparative analysis across 37 odontocete species revealed patterns of accelerated evolution within coastal and riverine lineages, supporting the hypothesis that shallow habitats pose specific selective pressures to sonar propagation, which are not found in the deep ocean. All toothed whales with genes evolving under positive selection are shallow coastal species, including three species that have recently diverged from freshwater lineages (Cephalorhynchus commersonii, Sotalia guianensis, and Orcaella heinsohni - CDH23), and three species that operate specialized Narrow Band High Frequency (NBHF) Sonars (Phocoena sinus - SLC26A5, Neophocaena phocaenoides and Cephalorhynchus commersonii - CDH23). For river dolphins and deep-diving toothed whales, we found signatures of positive selection and molecular convergence affecting specific sites on CDH23, TMC1, and SLC26A5. Positively selected sites (PSS) were different in number, identity, and substitution rates (dN/dS) across riverine, coastal, and oceanic toothed whales. ConclusionHere we shed light on potential molecular mechanisms underlying the diversification of toothed whale echolocation. Our results suggest that toothed whale hearing genes changed under different selective pressures in coastal, riverine, and oceanic environments.

molecular biology↗

bioRxiv2021

Positive selection in multiple salivary gland proteins of Anophelinae reveals potential targets for vector control

Anopheles is a genus belonging to the Culicidae family, which has great medical importance due to its role as a vector of Plasmodium, the parasite responsible for malaria. From Anopheles functional genomics, great focus has been given to the salivary gland proteins (SGPs) group. This class of proteins is essential to blood-feeding behavior as they have attributes such as vasodilators and anti-clotting properties. Recently, a comprehensive review on Anopheles SGPs was performed, however the authors did not deeply explore the adaptive molecular evolution of these genes. In this context, this work aimed to perform a more detailed analysis of the adaptive molecular evolution of SGPs in Anopheles, carrying out positive selection and gene families evolution analysis on 824 SGPs. Our results show that most SGPs have positively selected sites that can be used as targets in the development of new strategies for vector control. Notably, we were not able to find any evidence of an accelerated shift in the copy-number variation of SGPs compared with other proteins, as suggested in previous works. Significance StatementSalivary gland proteins (SGPs) are essential to blood-feeding behavior in Anopheles and they are the most studied class of proteins in blood-feeding insects. However a proper molecular evolution analysis on SGPs in Anopheles is missing. In our analyses we observed that most SGPs have positively selected sites and we were not able to find any evidence of an accelerated shift in the copy-number of SGPs compared with other proteins, as stated in the literature. Our results can open new venues in the development of new strategies for vector control.

evolutionary biology↗

bioRxiv2017

Neonatal Zika virus infection causes epileptic seizures, viral persistence and long-term behavioral impairment

A causal relationship between congenital Zika virus (ZIKV) exposure and microcephaly and other neurological disorders have been established, but long-term consequences of infection are still unknown. We evaluated acute and late neuropathological and behavioral consequences of ZIKV infection in a neonatal immunocompetent mouse model. ZIKV showed brain tropism, causing post-natal microcephaly and several behavioral dysfunctions. During the acute phase of infection, mice developed very frequent epileptic seizures, which are consistently reduced by TNF- neutralization. Although adult animals recover from seizures, they become more susceptible to chemically-induced crises. Intriguingly, the virus remained actively replicating in adult animals, which show persistent necrosis and calcifications in the mice brain. Altogether the results reveal late consequences of neonatal ZIKV exposure and suggest the early inhibition of neuroinflammation as a potential treatment.

neuroscience↗