Biology subjects

Godinho, R.

Publications and source records attributed to Godinho, R..

3 recordsLinked to original sources

bioRxiv2022

On taming the effect of transcript level intra-condition count variation during differential expression analysis: a story of dogs, foxes and wolves

The evolution of RNA-seq technologies has yielded datasets of high scientific value that are often generated as condition associated biological replicates within differential expression studies. As the number of replicates increase, so to does confidence in identifying differentially expressed transcripts. With rapidly expanding RNA-seq data archives there is opportunity to augment replicate numbers when conditions of interest overlap at an inter-study level. Despite correction procedures for estimating transcript abundance, a remaining source of error is transcript level intra-condition count variation; as partially indicated by the disjointed results between differential expression analysis tools. Such variation is amplified at an inter-study level. Here, we present TVscript, a tool that removes reference-based transcripts associated with intra-condition variation above specified thresholds. With this tool we explore the effects of removing transcripts associated with varying degrees of intra-condition variation on differential expression analysis. This is done in relation to inter- and intra-study datasets representing brain samples of dogs, wolves and foxes (wolves vs. dogs and aggressive vs. tame foxes). We demonstrate that 20% of the transcripts identified as being differentially expressed are associated with high levels of intra-condition variation. This is an over-representation relative to the reference set. As transcripts harbouring such variation are removed from the reference prior to differential expression analysis a discordance from 26 to 40% in the lists of differentially expressed transcripts is observed when compared to those obtained using the non-filtered reference. For our data, the removal of transcripts possessing intra-condition variation values within (and above) the 97th and 95th percentiles, for wolves vs. dogs and aggressive vs. tame foxes, maximized the detection of differentially expressed transcripts as a result of alterations within gene-wise dispersion estimates. Through this analysis the support for seven genes with potential for being involved with selection for tameness is provided. TVscript is available at: https://sourceforge.net/projects/tvscript/.

bioinformatics↗

bioRxiv2022

Genomes of the extinct Sicilian wolf reveal a complex history of isolation and admixture with ancient dogs

The Sicilian wolf represented the only population of wolves living on a Mediterranean island until the first half of the twentieth century (1930s-1960s) 1-7. Previous studies hypothesised that they remained isolated from mainland wolves from the end of the Last Glacial Maximum (LGM) 8,9, until human persecutions led them to extinction 1-7. There are only seven known Sicilian wolf specimens from the 19th and 20th century preserved in museums in Italy and recent morphometric analyses assigned them to the new subspecies Canis lupus cristaldii 10. To better understand the origins of the Sicilian wolf, and its relationship to other wolf populations, we sequenced four whole genomes (3.8x-11.6x) and five mitogenomes. We investigated the relationship between Sicilian wolves and other modern breeds to identify potential admixture. Furthermore, considering that the last land-bridge between Sicily and Italy disappeared after the LGM 11, around 17 kya, we explored the possibility that the Sicilian wolf retained ancestry from ancient wolf and dog lineages. Additionally, we explored whether the long-term isolation might have affected the genomic diversity, inbreeding levels and genetic load of the Sicilian wolf. Our findings show that the Sicilian wolves shared most ancestry with the modern Italian wolf population but are better modelled as admixed with European dog breeds, and shared traces of Eneolithic and Bronze age European dogs. We also find signatures of severe inbreeding and low genomic diversity at population and individual levels due to long-term isolation and drift, suggesting also low effective population size.

genomics↗

bioRxiv2020

Convergent evolution of increased urine concentrating ability in desert mammals

One of the most celebrated textbook examples of physiological adaptations to desert environments is the unique ability that desert mammals have to produce hyperosmotic urine. Commonly perceived as an adaptation mainly observed in small rodents, the extent to which urine concentrating ability has independently evolved in distinct lineages, including medium-sized and large desert mammals, has not previously been assessed using modern phylogenetic approaches. Here, we explicitly test the general hypothesis that desert-dwelling mammals have evolved increased ability to concentrate urine compared to non-desert species, controlling for body mass and other covariates. Phylogenetic generalized least-squares models show that the mean aridity index of a species distribution range largely predicts its urine concentrating ability, even when accounting for body mass differences and phylogenetic correlations. In contrast, we find much weaker correlations between mass-adjusted basal metabolic rate and environmental variables.

evolutionary biology↗