Biology subjects

D'Agostino, D.

Publications and source records attributed to D'Agostino, D..

7 recordsLinked to original sources

bioRxiv2025

Using the ancestral recombination graph to study the history of rare variants in founder populations

Gene genealogies represent the ancestry of a sample and are often encoded as ancestral recombination graphs (ARG). It has recently become possible to infer these gene genealogies from sequencing or genotyping data and use them for evolutionary and statistical genetics. Unfortunately, inferred gene genealogies can be noisy and subject to biases, making their applications more challenging. This project aims to study the application of ARG methods to systematically impute and trace the transmission of all disease variants in founder populations where long-shared haplotypes allow for accurate timing of relatedness. We applied these methods to the population of Quebec, where multiple founder events led to an uneven distribution of pathogenic variants across regions and where extensive population pedigrees are available. We validated our approach with nine founder mutations for the SLSJ region, demonstrating high accuracy for mutation age, imputation, and regional frequency estimation. Moreover, we showed that this subset of high-quality carriers is sufficient to capture previously described associations with pathogenic variants in the LPL gene. This method systematically characterizes rare variants in founder populations, establishing a fast and accurate approach to inform genetic screening programs.

genetics↗

bioRxiv2022

On the origins of phenotypic parallelism in benthic and limnetic stickleback

Rapid evolution of similar phenotypes in similar environments, giving rise to in situ parallel adaptation, is an important hallmark of ecological speciation. However, what appears to be in situ adaptation can also arise by dispersal of divergent lineages from elsewhere. We test whether two contrasting phenotypes repeatedly evolved in parallel, or have a single origin, in an archetypal example of ecological adaptive radiation: benthic-limnetic three-spined stickleback (Gasterosteus aculeatus) across species-pair and solitary lakes in British Columbia. We identify two genomic clusters across freshwater populations, which differ in benthic-limnetic divergent phenotypic traits and separate benthic from limnetic individuals in species pair lakes. Phylogenetic reconstruction and niche evolution modelling both suggest a single evolutionary origin for each of these clusters. We detected strong phylogenetic signal in benthic-limnetic divergent traits, suggesting they are ancestrally retained. Accounting for ancestral state retention, we identify local adaptation of body armour due to the presence of an intraguild predator, the sculpin (Cottus asper) and environmental effects of lake depth and pH on body size. Taken together, our results imply a predominant role for retention of ancestral characteristics in driving trait distribution, with further selection imposed on some traits by environmental factors.

evolutionary biology↗

bioRxiv2020

Growth impacts in a changing ocean: insights from two coral reef fishes in an extreme environment

Determining the life history consequences for fishes living in extreme and variable environments will be vital in predicting the likely impacts of ongoing climate change on reef fish demography. Here, we compare size-at-age and maximum body size of two common reef fish species (Lutjanus ehrenbergii and Pomacanthus maculosus) between the environmentally extreme Arabian/Persian Gulf (‘Arabian Gulf’) and adjacent comparably benign Oman Sea. Additionally, we use otolith increment width profiles to investigate the influence of temperature, salinity and productivity on the individual growth rates. Individuals of both species showed smaller size-at-age and lower maximum size in the Arabian Gulf compared to conspecifics in the less extreme and less variable environment of the Oman Sea, suggesting a life-history trade-off between size and metabolic demands. Salinity was the best environmental predictor of interannual growth across species and regions, with low growth corresponding to more saline conditions. However, salinity had a weaker negative effect on interannual growth of fishes in the Arabian Gulf than in the Oman Sea, indicating Arabian Gulf populations may be better able to acclimate to changing environmental conditions. Temperature had a weak positive effect on the interannual growth of fishes in the Arabian Gulf, suggesting that these populations may still be living within their thermal windows. Our results highlight the potential importance of osmoregulatory cost in impacting growth, and the need to consider the effect of multiple stressors when investigating the consequences of future climate change on fish demography.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗

bioRxiv2020

Behavioural traits and feeding ecology of Mediterranean lionfish and native species naivete to lionfish predation

The detrimental effects of invasion by Indo-Pacific lionfish (Pterois volitans/miles) on western Atlantic fishes have spurred concerns for Mediterranean fish biodiversity, where a Lessepsian invasion of lionfish has recently begun. In order to assess the potential impact on biodiversity, we examine key behavioural and ecological traits of lionfish, and the resident fish community in the Mediterranean, that may contribute to lionfish invasion success. We focus on Cyprus, where lionfish populations were first sighted in 2012 and have now established abundant and stable populations. Using field observations, we examine lionfish predatory behaviour and feeding ecology, and resident fish species naivete to hunting lionfish. Our findings suggest that lionfish in the Mediterranean are crepuscular generalist predators, with prey targeted dominated by small-bodied benthic or bentho-pelagic associated species. Such prey are more likely to be native than introduced (Lessepsian) fishes, with native prey fishes showing greater naivete towards lionfish than Lessepsian prey species. Notably, one of the Mediterraneans key ecological fish species (the native damselfish Chromis chromis), showed the highest level of naivete and was the most heavily targeted prey. Overall, lionfish in the Mediterranean show similar predatory behaviour and ecology to their western Atlantic counterparts. Although the Mediterranean invasion is still relatively recent, it may result in a similar disruption to reef fish biomass to that recorded in the Atlantic, with impact to the structure and biodiversity of reef fish communities and the services they provide.

ecology↗

bioRxiv2019

Metabolic switching is impaired by aging and facilitated by ketosis independent of glycogen

The ability to switch between glycolysis and ketosis promotes survival by enabling metabolism through fat oxidation during periods of fasting. Carbohydrate restriction or stress can also elicit metabolic switching. Keto-adapting from glycolysis is delayed in aged rats, but factors mediating this age-related impairment have not been identified. We measured metabolic switching between glycolysis and ketosis, as well as glycogen dynamics, in young and aged rats undergoing time-restricted feeding (TRF) with a standard diet or a low carbohydrate ketogenic diet (KD). TRF alone reversed markers of insulin-related metabolic deficits and accelerated metabolic switching in aged animals. A KD+TRF, however, provided additive benefits on these variables. Remarkably, the ability to keto-adapt was not related to glycogen levels and KD-fed rats showed an enhanced elevation in glucose following epinephrine administration. This study provides new insights into the mechanisms of keto-adaptation demonstrating the utility of dietary interventions to treat metabolic impairments across the lifespan.

biochemistry↗

bioRxiv2019

Intercontinental genomic parallelism in multiple adaptive radiations

Parallelism, the evolution of similar traits in populations diversifying in similar conditions, provides good evidence of adaptation by natural selection. Many studies of parallelism have focused on comparisons of strongly different ecotypes or sharply contrasting environments, defined a priori, which could upwardly bias the apparent prevalence of parallelism. Here, we estimated genomic parallelism associated with individual components of environmental and phenotypic variation at an intercontinental scale across four adaptive radiations of the three-spined stickleback (Gasterosteus aculeatus), by associating genome-wide allele frequencies with continuous distributions of environmental and phenotypic variation. We found that genomic parallelism was well predicted by parallelism of phenotype-environment associations, suggesting that a quantitative characterization of phenotypes and environments can provide a good prediction of expected genomic parallelism. Further, we examined the explanatory power of genetic, phenotypic, and environmental similarity in predicting parallelism. We found that parallelism tended to be greater for geographically proximate, genetically similar radiations, highlighting the significant contingency of standing variation in the early stages of adaptive radiations, before new mutations accumulate. However, we also demonstrate that distance within multivariate environmental space predicts parallelism, after correction for genetic distance. This study thus demonstrates the relative influences of environment, phenotype and genetic contingency on repeatable signatures of adaptation in the genome.

evolutionary biology↗

bioRxiv2019

The influence of thermal extremes on coral reef fish behaviour in the Persian Gulf

Despite increasing environmental variability within marine ecosystems, little is known about how coral reef fish species will cope with future climate scenarios. The Arabian/Persian Gulf is an extreme environment, providing an opportunity to study fish behaviour on reefs with seasonal temperature ranges which include both values above the mortality threshold of Indo-Pacific reef fish, and values below the optimum temperature for growth. Summer temperatures in the Gulf are comparable to those predicted for the tropical ocean by 2090-2099. Using field observations in winter, spring and summer, and laboratory experiments, we examined the foraging activity, distance from refugia and resting time of Pomacentrus trichrourus (pale-tail damselfish). Observations of fish behaviour in natural conditions showed that individuals substantially reduced distance from refugia and feeding rate and increased resting time at sub-optimal environmental temperatures in winter (average SST = 21{degrees}C) and summer (average SST = 34{degrees}C), while showing high movement and feeding activity in spring (average SST= 27{degrees}C). Diet was dominated by plankton in winter and spring, while fish used both plankton and benthic trophic resources in summer. These findings were corroborated under laboratory conditions: in a replicated aquarium experiment, time away from refugia and activity were significantly higher at 28{degrees}C (i.e., spring temperature conditions) compared to 21 {degrees}C (i.e., winter temperature conditions). Our findings suggest that P. trichrourus may have adapted to the Arabian/Persian Gulf environment by downregulating costly activity during winter and summer and upregulating activity and increasing energy stores in spring. Such adaptive behavioural plasticity may be an important factor in the persistence of populations within increasing environmentally variable coral reef ecosystems.

animal behavior and cognition↗