Biology subjects

Fuentes-Pardo, A. P.

Publications and source records attributed to Fuentes-Pardo, A. P..

4 recordsLinked to original sources

bioRxiv2026

Experimental evolution unveils a role for structural variants and sex-specificity in the genetic architecture of lifespan

Insights into the genetic basis of lifespan evolution can link evolutionary theory with an understanding of health, disease and adaptation. We leverage the power of >200 generations of experimental evolution in a seed beetle to unveil the genomic architecture of lifespan evolution. Replicated populations evolved under regimes favoring either a short or long life, resulting in a near doubling of lifespan. Whole genome re-sequencing revealed that short- and long-lived lines were strongly differentiated (global FST = 0.41) and more than 700 genes showed consistent signs of divergent selection. Remarkably, short- and long-lived lines were consistently divergent in a large number of regions harboring copy-number variants (CNVs), involving >600 genes. The evolution of a long life involved many distinct biological processes, such as DNA fidelity, mitotic integrity, reproduction, metabolism, immunity and stress response. A pedigree-based genome scan for quantitative trait loci (QTLs) uncovered several QTLs with large effects on lifespan, but the genetic basis of a long life was dominated by a very large number of regions with medium and small effects. The genome-wide spatial association with QTL effects was, if anything, stronger for CNVs than for sequence variants. The genetic effects of QTLs on lifespan were positively correlated overall between the sexes, but four regions showed pronounced sex-differences. Our results show that structural variants play a significant role in the evolution of an extended lifespan and the highly polygenic genomic architecture is to some extent sex-specific, consistent with differences in physiology and life history tradeoffs between the sexes.

evolutionary biology↗

bioRxiv2025

Adaptive introgression from Pacific herring to Atlantic herring in the brackish Baltic Sea

The genomic era has revealed that interspecific gene flow can play an important role in adaptive evolution. Here, we report a striking case of adaptive introgression from Pacific into Atlantic herring following the colonization of the brackish Baltic Sea. Gene flow likely occurred in the Arctic, where the distributions of the two species overlap. Although introgression affected only 0.29% of the genome, these regions encompass about 10% of the loci showing strong differentiation between Atlantic and Baltic herring, indicating that natural selection has favored introgressed alleles in functionally important parts of the genome. Adaptive introgression may have been facilitated by shared spawning depths and salinity preferences between Pacific and Baltic herring, in contrast to Atlantic herring, which spawn in deeper, fully marine waters. Introgressed genes such as THRB and SEC16B may have enhanced visual acuity and lipid metabolism, respectively, promoting adaptation to the brackish Baltic environment.

evolutionary biology↗

bioRxiv2022

The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (Trachurus trachurus)

Understanding how populations adapt to local environments is increasingly important to prevent biodiversity loss due to climate change. Here we examined whole-genome variation of twelve Atlantic horse mackerel samples from the North Sea to North Africa, and the western Mediterranean Sea. This marine migratory benthopelagic fish is one of the most widely distributed and commercially important species in the eastern Atlantic. We found low population structure at neutral loci, but high differentiation at adaptive loci distinguishing the western Mediterranean and the North Sea populations from other Atlantic locations. Candidate genes distinctive of the Mediterranean include a green-sensitive-opsin harbouring two missense mutations that might fine-tune the spectral sensitivity to blue-green light conditions. Candidate genes characteristic of the North Sea could play a critical role in cold tolerance (energy metabolism and cell membrane structure) and increased sensitivity to odours, presumably to compensate reduced visibility in turbid waters. We also discovered a putative chromosomal inversion (9.9 Mb) that follows a climate-related latitudinal cline with a break near mid Portugal. Genome-environment association analysis indicated that seawater-dissolved oxygen concentration and temperature are likely the main environmental drivers of local adaptation. Our genomic data broadly supports the current stock divisions, but recommends revision of the western and southern stock boundaries. We developed a reduced SNP panel that genetically discriminate the North Sea and North Africa from neighbouring populations. Our study highlights the importance of life history and chromosomal inversions in adaptation with gene flow, and the complexity of evolutionary and ecological processes involved in local adaptation.

genomics↗

bioRxiv2019

Adaptation to seasonal reproduction and thermal minima-related factors drives fine-scale divergence despite gene flow in Atlantic herring populations

Natural selection can maintain local adaptation despite the presence of gene flow. However, the genomic basis and environmental factors involved in adaptation at fine-spatial scales are not well understood. Here, we address these questions using Atlantic herring (Clupea harengus), an abundant, migratory, and widely distributed marine species with substantial genomic resources including a chromosome-level genome assembly and genomic data from the eastern Atlantic and Baltic populations. We analysed whole-genome sequence and oceanographic data to examine the genetic variation of 15 spawning aggregations across the northwest Atlantic Ocean ([~]1,600 km of coastline) and the association of this variation with environmental variables. We found that population structure lies in a small fraction of the genome involving adaptive genetic variants of functional importance. We discovered 10 highly differentiated genomic regions distributed across four chromosomes. Two of these loci appear to be private to the northwest, four loci share a large number of adaptive variants between northwest and northeast Atlantic, and four shared loci exhibit an outstanding diversity in haplotype composition, including a novel putative inversion on chromosome 8. Another inversion on chromosome 12 underlies a latitudinal genetic pattern discriminating populations north and south of a biogeographic transition zone on the Scotian Shelf. Our genome-environment association analysis indicates that sea water temperature during winter is the environmental factor that best correlates with the latitudinal pattern of this inversion. We conclude that the timing and geographic location of spawning and early development are under diverse selective pressures related to environmental gradients. Natural selection appears to act on early-life performance traits with differential fitness across environments. Our study highlights the role of genomic architecture, ancestral haplotypes, and selection in maintaining adaptive divergence in species with large population sizes and presumably high gene flow.

genomics↗