Biology subjects

Ferreira, M. S.

Publications and source records attributed to Ferreira, M. S..

3 recordsLinked to original sources

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↗

bioRxiv2023

The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring

Chromosomal inversions are associated with local adaptation in many species. However, questions regarding how they are formed, maintained and impact various other evolutionary processes remain elusive. Here, using a large genomic dataset of long-read and short-read sequencing, we ask these questions in one of the most abundant vertebrates on Earth, the Atlantic herring. This species has four megabase-sized inversions associated with ecological adaptation that correlate with water temperature. The S and N inversion alleles at these four loci dominate in the southern and northern parts, respectively, of the species distribution in the North Atlantic Ocean. By determining breakpoint coordinates of the four inversions and the structural variations surrounding them, we hypothesize that these inversions are formed by ectopic recombination between duplicated sequences immediately outside of the inversions. We show that these are old inversions (>1 MY), albeit formed after the split between Atlantic herring and its sister species, the Pacific herring. They are yet to reach mutation-flux equilibrium, but the large Ne of herring combined with the common occurrence of opposite homozygotes across the species distribution has allowed effective purifying selection to prevent accumulation of genetic load and repeats within the inversions.

evolutionary biology↗

bioRxiv2020

The legacy of recurrent introgression during the radiation of hares

AO_SCPLOWBSTRACTC_SCPLOWHybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1- 4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum, but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation within and among species.

evolutionary biology↗