Maëva Gabrielli

Examining genomic patterns of differentiation across lineage pairs at different stages of the speciation continuum, in combination with recombination maps, can help disentangle the effects of linked and divergent selection and identify lineage-specific targets of selection that may act as barrier loci during speciation. Here, we apply this framework to genomic data from African and Indian Ocean bird species of the genus Zosterops (Zosteropidae) to identify candidate barrier loci between ecologically, phenotypically, and genetically distinct Reunion gray white-eye (Zosterops borbonicus) parapatric geographic forms. Using analyses that account for recombination rate variation, we show that putative targets of divergent selection are primarily located on the Z chromosome, except in comparisons between geographic forms that differ in their ecologies. Functional annotation revealed that candidate barrier loci between forms with similar environmental niches are associated with genes involved in song formation and immune function, whereas those between forms with different environmental niches are associated with adaptation to altitude, morphology, and song behavior. Our results highlight the combined roles of natural and sexual selection in the evolution of reproductive barriers in this incipient species radiation.

Small populations face high extinction risks. This can be explained by several non-genetic and genetic factors, the latter including the loss of genetic diversity and evolutionary potential, as well as the accumulation of harmful mutations (genetic load). Using whole-genome data from island populations with different effective sizes, we estimated genetic variation and load and explored the relationship between these quantities. An extremely small population of the Aeolian wall lizard, Podarcis raffonei , likely isolated for tens of thousands of years, shows the lowest genome-wide heterozygosity observed in wild eukaryotes (one polymorphic site every 300 kb on average). Despite this, its realized genetic load is comparable to that observed in another larger and more genetically variable population. Both populations have lower variation and higher load than the much more abundant sister species, the Sicilian wall lizard. These observations are consistent with the hypothesis that populations experiencing severe bottlenecks may persist for extended periods with extremely low genomic variation, provided that their burden of deleterious mutations remains within tolerable bounds.

Small populations face high extinction risks. This can be explained by several non-genetic and genetic factors, the latter including the loss of genetic diversity and evolutionary potential, as well as the accumulation of harmful mutations (genetic load). Using whole-genome data from island populations with different effective sizes, we estimated genetic variation and load and explored the relationship between these quantities. An extremely small population of the Aeolian wall lizard, Podarcis raffonei , likely isolated for tens of thousands of years, shows the lowest genome-wide heterozygosity observed in wild eukaryotes (one polymorphic site every 300 kb on average). Despite this, its realized genetic load is comparable to that observed in another larger and more genetically variable population. Both populations have lower variation and higher load than the much more abundant sister species, the Sicilian wall lizard. These observations are consistent with the hypothesis that populations experiencing severe bottlenecks may persist for extended periods with extremely low genomic variation, provided that their burden of deleterious mutations remains within tolerable bounds.

Islands provide unparalleled natural laboratories for understanding how small, isolated populations persist and evolve. Our synthesis of island population studies reveals that 50–70% report effective population sizes below 100, yet many taxa have sustained such small populations for millions of years. Strikingly, only 4% and 27% of studies examined genetic load and genomic diversity, exposing major blind spots in our understanding of genomic erosion. We argue that island systems offer critical insights into how limited populations retain viability and adaptive potential. Future work should expand taxonomic and geographic coverage, exploit temporal genomic data, and integrate genomic, demographic, and fitness information to link evolutionary resilience on islands to the conservation of increasingly fragmented populations worldwide.

Examining patterns of differentiation among lineage pairs at different stages of the speciation continuum can help disentangle the effects of linked and divergent selection, and identify lineage-specific targets of selection that may act as barrier loci during speciation. Here, we developed this approach using genomic data from a set of African and Indian Ocean belonging to the Zosteropidae family, commonly referred to as a “Great Speciator”. We sampled a divergence continuum aiming to identify candidate barrier loci in phenotypically, genetically distinct, and parapatrically distributed, forms from a species complex, through comparisons with closely related species. Using three independent approaches, we showed that divergence at selected loci between geographic forms is mainly concentrated on the Z chromosome, unless forms differ in their ecologies. Functional annotation revealed that genes linked to song formation and immunity could be involved in reproductive isolation between forms only separated by physical barriers, while it is mostly genes related to adaptation to local conditions, morphology, and song behaviour that may explain reproductive isolation between forms with different ecologies, highlighting a role for combined effects of natural and sexual selection in driving the evolution of reproductive barriers in this rapidly speciating lineage

Organisms can experience very different selective pressures across their latitudinal range, yet the genetic changes that underlie phenotypic differences across latitudes are poorly understood. Pacific salmon are renowned for their extreme life history variation and local adaptation to specific environments. We sequenced 137 whole-genomes of Chinook salmon (Oncorhynchus tshawytscha) sampled along the Pacific Coast of north America to study how adaptation across latitudes has evolved. We tested latitudinal gradients in five genes previously linked to polymorphisms in timing of migration and rate of maturation in salmonids: CLOCK1A, CLOCK1B, VGLL3, SIX6, ROCK1/GREB1L. Allelic variation in all five candidate genes was steeply associated with latitude. Many of the SNPs in ROCK1/GREB1L overlapped with those previously linked to a polymorphism in timing of adult migration in the south of the range. Additionally, we found that many other genes having strong correlations with latitude interact with the gene pathways previously linked to migration or maturation (including circadian clock and Hippo signaling pathways) and in multiple organs (especially the hypothalamic-pituitary-gonadal axis). We suggest that changes in functional clusters of interacting genes rather than a small number of disconnected changes influence life history adaptations to latitude. This has implications for the conservation of this iconic species and its adaptation to future climates.

Climate and land use change have increased human–wildlife interactions, potentially reducing wild species density and prompting behavioral adaptations to urbanized environments. It is still debated if behavioral responses are mainly the result of phenotypic plasticity or if they were driven by anthropic selective pressures, especially in small populations where genetic drift is strong. Our study focused on the small Apennine brown bear population (Ursus arctos marsicanus), which has coexisted with humans in Central Italy for millennia. We characterized genomic diversity and identified adaptation signals distinctive to this population by comparing newly generated and published whole-genome resequencing data from Apennine, Central European, and North American brown bears. Apennine brown bears exhibited reduced genomic diversity, higher inbreeding, and larger realized genetic load compared to other brown bears. We showed that Apennine brown bears possess a unique genomic diversity pattern including selective signatures at genes associated with reduced aggressiveness (eg DCC, SLC13A5). Within these genes, most of the newly discovered variants were located in noncoding regions and some of them were predicted to alter splicing factor binding sites, highlighting the contribution of noncoding variation in shaping complex phenotypes. Our results support the hypothesis that human-induced selection has promoted behavioral changes even in small- and long-isolated populations, reducing conflicts and contributing to the long-term persistence of a large mammal species and its coexistence with humans.

Climate and land use change have increased human-wildlife interactions, potentially reducing wild species density and prompting behavioural adaptations to urbanised environments. It is still debated if behavioural responses are mainly the result of phenotypic plasticity or if they were driven by anthropic selective pressures, especially in small populations. Our study focused on the Apennine brown bear population ( Ursus arctos marsicanus ), which has coexisted with humans in Central Italy for millennia. We characterised genomic diversity and identified adaptation signals distinctive to this population by comparing whole genome resequencing data across the Holarctic species range. We show that Apennine brown bears possess a unique genomic diversity pattern including selective signatures at genes associated with reduced aggressiveness, possibly involving alternative splicing mechanism. Our findings suggest that even in small and long-isolated populations, selection may shape behavioural traits. We hypothesise that human-induced selection has influenced these changes, reducing conflicts and contributing to the long-term persistence of the Apennine bear and its coexistence with humans.

Disentangling the effects of ecological disruptions operating at different spatial and temporal scales in shaping past species' demography is particularly important in the current context of rapid environmental changes driven by both local and regional factors. We argue that volcanic oceanic islands provide useful settings to study the influence of past ecological disruptions operating at local and regional scales on population demographic histories. We investigate potential drivers of past population dynamics for three closely related species of passerine birds from two volcanic oceanic islands, Reunion and Mauritius (Mascarene archipelago), with distinct volcanic history. Using ABC and PSMC inferences from complete genomes, we reconstructed the demographic history of the Reunion Grey White‐eye (Zosterops borbonicus (Pennant, 1781)), the Reunion Olive White‐eye (Z. olivaceus (Linnaeus, 1766)) and the Mauritius Grey White‐eye (Z. mauritianus (Gmelin, 1789)) and searched for possible causes underlying similarities or differences between species living on the same or different islands. Both demographic inferences strongly support ancient and long‐term expansions in all species. They also reveal different trajectories between species inhabiting different islands, but consistent demographic trajectories in species or populations from the same island. Species from Reunion appear to have experienced synchronous reductions in population size during the Last Glacial Maximum, a trend not seen in the Mauritian species. Overall, this study suggests that local events may have played a role in shaping population trajectories of these island species. It also highlights the potential of our conceptual framework to disentangle the effects of local and regional drivers on past species' demography and long‐term population processes.