Mark Ravinet

Ancestral adaptive variation is thought to play an important role in facilitating adaptation to insular environments. However, to properly evaluate its role, we need to determine the age of genetic variation. In this study, we investigate the Iago sparrow ( Passer iagoensis ), a generalist endemic to the Cabo Verde archipelago, to understand how genetic diversity is maintained in an island lineage where populations are likely ephemeral and adaptation to environmental extremes is ongoing. Using whole‐genome sequencing and phenotypic data, we inferred the species' evolutionary history, population structure, and signatures of selection. Our results show that the Iago sparrow diverged from its closest mainland relative approximately 4.26 million years ago, although the colonisation likely occurred only around 2 million years ago. Population structure analyses reveal three distinct lineages, corresponding to geographic divisions within the archipelago, with the Rombos islets population exhibiting significant phenotypic divergence, particularly in bill morphology. Genome scans and phenotypic measurements identified signatures of divergent selection in genes associated with bill size ( HMG20B ) and bill shape ( ALX1 ), suggesting adaptive evolution in response to local environmental conditions. Our ancestral recombination graph analysis provided temporal estimates for adaptive variation associated with these genes, suggesting that adaptive haplotypes observed in the Rombos population arose after colonisation of the archipelago. This contrasts with patterns described in Darwin's finches, where ancestral variation likely originated prior to colonisation. Our findings highlight the interplay of genetic drift, gene flow, and selection in shaping island species' genetic diversity. The Iago sparrow, a generalist thriving across diverse habitats, provides insights into the mechanisms that maintain genetic diversity in island lineages despite small population sizes and pronounced environmental heterogeneity.

Natal dispersal is a key life history trait determining fitness and driving population dynamics, genetic structure, and species distributions. Despite existing evidence that not all phenotypes are equally likely to successfully establish in new areas, the mechanistic underpinnings of natal dispersal remain poorly understood. The propensity to disperse into a new environment can be favoured by a high degree of phenotypic plasticity, which facilitates local adaptation and may be achieved via epigenetic mechanisms, which modify gene expression and enable rapid phenotypic changes. Epigenetic processes occur in particular genomic regions—DNA methylation on CpG sites in vertebrates—and thus individual genomes may differ in their capacity to be modified epigenetically. This ‘Epigenetic potential’ (EP) may represent the range of phenotypic plasticity attainable by an individual and be a key determinant of successful settlement in novel areas. We investigated the association between EP—quantified as the number of genome‐wide CpG variants—and natal dispersal propensity in a long‐term study population of Pied flycatchers ( Ficedula hypoleuca ) monitored since colonisation of a new habitat 35 years ago. We tested this association at three levels, comparing EP between: (i) individuals dispersing between and within habitat patches; (ii) immigrants to the population and locally born individuals; and (iii) individuals from first (comprising colonisers or their direct descendants) and later generations of the population (consisting of locally born individuals, which did not show natal dispersal between habitat patches). Results show a significant, positive association between EP and dispersal propensity in comparisons (i)—only in females—and (iii), but not (ii). Furthermore, CpG variants were non‐randomly distributed across the genome, suggesting species‐ and/or population‐specific CpGs being more frequent in promoters and exons. Our findings point to EP playing a role in dispersal propensity at spatial and temporal scales, supporting the idea that epigenetically driven phenotypic plasticity facilitates dispersal and environmental coping in free‐living birds.

Background: Whole-genome sequencing efforts, have during the past decade, unveiled the central role of genomic rearrangements—such as chromosomal inversions—in evolutionary processes, including local adaptation in a wide range of taxa. However, employment of reference genomes from distantly or even closely related species for mapping and the subsequent variant calling can lead to errors and/or biases in the datasets generated for downstream analyses. Results: Here, we capitalize on the recently generated chromosome-anchored genome assemblies for Arctic cod ( Arctogadus glacialis ), polar cod ( Boreogadus saida ), and Atlantic cod ( Gadus morhua ) to evaluate the extent and consequences of reference bias on population sequencing datasets (approx. 15–20 × coverage) for both Arctic cod and polar cod. Our findings demonstrate that the choice of reference genome impacts the mapping statistics, including mapping depth and mapping quality, as well as core population genetic estimates, such as heterozygosity levels, nucleotide diversity (π), and cross-species genetic divergence (D _XY ). Furthermore, using a more distantly related reference genome can lead to inaccurate detection and characterization of chromosomal inversions, i.e., in terms of size (length) and location (position), due to inter-chromosomal reorganizations between species. Additionally, we observe that some of the verified species-specific inversions are split across multiple genomic regions when mapped against a heterospecific reference. Conclusions: Inaccurate identification of chromosomal rearrangements as well as biased population genetic measures could potentially lead to erroneous interpretation of species-specific genomic diversity, impede the resolution of local adaptation, and thus, impact predictions of their genomic potential to respond to climatic and other environmental perturbations.

Gut microbiomes are central to host ecology and evolution, yet the mechanisms driv-ing their diversification remain elusive, partly because host evolution and biogeography are often confounded. The recent radiation of chaffinches in Macaronesia, coupled with their broadly similar ecologies across islands, makes them an ideal replicated natural experiment to separate spatial from host-driven effects on microbiome structure. Us-ing long-read 16S rRNA gene sequencing, diet metabarcoding, and whole-genome host data, we show that gut microbiome diversity aligns with predictions of island biogeog-raphy theory rather than host colonization history, revealing that microbial dispersal limitation independent of the host is a dominant mechanism of community assembly. Geography and diet primarily explain bacterial presence–absence patterns, whereas host genetic differentiation and heterozygosity influence abundant, potentially resident taxa. Challenging previous assumptions about birds, we detect clear signals of phylosymbiosis (i.e. similar microbiome composition among closely related hosts), however phylogenetic reconciliation reveals these associations result from convergent host filtering of environ-mentally acquired bacteria, likely via shared diets or physiological traits, rather than de-tectable co-diversification. Our study reframes our understanding of avian host-microbe relationships, revealing that birds maintain host-specific microbiome associations within biogeographic constraints, but these arise from ecological filtering processes rather than co-evolutionary partnerships.

Natal dispersal is a key life-history trait determining fitness and driving population dynamics, genetic structure and species distributions. Despite existing evidence that not all phenotypes are equally likely to successfully establish in new areas, the mechanistic underpinnings of natal dispersal remain poorly understood. The propensity to disperse into a new environment can be favored by a high degree of phenotypic plasticity which facilitates local adaptation and may be achieved via epigenetic mechanisms, which modify gene expression and enable rapid phenotypic changes. Epigenetic processes occur in particular genomic regions - DNA methylation on CpG sites in vertebrates -, and thus individual genomes may differ in their capacity to be modified epigenetically. This “Epigenetic potential” (EP) may represent the range of phenotypic plasticity attainable by an individual, and be a key determinant of successful settlement in novel areas. We investigated the association between EP – quantified as the number of genome-wide CpG variants – and natal dispersal propensity in a long-term study population of Pied flycatchers ( Ficedula hypoleuca ) monitored since colonization of a new habitat 35 years ago. We tested this association at three levels, comparing EP between: i) individuals dispersing between and within habitat patches; ii) immigrants to the population and locally-born individuals; and iii) individuals from first (comprising colonizers or their direct descendants) and later generations of the population (consisting of locally-born individuals, which did not show natal dispersal). Results show a significant, positive association between EP and dispersal propensity in comparisons i) and iii), but not ii). Furthermore, CpG variants were non-randomly distributed across the genome, suggesting species- and/or population-specific CpGs being more frequent in promoters and exons. Our findings point to EP playing a role in dispersal propensity at spatial and temporal scales, supporting the idea that epigenetically-driven phenotypic plasticity facilitates dispersal and environmental coping in free-living birds.

Genomic rearrangements have in recent years gained attention due to their evolutionary role in processes related to adaptation to local environmental conditions as well as diversification and speciation. In this study, we report on genomic rearrangements in the cold-water adapted polar cod ( Boreogadus saida ), a keystone Arctic fish species. By taking advantage of a new chromosome-level genome assembly in combination with whole-genome population sequencing data from specimens across the northern Barents Sea and adjacent regions, we identified a substantial number of larger chromosomal inversions (n=20) and characterized the previously identified chromosomal fusions (n=5). These genomic features — encompassing over 20% of the genome — exhibited genetic divergence, strong internal linkage disequilibrium, and signals of selection. Two of the identified inversions were associated with the two previously described hemoglobin clusters, while a third chromosomal region was found to differentiate between males and females. Moreover, clustering analyses on genotype frequencies of inversions revealed sub- structuring according to five geographic sub-groups suggesting sub-populations and/or the existence of cryptic ecotypes. These results provide novel insights into the impact of genomic rearrangements in population divergence and thus, potentially local adaptation, especially in species with high gene flow.

Summary: Whole-genome sequencing efforts has during the past decade unveiled the central role of genomic rearrangements—such as chromosomal inversions—in evolutionary processes, including local adaptation in a wide range of taxa. However, employment of reference genomes from distantly or even closely related species for mapping and the subsequent variant calling, can lead to errors and/or biases in the datasets generated for downstream analyses. Here, we capitalize on the recently generated chromosome-anchored genome assemblies for Arctic cod ( Arctogadus glacialis ), polar cod ( Boreogadus saida ), and Atlantic cod ( Gadus morhua ) to evaluate the extent and consequences of reference bias on population sequencing datasets (approx. 15-20x coverage) for both Arctic cod and polar cod. Our findings demonstrate that the choice of reference genome impacts population genetic statistics, including individual mapping depth, heterozygosity levels, and cross-species comparisons of nucleotide diversity (π) and genetic divergence (D _XY ). Further, it became evident that using a more distantly related reference genome can lead to inaccurate detection and characterization of chromosomal inversions, i.e., in terms of size (length) and location (position), due to inter-chromosomal reorganizations between species. Additionally, we observe that several of the detected species-specific inversions were split into multiple genomic regions when mapped towards a heterospecific reference. Inaccurate identification of chromosomal rearrangements as well as biased population genetic measures could potentially lead to erroneous interpretation of species-specific genomic diversity, impede the resolution of local adaptation, and thus, impact predictions of their genomic potential to respond to climatic and other environmental perturbations.

Interspecific hybridization events are on the rise in natural systems due to climate change disrupting species barriers. Across taxa, microsatellites have long been the molecular markers of choice to identify admixed individuals. However, with the advent of high-throughput sequencing easing the generation of genome-wide datasets, incorrect reports of hybridization resulting from microsatellite technical artefacts have been uncovered in a growing number of taxa. In the marine zooplankton genus Calanus (Copepoda), whose species are used as climate change indicators, microsatellite markers have suggested hybridization between C. finmarchicus and C. glacialis, while other nuclear markers (InDels) never detected any admixed individuals, leaving the scientific community divided. Here, for the first time, we investigated the potential for hybridization among C. finmarchicus, C. glacialis, C. helgolandicus and C. hyperboreus using two large and independent SNP datasets. These were derived firstly from a protocol of target-capture applied to 179 individuals collected from 17 sites across the North Atlantic and Arctic Oceans, including sympatric areas, and second from published RNA sequences. All SNP-based analyses were congruent in showing that Calanus species are distinct and do not appear to hybridize. We then thoroughly re-assessed the microsatellites showing hybrids, with the support of published transcriptomes, and identified technical issues plaguing eight out of 10 microsatellites, including size homoplasy, paralogy, potential for null alleles and even two primer pairs targeting the same locus. Our study illustrates how deceptive microsatellites can be when applied to the investigation of hybridization.

Anthropogenic impacts on the environment alter speciation processes by affecting both geographical contexts and selection patterns on a worldwide scale. Here we review evidence of these effects. We find that human activities often generate spatial isolation between populations and thereby promote genetic divergence but also frequently cause sudden secondary contact and hybridization between diverging lineages. Human-caused environmental changes produce new ecological niches, altering selection in diverse ways that can drive diversification; but changes also often remove niches and cause extirpations. Human impacts that alter selection regimes are widespread and strong in magnitude, ranging from local changes in biotic and abiotic conditions to direct harvesting to global climate change. Altered selection, and evolutionary responses to it, impacts early-stage divergence of lineages, but does not necessarily lead toward speciation and persistence of separate species. Altogether, humans both promote and hinder speciation, although new species would form very slowly relative to anthropogenic hybridization, which can be nearly instantaneous. Speculating about the future of speciation, we highlight two key conclusions: (1) Humans will have a large influence on extinction and “despeciation” dynamics in the short term and on early-stage lineage divergence, and thus potentially speciation in the longer term, and (2) long-term monitoring combined with easily dated anthropogenic changes will improve our understanding of the processes of speciation. We can use this knowledge to preserve and restore ecosystems in ways that promote (re-)diversification, increasing future opportunities of speciation and enhancing biodiversity.

To understand how species evolve and adapt to changing environments, it is important to study gene flow and introgression due to their influence on speciation and radiation events. Here, we apply a novel experimental system for investigating these mechanisms using natural populations. The system is based on two fungal sister species with morphological and ecological similarities occurring in overlapping habitats. We examined introgression between these species by conducting whole genome sequencing of individuals from populations in North America and Europe. We assessed genome-wide nucleotide divergence and performed crossing experiments to study reproductive barriers. We further used ABBA–BABA statistics together with a network analysis to investigate introgression, and conducted demographic modelling to gain insight into divergence times and introgression events. The results revealed that the species are highly divergent and incompatible in vitro. Despite this, small regions of introgression were scattered throughout the genomes and one introgression event likely involves a ghost population (extant or extinct). This study demonstrates that introgression can be found among divergent species and that population histories can be studied without collections of all the populations involved. Moreover, the experimental system is shown to be a useful tool for research on reproductive isolation in natural populations. Abstract We studied population histories with demographic modelling and found introgression between highly divergent fungal sister species, involving a ghost population.