Biology subjects

Eroukhmanoff, F.

Publications and source records attributed to Eroukhmanoff, F..

9 recordsLinked to original sources

bioRxiv2025

Signatures of genomic adaptation to Cuckoo brood parasitism in Reed Warbler hosts across Europe

Behaviour is a fundamental defence mechanism for animals facing enemies, yet its plasticity makes finding associated genomic evidence for coevolution challenging. As a solution, we apply landscape genomics methods more typically deployed with abiotic variables to a coevolutionary model system: Reed Warblers (Acrocephalus scirpaceus) and their Cuckoo (Cuculus canorus) brood parasites. Using continental sampling of genome-wide data from hosts breeding under varying brood parasitism rates, we reveal that gene flow varies among populations, and, controlling for variation due to environmental differences, identify genomic regions and putative genes that differ with exposure to brood parasitism. Therefore, our results suggest that variable host responses to selection are possible, even by highly mobile and connected populations, supporting long-held assumptions that behavioural defences may reflect genomic adaptation despite their plasticity. Further studies, including those linking genetic variation to individual-level behaviours involved in parental responses to brood parasitism, are required to confirm a genetic basis to specific coevolutionary adaptations, and to test for other biotic or abiotic variables potentially confounding with local parasitism rate.

evolutionary biology↗

bioRxiv2025

High genetic diversity and no detectable founder effects following a rapid range expansion of a long-distance migrant (Acrocephalus scirpaceus)

Many species are currently experiencing range shifts in response to changing environmental conditions, but with potentially serious genetic consequences. Repeated founder events and strong genetic drift are expected to erode genetic variation at the range front, reducing adaptive potential and slowing or even halting the expansion. However, the severity of these consequences for the more common and highly mobile species undergoing environment-driven range shifts (c.f. invasions) is less clear. Here we combined historical observations and contemporary movement data of the common reed warbler (Acrocephalus scirpaceus) with genomic evidence from across its European breeding range to (1) infer the origin and (2) quantify the genetic consequences of a recent and rapid northward range expansion. While there were no reductions in levels of nucleotide diversity or allelic richness, nor a signal of founder effect in the directionality index ({psi}), our combined dataset approach was able to infer an expansion origin from the southwest. Furthermore, we found that private allelic richness retained a slight but significant linear decline along the colonisation route. These results suggest that high dispersal capabilities can allow even philopatric species to avoid the loss of genetic diversity during rapid range expansions. Nevertheless, if multiple lines of evidence enable identification of an expansion pathway, we may still detect genetic signals of expansion.

evolutionary biology↗

bioRxiv2022

Genomic consequences of range expansion and colonisation in the reed warbler (Acrocephalus scirpaceus)

Range expansion is a common natural phenomenon, which may be intensified by human-induced drivers such as climate change and alterations of habitat. The genetic consequences of range expansion are potentially major, and it is important to study known cases of range expansion to understand how human activities affect contemporary evolution, and to learn more about the genetic adaptive potential of species. The reed warbler (Acrocephalus scirpaceus) is a long-distance migratory bird breeding in Eurasia and wintering south of Sahara. It is currently expanding its range northwards, likely as a consequence of climate change. Interestingly, however, reed warblers have also recently colonised new territory southwards, following habitat restoration at the southern range margin. In this study, we investigate the genetic consequences of these two-directional range expansions with RAD-seq, looking at 10 populations from north to south in Europe. We investigate population structure and genome diversity, and assess the role of selection in divergence between populations across the species range. We do not find evidence of strong genetic structure in the reed warbler populations, and the youngest edge populations do not exhibit any substantial loss in genetic diversity, suggesting ongoing gene flow. On a smaller scale, the edge populations are the most genetically distinct, and we identify environmental disparity, especially in precipitation variability, as the main barrier of gene flow, to a greater extent than geographic distance. We find no evidence that the loci involved in population divergence and adaptation in the core populations are the same that are involved in adaptation at the range edges. Using three genome scan methods to identify selection, we found 49 SNPs putatively under selection, of which 33 were located in introns of 28 unique genes. Most of these are correlated with differences in climatic variables of temperature and precipitation. Some genome scan outliers show signs of being part of nascent selective sweeps, especially one which is distinct for the northern range edge. Our results suggest that in the reed warbler, contemporary range expansion has had little effect on molecular diversity and has been rapidly followed by local adaptation to climatic conditions, which could further corroborate the rapid pace at which colonisation of novel environments has occurred both northwards and southwards.

evolutionary biology↗

bioRxiv2021

Predictors of genomic differentiation within a hybrid taxon

Hybridization is increasingly recognized as an important evolutionary force. Novel genetic methods now enable us to address how the genomes of parental species are combined to build hybrid genomes. However, we still do not know the relative importance of contingencies, genome architecture and local selection in shaping hybrid genomes. Here, we take advantage of the genetically divergent island populations of Italian sparrow on Crete, Corsica and Sicily to investigate the predictors of genomic variation within a hybrid taxon. We test if differentiation is affected by recombination rate, selection, or variation in ancestry proportion from each parent species. We find that the relationship between recombination rate and differentiation is less pronounced within hybrid lineages than between the parent species, as expected if purging of minor parent ancestry in low recombination regions reduces the variation available for differentiation. In addition, we find that differentiation between islands is correlated with differences in selection in two out of three comparisons. Patterns of within-island selection are correlated across all islands, suggesting that shared selection may mould genomic differentiation. The best predictor of strong differentiation within islands is the degree of differentiation from house sparrow, and hence loci with Spanish sparrow ancestry may vary more freely. Jointly, this suggests that constraints and selection interact in shaping the genomic landscape of differentiation in this hybrid species.

evolutionary biology↗

bioRxiv2019

Intraspecific genomic variation and local adaptation in a young hybrid species

Hybridization increases genetic variation, hence hybrid species may have a strong evolutionary potential once their admixed genomes have stabilized and incompatibilities have been purged. Yet, little is known about how such hybrid lineages evolve at the genomic level following their formation, in particular the characteristics of their adaptive potential, i.e. constraints and facilitations of diversification. Here we investigate how the Italian sparrow (Passer italiae), a homoploid hybrid species, has evolved and locally adapted to its variable environment. Using restriction site-associated DNA sequencing (RAD-seq) on several populations across the Italian peninsula, we evaluate how genomic constraints and novel genetic variation have influenced population divergence and adaptation. We show that population divergence within this hybrid species has evolved in response to climatic variation. As in non-hybrid species, climatic differences may even reduce gene flow between populations, suggesting ongoing local adaptation. We report outlier genes associated with adaptation to climatic variation, known to be involved in beak morphology in other species. Most of the strongly divergent loci among Italian sparrow populations seem not to be differentiated between its parent species, the house and Spanish sparrow. Within the parental species, population divergence has occurred mostly in loci where different alleles segregate in the parent species, unlike in the hybrid, suggesting that novel combinations of parental alleles in the hybrid have not necessarily enhanced its evolutionary potential. Rather, our study suggests that constraints linked to incompatibilities may have restricted the evolution of this admixed genome, both during and after hybrid species formation.

evolutionary biology↗

bioRxiv2018

Hybridization, sex specific genomic architecture and local adaptation

While gene flow can reduce the potential for local adaptation, hybridization may conversely provide genetic variation that increases the potential for local adaptation. Hybridization may also affect adaptation through altering sexual dimorphism and sexual conflict, but this remains largely unstudied. Here, we discuss how hybridization may affect sexual dimorphism and conflict due to differential effects of hybridization on males and females, and then how this in turn may affect local adaptation. First, the lower viability of the heterogametic sex in hybrids could shift the balance in sexual conflict. Second, sex-specific inheritance of the mitochondrial genome in hybrids may lead to cyto-nuclear mismatches, for example in the form of \"mothers curse\", with potential consequences for sex-ratio and sex specific expression. Third, transgressive segregation of sexually antagonistic alleles could lead to greater sexual dimorphism in hybrid populations. These mechanisms can reduce sexual conflict and enhance intersexual niche partitioning, increasing the fitness of hybrids. Adaptive introgression of alleles reducing sexual conflict or enhancing intersexual niche partitioning may facilitate local adaptation, and could favour the colonization of novel habitats. We review these consequences of hybridization on sex differences and local adaptation, and discuss how their prevalence and importance could be tested empirically.

evolutionary biology↗

bioRxiv2017

Genomic contingencies and beak shape variation in a hybrid species

Hybridization is increasingly recognized as a potent evolutionary force. Though additive genetic variation and novel combinations of parental genes theoretically increase the potential for hybrid species to adapt, few empirical studies have investigated the adaptive potential within a hybrid species. Here, we investigate factors promoting phenotypic divergence using genomically diverged island populations of the homoploid hybrid Italian sparrow Passer italiae from Crete, Corsica, and Sicily. We address whether genomic contingencies, adaptation to climate or diet best explain divergence in beak morphology. Populations vary significantly in beak morphology, both between and within islands of origin. Temperature seasonality best explains population divergence in beak size. Interestingly, beak shape along all significant dimensions of variation was best explained by annual precipitation, genomic composition and their interaction, suggesting a role for contingencies. Moreover, beak shape similarity to a parent species correlates with proportion of the genome inherited from that species, consistent with the presence of contingencies. In conclusion, adaptation to local conditions and genomic contingencies arising from putatively independent hybridization events jointly explain beak morphology in the Italian sparrow. Hence, hybridization may induce contingencies and restrict evolution in certain directions dependent on the genetic background.

evolutionary biology↗

bioRxiv2017

Variation and constraints in hybrid genome formation

Recent genomic investigations have revealed hybridization to be an important source of variation, the working material of natural selection1,2. Hybridization can spur adaptive radiations3, transfer adaptive variation across species boundaries4, and generate species with novel niches5. Yet, the limits to viable hybrid genome formation are poorly understood. Here we investigated to what extent hybrid genomes are free to evolve or whether they are restricted to a specific combination of parental alleles by sequencing the genomes of four isolated island populations of the homoploid hybrid Italian sparrow Passer italiae6,7. Based on 61 Italian sparrow genomes from Crete, Corsica, Sicily and Malta, and 10 genomes of each of the parent species P. domesticus and P. hispaniolensis, we report that a variety of novel and fully functional hybrid genomic combinations have arisen on the different islands, with differentiation in candidate genes for beak shape and plumage colour. There are limits to successful genome fusion, however, as certain genomic regions are invariably inherited from the same parent species. These regions are overrepresented on the Z-chromosome and harbour candidate incompatibility loci, including DNA-repair and mito-nuclear genes; loci that may drive the general reduction of introgression on sex chromosomes8. Our findings demonstrate that hybridization is a potent process for generating novel variation, but variation is limited by DNA-repair and mito-nuclear genes, which play an important role in reproductive isolation and thus contribute to speciation.

evolutionary biology↗

bioRxiv2017

Resolution of conflict between parental genomes in a hybrid species

The development of reproductive barriers against parent species is crucial during hybrid speciation, and post-zygotic isolation can be important in this process. Genetic incompatibilities that normally isolate the parent species can become sorted in hybrids to form reproductive barriers towards either parent. However, the extent to which this sorting process is systematically biased and therefore predictable in which loci are involved and which alleles are favored is largely unknown. Theoretically, reduced fitness in hybrids due to the mixing of differentiated genomes can be resolved through rapid evolution towards allelic combinations ancestral to lineage-splitting of the parent species, as these alleles have successfully coexisted in the past. However, for each locus, this effect may be influenced by its chromosomal location, function, and interactions with other loci. We use the Italian sparrow, a homoploid hybrid species that has developed post-zygotic barriers against its parent species, to investigate this prediction. We show significant bias towards fixation of the ancestral allele among 57 nuclear intragenic SNPs, particularly those with a mitochondrial function whose ancestral allele came from the same parent species as the mitochondria. Consistent with increased pleiotropy leading to stronger fitness effects, genes with more protein-protein interactions were more biased in favor of the ancestral allele. Furthermore, the number of protein-protein interactions was especially low among candidate incompatibilities still segregating within Italian sparrows, suggesting that low pleiotropy allows steep intraspecific clines in allele frequencies to form. Finally, we report evidence for pervasive epistatic interactions within one Italian sparrow population, particularly involving loci isolating the two parent species but not hybrid and parent. However there was a lack of classic incompatibilities and no admixture linkage disequilibrium. This suggests that parental genome admixture can continue to constrain evolution and prevent genome stabilization long after incompatibilities have been purged.

evolutionary biology↗