Biology subjects

Nocchi, G.

Publications and source records attributed to Nocchi, G..

5 recordsLinked to original sources

bioRxiv2026

Genomic basis for resistance to acute oak decline and mildew infection in English oak

English oak (Q. robur) in Britain is at risk from a young age due to powdery mildew and at maturity due to acute oak decline (AOD). The contribution of oak genetic diversity to these conditions is a critical question that until recently would have required extensive clonal or family trials of juvenile and mature oak trees. Here we overcome this practical burden with genomic approaches inspired by medicine. We sequence 1868 oak trees from 78 sites and identify 1491 trees exclusively of the species Q. robur, which we analyse. Using single nucleotide polymorphism (SNP) based estimates of heritability ([Formula]), we estimate 20.9% of variation in AOD presence is genetically determined. For mildew symptoms, [Formula] is 27.8%. Using genome-wide association studies, no SNP markers show a significant association with AOD, but 183 are significantly associated with mildew. Genomic prediction models for AOD and its symptoms, using thousands of loci, give low to moderate accuracies, ranging from 0.187 to 0.617. These results suggest a highly polygenic heritable component of susceptibility to AOD, which perhaps reflects the number of biotic and abiotic factors known to contribute to it. In contrast, powdery mildew, caused by a single fungus, has an oligogenic heritable component controlled by fewer loci of large effect. These results could be used to inform breeding programs to develop trees more resistant to AOD and mildew.

evolutionary biology↗

bioRxiv2025

The genomic basis of local adaptation in the white x Engelmann spruce hybrid zone

Hybridization between species can occur along repeated zones of contact, providing a natural laboratory for studying the interplay between migration and selection, and identifying loci involved in adaptation and reproductive isolation. However, interpreting how evolutionary processes shape genomic patterns can be challenging: repeatability of genotype-environment association alone is not strong evidence for selection, as hybrid zones derived from the same parental species are not evolutionarily independent. Conversely, processes that operate within the middle of each hybrid zone, such as selection driving directional introgression, may be more evolutionarily independent, and therefore provide stronger evidence of selection. Here we compared hybridization and local adaptation patterns between two replicated regions within the western Canada interior spruce hybrid zone: a broad latitudinal transect with gradual environmental variation and a narrow elevational transect with substantial topographical and environmental variation. We discovered a complex pattern of introgression, with strong differences in ancestry maintained even across small spatial scales at several locations along the elevational transect. Despite differences in their spatial scales, the elevational and latitudinal transects revealed strikingly similar genome-wide patterns of differentiation and adaptation, and consistent patterns of directional introgression. We explore the extent to which the evolutionary non-independence of these hybrid zones allows inferences about the role of natural selection and drift in shaping these patterns. Consistent with theory, we found longer genomic tracts in the elevational transect, likely because the steeper environmental gradients over shorter distances limit the rate of mixing by migration and recombination relative to drift and selection.

evolutionary biology↗

bioRxiv2024

Repeated global adaptation across plant species

Global adaptation occurs when all populations of a species undergo selection toward a common optimum. This can occur by a hard selective sweep with the emergence of a new globally advantageous allele that spreads throughout a species natural range until reaching fixation. This evolutionary process leaves a temporary trace in the region affected, which is detectable using population genomic methods. While selective sweeps have been identified in many species, there have been few comparative and systematic studies of the genes involved in global adaptation. Building upon recent findings showing repeated genetic basis of local adaptation across independent populations and species, we asked whether certain genes play a more significant role in driving global adaptation across plant species. To address this question, we scanned the genomes of 17 plant species to identify signals of repeated global selective sweeps. Despite the substantial evolutionary distance between the species analysed, we identified several gene families with strong evidence of repeated positive selection. These gene families tend to be enriched for reduced pleiotropy, consistent with predictions from Fishers evolutionary model and the cost of complexity hypothesis. We also found that genes with repeated sweeps exhibit elevated levels of gene duplication. Our findings contrast with recent observations of increased pleiotropy in genes driving local adaptation, consistent with predictions based on the theory of migration-selection balance. SignificanceGlobal adaptation occurs when a species undergoes selection toward a common optimum throughout its natural range. While instances of global adaptation are widespread in the literature, there is a shortage of comparative studies aimed at understanding its genetic architecture and how it contrasts with that of local adaptation. This research compares global selective sweeps across 17 plant species to uncover the attributes of the genetic loci repeatedly involved in adaptation. We show that global adaptation tends to rely on genes with reduced pleiotropy and is characterized by increased levels of gene duplication. This finding contrasts with recent observations of increased pleiotropy in genes driving local adaptation, reflecting the opposing dynamics underlying these two evolutionary processes.

evolutionary biology↗

bioRxiv2022

Genomic signals of local adaptation and hybridization in Asian white birch

Disentangling the numerous processes that affect patterns of genome-wide diversity in widespread tree species has important implications for taxonomy, conservation, and forestry. Here, we investigate the population genomic structure of Asian white birch (Betula platyphylla) in China and seek to explain it in terms of hybridization, demography and adaptation. We generate whole genome sequence data from 83 individuals across the species range in China. Combining this with an existing dataset for 79 European and Russian white birches, we show a clear distinction between B. pendula and B. platyphylla, which have sometimes been lumped taxonomically. Genomic diversity of B. platyphylla in north-western China and Central Russia is affected greatly by hybridization with B. pendula. Excluding these hybridized populations, B. platyphylla in China has a linear distribution from north-eastern to south-western China, along the edge of the inland mountainous region. Within this distribution, three genetic clusters are found, which we model as long diverged with subsequent episodes of gene flow. Patterns of co-variation between allele frequencies and environmental variables in B. platyphylla suggest the role of natural selection in the distribution of diversity at 7,609 SNPs of which 3,767 were significantly differentiated among the genetic clusters. The putative adaptive SNPs are distributed throughout the genome and span 1,633 genic regions. Of these genic regions, 87 were previously identified as candidates for selective sweeps in Eurasian B. pendula. We use the 7,609 environmentally associated SNPs to estimate the risk of non-adaptedness for each sequenced B. platyphylla individual under a scenario of future climate change, highlighting areas where populations may be under future threat from rising temperatures.

evolutionary biology↗

bioRxiv2021

Genomic structure and diversity of oak populations in British Parklands

The two predominant oak species in Britain are Quercus robur (English or pedunculate oak) and Q. petraea (sessile oak). We sequenced the whole genomes of 386 oak trees from four British parkland sites and found over 50 million nuclear single nucleotide polymorphisms (SNPs), allowing us to identify 360 Q. robur, ten Q. petraea and 16 hybrid individuals using clustering methods. Comparing Q. robur and Q. petraea trees from Attingham Park, we found that the nuclear genomes of the two species are largely undifferentiated but identified 81 coding regions exhibiting strong interspecific differentiation. The nuclear genomes of our 360 Q. robur individuals showed no clear differentiation among the four parkland sites. Scans for selective sweeps in Q. robur highlighted regions containing genes with putative involvement in stress tolerance, one of which was moderately differentiated from Q. petraea. Reconstructions of past effective population sizes suggested a long population size decline in both Q. robur and Q. petraea over the Pleistocene, but population growth after the last glacial maximum. We assembled the whole chloroplast genomes of 287 Q. robur, 8 Q. petraea and 14 hybrid trees. In a phylogenetic network, these fell into five major haplotypes, which were shared among species but differed in frequency among parkland sites. We matched our chloroplast genome haplotypes to restriction enzyme fragment haplotypes identified in older studies that had surveyed ancient woodlands in Britain and much of Europe. This suggested that the parkland populations in our study derive from local seed sources.

genomics↗