Biology subjects

Gugerli, F.

Publications and source records attributed to Gugerli, F..

4 recordsLinked to original sources

bioRxiv2023

Local-scale divergent selection in a Mediterranean pine

The effects of selection on an organisms genome are hard to detect on small spatial scales, as gene flow can erase signatures of local adaptation. Most genome scans to detect signatures of environmental selection are performed on large spatial scales, however divergent selection on the local scale (e.g. between contrasting soil conditions) has also been demonstrated, in particular for herbaceous plants. Here we hypothesize that in topographically complex landscapes, microenvironment variability is strong enough to leave a selective footprint in genomes of long-lived organisms. To test this, we investigated paired south- versus north-facing Pinus pinaster stands in a Mediterranean mountain area. While north-facing (mesic) stands experience less radiation, south facing (xeric) stands represent especially harsh conditions, particularly during the dry summer season. Outlier detection revealed five putatively adaptive loci out of 4,034, two of which encoded non-synonymous substitutions. Additionally, one locus showed consistent allele frequency differences in all three stand pairs indicating divergent selection despite high gene flow on the local scale. Functional annotation of these candidate genes revealed biological functions related to abiotic stress response in other species. Our study highlights how divergent selection shapes the functional genetic variation within populations of long-lived forest trees on local spatial scales.

plant biology↗

bioRxiv2023

Synchronous effective population size changes and genetic stability of forest trees through glacial cycles

The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we performed comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasted European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, Ne, increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Hence, surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of Ne over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity, over time. Altogether, our results indicate that forest trees were able to retain their evolutionary potential over very long periods of time despite strong environmental changes. One-Sentence SummaryPopulation genomic analyses reveal that forest trees retained their evolutionary potential over the Quaternary.

evolutionary biology↗

bioRxiv2018

Using transcriptome sequencing and pooled exome capture to study local adaptation in the giga-genome of Pinus cembra

Despite decreasing sequencing costs, whole-genome sequencing for population-based genome scans for selection is still prohibitively expensive for organisms with large genomes. Moreover, the repetitive nature of large genomes often represents a challenge in bioinformatic and downstream analyses. Here we use in-depth transcriptome sequencing to design probes for exome capture in Swiss stone pine (Pinus cembra), a conifer with an estimated genome size of 29.3 Gbp and no reference genome available. We successfully applied around 55,000 self-designed probes, targeting 25,000 contigs, to DNA pools of seven populations from the Swiss Alps and identified > 140,000 SNPs in around 13,000 contigs. The probes performed equally well in pools of the closely related species Pinus sibirica; in both species, more than 70% of the targeted contigs were sequenced at a depth [≥] 40x, i.e. the number of haplotypes in the pool. However, a thorough analysis of individually sequenced P. cembra samples indicated that a majority of the contigs (63%) represented multi-copy genes. We therefore removed paralogous contigs based on heterozygote excess and deviation from allele balance. Without putatively paralogous contigs, allele frequencies of population pools represented accurate estimates of individually determined allele frequencies. Using population genetic and landscape genomic methods, we show that inferences of neutral and adaptive genetic variation may be biased when not accounting for such multi-copy genes. Future studies should therefore put more emphasis on identifying paralogous loci, which will be facilitated by the establishment of additional high-quality reference genomes.

genomics↗

bioRxiv2018

Adaptation to local climate in size, growth and phenology across 19 silver fir (Abies alba Mill.) populations from Switzerland

Attempts to identify and understand selection pressures responsible for local adaptation are central to evolutionary research. We tested whether populations of silver fir (Abies alba Mill.), sampled across a heterogeneous environment, have more strongly diverged at quantitative traits than expected from genetic drift. We genotyped 387 trees from 19 Swiss populations at 374 single-nucleotide polymorphisms (SNPs) to estimate their demographic distances, and used these to generate a null expectation for divergence in a multi-trait space including morphology and life-history traits obtained from a published common garden trial. Local soil and historical climate data were used to identify the selective environment of the source populations. Our results revealed a strong selection on height driven by temperature: trees from warm sites evolved to become taller than those from cooler sites. The evolution of growth rate, growth duration and bud break were correlated, and populations evolved towards two extreme strategies, \"start early and grow slow\" or \"start late and grow fast\", driven by precipitation seasonality. We conclude that local climate has shaped the morphology and life-history of silver fir populations since they recolonized the Alps. Our methodology provides a show-case for empirical evaluation of adaptive evolutionary strategies combining genetic data and common gardens.

evolutionary biology↗