Combining GWAS and FST-based approaches to identify targets of Borrelia-mediated selection in natural rodent hosts

This is the author accepted manucript. The final version is available from Wiley via the DOI in this recordData accessibility: The Genotyping-by-Sequencing data are deposited in NCBI BioProject PRJNA306409, SRA experiment SRR3031372. The quality filtered SNP file used for population genomic analyses and information on population and infection status of individual bank voles are deposited in the Dryad repository doi:10.5061/dryad.c866t1g3tRecent advances in high-throughput sequencing technologies provide opportunities to gain novel insights into the genetic basis of phenotypic trait variation. Yet to date, progress in our understanding of genotype-phenotype associations in non-model organisms in general and natural vertebrate populations in particular has been hampered by small sample sizes typically available for wildlife populations and a resulting lack of statistical power, as well as a limited ability to control for false positive signals. Here we propose to combine a genome-wide association (GWAS) and FST-based approach with population-level replication to partly overcome these limitations. We present a case study in which we used this approach in combination with Genotyping-by-Sequencing (GBS) SNP data to identify genomic regions associated with Borrelia afzelii resistance or susceptibility in the natural rodent host of this Lyme disease-causing spirochete, the bank vole (Myodes glareolus). Using this combined approach we identified four consensus SNPs located in exonic regions of the genes Slc26a4, Tns3, Wscd1 and Espnl, which were significantly associated with the voles’ Borrelia infectious status within and across populations. Functional links between host responses to bacterial infections and most of these genes have previously been demonstrated in other rodent systems, making them promising new candidates for the study of evolutionary host responses to Borrelia emergence. Our approach is applicable to other systems and may facilitate the identification of genetic variants underlying disease resistance or susceptibility, as well as other ecologically relevant traits, in wildlife populations.University of Zuric

The Genome of the "Great Speciator" Provides Insights into Bird Diversification

Among birds, white-eyes (genus Zosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the “great speciator.” The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation

Small-scale spatial variation in infection risk shapes the evolution of a Borrelia resistance gene in wild rodents

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordSpatial variation in pathogen-mediated selection is predicted to influence the evolutionary trajectory of host populations and lead to spatial variation in their immunogenetic composition. However, to date few studies have been able to directly link small-scale spatial variation in infection risk to host immune gene evolutionin natural,non-human populations. Here we use a natural rodent-Borrelia system to test for associations between landscape-level spatial variation in Borrelia infection risk along replicated elevational gradients in the Swiss Alps and Toll-like receptor 2(TLR2) evolution, a candidate gene for Borrelia resistance, across bank vole (Myodes glareolus) populations.We found that Borrelia infection risk (i.e. the product of Borrelia prevalence in questing ticks and the average tick load of voles at a sampling site) was spatially variable and significantly negatively associated with elevation. Across sampling sites, Borrelia prevalence in bank voles was significantly positively associated with Borrelia infection risk along the elevational clines. We observed a significant association between naturally occurring TLR2 polymorphisms in hosts and their Borrelia infection status. The TLR2 variant associated with a reduced likelihood of Borrelia infection was most common in rodent populations at lower elevations that face a high Borreliainfection risk, and its frequency changed in accordance with the change in Borrelia infection risk along the elevational clines. These results suggest that small-scale spatial variation in parasite-mediated selection affects the immunogenetic composition of natural host populations, providing a striking example that the microbial environment shapes the evolution of the host’s immune system in the wild.Swiss National Science FoundationStiftung für wissenschaftliche Forschung an der Universität ZürichFaculty of Science of the University of ZurichBaugarten StiftungGeorges und Antoine Claraz‐Schenkun

Tick range expansion to higher elevations: does Borrelia burgdorferi sensu lato facilitate the colonisation of marginal habitats?

This is the final version. Available on open access from BMC via the DOI in this recordAvailability of data and materials: The dataset supporting the conclusions of this article is included within the article and its additional files.Background Parasites can alter host and vector phenotype and thereby affect ecological processes in natural populations. Laboratory studies have suggested that Borrelia burgdorferi sensu lato, the causative agent of human Lyme borreliosis, may induce physiological and behavioural alterations in its main tick vector in Europe, Ixodes ricinus, which increase the tick’s mobility and survival under challenging conditions. These phenotypic alterations may allow I. ricinus to colonise marginal habitats (‘facilitation hypothesis’), thereby fuelling the ongoing range expansion of I. ricinus towards higher elevations and latitudes induced by climate change. To explore the potential for such an effect under natural conditions, we studied the prevalence of B. burgdorferi s.l. in questing I. ricinus and its variation with elevation in the Swiss Alps. Results We screened for B. burgdorferi s.l. infection in questing nymphs of I. ricinus (N = 411) from 15 sites between 528 and 1774 m.a.s.l to test if B. burgdorferi s.l. prevalence is higher at high elevations (i.e. in marginal habitats). Opposite of what is predicted under the facilitation hypothesis, we found that B. burgdorferi s.l. prevalence in I. ricinus nymphs decreased with increasing elevation and that Borrelia prevalence was 12.6% lower in I. ricinus nymphs collected at the range margin compared to nymphs in the core range. But there was no association between Borrelia prevalence and elevation within the core range of I. ricinus. Therefore the observed pattern was more consistent with a sudden decrease in Borrelia prevalence above a certain elevation, rather than a gradual decline with increasing elevation across the entire tick range. Conclusions In conclusion, we found no evidence that B. burgdorferi s.l.-induced alterations of I. ricinus phenotype observed in laboratory studies facilitate the colonisation of marginal habitats in the wild. Rather, ticks in marginal habitats are substantially less likely to harbour the pathogen. These findings have implications for a better understanding of eco-evolutionary processes in natural host-parasite systems, as well as the assessment of Lyme borreliosis risk in regions where I. ricinus is newly emerging.University of ZurichSwiss National Science FoundationBaugarten Stiftung & Stiftung für wissenschaftliche Forschung an der Universität ZürichGeorges und Antoine Claraz-Schenkun

Mechanics of fragmentation of crocodile skin and other thin films

Fragmentation of thin layers of materials is mediated by a network of cracks on its surface. It is commonly seen in dehydrated paintings or asphalt pavements and even in graphene or other two-dimensional materials, but is also observed in the characteristic polygonal pattern on a crocodile’s head. Here, we build a simple mechanical model of a thin film and investigate the generation and development of fragmentation patterns as the material is exposed to various modes of deformation. We find that the characteristic size of fragmentation, defined by the mean diameter of polygons, is strictly governed by mechanical properties of the film material. Our result demonstrates that skin fragmentation on the head of crocodiles is dominated by that it features a small ratio between the fracture energy and Young’s modulus, and the patterns agree well with experimental observations. Understanding this mechanics-driven process could be applied to improve the lifetime and reliability of thin film coatings by mimicking crocodile skin

A simple dynamic model explains the diversity of island birds worldwide

International audienc

Widespread adaptive evolution during repeated evolutionary radiations in New World lupins

The evolutionary processes that drive rapid species diversification are poorly understood. In particular, it is unclear whether Darwinian adaptation or non-adaptive processes are the primary drivers of explosive species diversifications. Here we show that repeated rapid radiations within New World lupins (Lupinus, Leguminosae) were underpinned by a major increase in the frequency of adaptation acting on coding and regulatory changes genome-wide. This contrasts with far less frequent adaptation in genomes of slowly diversifying lupins and all other plant genera analysed. Furthermore, widespread shifts in optimal gene expression coincided with shifts to high rates of diversification and evolution of perenniality, a putative key adaptation trait thought to have triggered the evolutionary radiations in New World lupins. Our results reconcile long-standing debate about the relative importance of protein-coding and regulatory evolution, and represent the first unambiguous evidence for the rapid onset of lineage- and genome-wide accelerated Darwinian evolution during rapid species diversification

Small effective population size and fragmentation in Alpine populations of Bombina variegata: the combined effects of recent bottlenecks and postglacial recolonization

Amphibians are experiencing population declines in all continents due to anthropogenic factors. Evidence of demographic reduction and local extinction have been reported also for the yellow-bellied toad, Bombina variegata, along all its distributional range, which includes the Italian Alps. Here we genotyped at the mtDNA cytb and at 11 nuclear microsatellites 200 individuals of B. variegata from 9 populations sampled in Trentino (north-eastern Italy). We investigated the fine-scale population structure and we tested for genetic traces of population decline using different methods. We found that all populations showed low level of genetic diversity in comparison with other studies, low estimates of effective population size, and clear evidence of demographic decline. When the age of the decline is estimated, contrasting results are found. Some methods suggest a recent reduction of population size possibly associated with anthropogenic environmental changes, and others support a more ancient bottleneck dating back to the postglacial recolonization of the Alps. We suggest that both demographic processes occurred in the evolutionary history of the yellow-bellied toad populations, and we are now testing this hypothesis by simulation

NGS approach for investigating evolutionary transition form oviparity to viviparity in squamate reptiles

Some squamate reptile species provide a unique model system for gaining crucial information about the evolutionary transition from oviparity to viviparity in vertebrates. The lizard Zootoca vivipara is one of the few species with distinct reproductive modalities in different subspecies; in particular, Z. v. carniolica is an egg-laying lizard while Z. v. vivipara is a live-bearing one; they both live in the Eastern Italian Alps, sometimes in sintopy. This provides an interesting natural setting for studying the evolutionary shift in reproductive mode. Some populations were analysed using classical genetic markers (mitochondrial, nuclear DNA sequences and autosomal microsatellites). The mtDNA results indicated a marked divergence between the two subspecies (around 5% at the cytochrome B), as well as nuclear microsatellites. Possible existence of hybrid individuals in Carnic Alps, as recently reported by morphological evidences, has boosted the interest on this topic. RAD-tag sequencing, a next-generation sequencing technique that allows simultaneously discovering and analyzing hundreds of thousands of SNPs, was then applied to Zootoca vivipara subspecies in order to identify mutations correlated with the reproductive modality and with related adaptive traits

A simplified approach to hydraulic fracturing of rocks based on Finite Fracture Mechanics

This work presents a coupled approach, based on Finite Fracture Mechanics (FFM), to preliminarily investigate hydraulic fracturing of rocks. The novelty of the criterion relies on the assumption of a finite crack extension and on the simultaneous fulfilment of a stress requirement and the energy balance. Two material constants are involved, namely the tensile strength and the fracture toughness. The FFM unknowns are represented by the critical crack advance, which results a structural parameter and not a simple material one, and the breakdown pressure. The study investigates the longitudinal failure behaviour of both impermeable and permeable rocks by supposing that growing cracks are loaded by a pressure proportional to that acting on the borehole wall. The stability growth of hydraulic fractures is discussed case by case. The approach is validated against experimental data available in the literature by considering the effect of rock permeability, fluid viscosity and flow rate