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The tick Ixodes ricinus is the vector of various pathogens, including Chlamydiales bacteria, which potentially cause respiratory infections. In this study, we modeled the spatial distribution of I. ricinus and associated Chlamydiales over Switzerland from 2009 to 2019. We used a total of 2,293 ticks and 186 Chlamydiales occurrences provided by a Swiss Army field campaign, a collaborative smartphone application, and a prospective campaign. For each tick location, we retrieved from Swiss federal data sets the environmental factors reflecting the topography, climate, and land cover. We then used the Maxent modeling technique to estimate the suitability of particular areas for I. ricinus and to subsequently build the nested niche of Chlamydiales bacteria. Results indicate that I. ricinus habitat suitability is determined by higher temperature and normalized difference vegetation index (NDVI) values, lower temperature during the driest months, and a higher percentage of artificial and forest areas. The performance of the model was improved when extracting the environmental variables for a 100-m radius buffer around the sampling points and when considering the climatic conditions of the 2 years previous to the sampling date. Chlamydiales bacteria were favored by a lower percentage of artificial surfaces, drier conditions, high precipitation during the coldest months, and short distances to wetlands. From 2009 to 2018, we observed an extension of areas suitable to ticks and Chlamydiales, associated with a shift toward higher altitude. The importance of considering spatiotemporal variations in the environmental conditions for obtaining better prediction was also demonstrated., IMPORTANCE Ixodes ricinus is the vector of pathogens including the agent of Lyme disease, the tick-borne encephalitis virus, and the less well-known Chlamydiales bacteria, which are responsible for certain respiratory infections. In this study, we identified the environmental factors influencing the presence of I. ricinus and Chlamydiales in Switzerland and generated maps of their distribution from 2009 to 2018. We found an important expansion of suitable areas for both the tick and the bacteria during the last decade. Results also provided the environmental factors that determine the presence of Chlamydiales within ticks. Distribution maps as generated here are expected to bring valuable information for decision makers in controlling tick-borne diseases in Switzerland and establishing prevention campaigns. The methodological framework presented could be used to predict the distribution and spread of other host-pathogen pairs to identify environmental factors driving their distribution and to develop control or prevention strategies accordingly.

Background The clinical decisions of emergency department triage nurses need to be of the highest accuracy. However, studies have found repeatedly that these nurses over- or underestimate the severity of patient health conditions. This has major consequences for patient safety and patient flow management. Workplace distractors such as noise and task interruptions have been pointed to as factors that might explain this inaccuracy. The use of a serious game reproducing the work environment during triage affords the opportunity to explore the impact of these distractors on nurse emergency triage accuracy, in a safe setting. Methods/design A pilot study with a factorial design will be carried out to test the acceptability and feasibility of a serious game developed specifically to simulate the triage process in emergency departments and to explore the primary effects of distractors on nurse emergency triage accuracy. Eighty emergency nurses will be randomized into four groups: three groups exposed to different distractors (A, noise; B, task interruptions; C, noise and task interruptions) and one control group. All nurses will have to complete 20 clinical vignettes within 2 h. For each vignette, a gold standard assessment will be determined by experts. Pre-tests will be conducted with clinicians and certified emergency nurses to evaluate the appeal of the serious game. Discussion Study results will inform the design of large-scale investigations and will help identify teaching, training, and research areas that require further development.

The rate of aquatic invasions by planktonic organisms has increased considerably in recent decades. In order to effectively direct funding and resources to control the spread of such invasions, a methodological framework for identifying high-risk transport vectors, as well as ruling out vectors of lesser concern will be necessary. A number of estuarine ecosystems on the North American Pacific Northwest coast have experienced a series of high impact planktonic invasions that have slowly unfolded across the region in recent decades, most notably, that of the planktonic copepod crustacean Pseudodiaptomus inopinus. Although introduction of P. inopinus to the United States almost certainly occurred through the discharge of ballast water from commercial vessels originating in Asia (the species’ native range), the mechanisms and patterns of subsequent spread remain unknown. In order to elucidate the migration events shaping this invasion, we sampled the genomes of copepods from seven invasive and two native populations using restriction-site associated DNA sequencing. This genetic data was evaluated against spatially-explicit genetic simulation models to evaluate competing scenarios of invasion spread. Our results indicate that invasive populations of P. inopinus exhibit a geographically unstructured genetic composition, likely arising from infrequent and large migration events. This pattern of genetic patchiness was unexpected given the linear geographic structure of the sampled populations, and strongly contrasts with the clear invasion corridors observed in many aquatic systems.

Ease of worldwide travel provides increased opportunities for organisms not only to colonize new environments but also to encounter related but diverged populations. Such events of reconnection and secondary contact of previously isolated populations are widely observed at different time scales. For example, during the quaternary glaciation, sea water level fluctuations caused temporal isolation of populations, often to be followed by secondary contact. At shorter time scales, population isolation and reconnection of viruses are commonly observed, and such events are often associated with epidemics and pandemics. Here, using coalescent theory and simulations, we describe the temporal impact of population reconnection after isolation on nucleotide differences and the site frequency spectrum, as well as common summary statistics of DNA variation. We identify robust genomic signatures of population reconnection after isolation. We utilize our development to infer the recent evolutionary history of human immunodeficiency virus 1 (HIV-1) in Asia and South America, successfully retrieving the successive HIV subtype colonization events in these regions. Our analysis reveals that divergent HIV-1 subtype populations are currently admixing in these regions, suggesting that HIV-1 may be undergoing a process of homogenization, contrary to popular belief.

A workshop recently held at the Ecole Polytechnique Federale de Lausanne (EPFL, Switzerland) was dedicated to understanding the genetic basis of adaptive change, taking stock of the different approaches developed in theoretical population genetics and landscape genomics and bringing together knowledge accumulated in both research fields. Indeed, an important challenge in theoretical population genetics is to incorporate effects of demographic history and population structure. But important design problems (e.g. focus on populations as units, focus on hard selective sweeps, no hypothesis-based framework in the design of the statistical tests) reduce their capability of detecting adaptive genetic variation. In parallel, landscape genomics offers a solution to several of these problems and provides a number of advantages (e.g. fast computation, landscape heterogeneity integration). But the approach makes several implicit assumptions that should be carefully considered (e.g. selection has had enough time to create a functional relationship between the allele distribution and the environmental variable, or this functional relationship is assumed to be constant). To address the respective strengths and weaknesses mentioned above, the workshop brought together a panel of experts from both disciplines to present their work and discuss the relevance of combining these approaches, possibly resulting in a joint software solution in the future.

Many features of virus populations make them excellent candidates for population genetic study, including a very high rate of mutation, high levels of nucleotide diversity, exceptionally large census population sizes, and frequent positive selection. However, these attributes also mean that special care must be taken in population genetic inference. For example, highly skewed offspring distributions, frequent and severe population bottleneck events associated with infection and compartmentalization, and strong purifying selection all affect the distribution of genetic variation but are often not taken into account. Here, we draw particular attention to multiple-merger coalescent events and background selection, discuss potential misinference associated with these processes, and highlight potential avenues for better incorporating them into future population genetic analyses.

Self-incompatibility (SI), a reproductive system broadly present in plants, chordates, fungi, and protists, might be controlled by one or several multiallelic loci. How a transition in the number of SI loci can occur and the consequences of such events for the population's genetics and dynamics have not been studied theoretically. Here, we provide analytical descriptions of two transition mechanisms: linkage of the two SI loci (scenario 1) and the loss of function of one incompatibility gene within a mating type of a population with two SI loci (scenario 2). We show that invasion of populations by the new mating type form depends on whether the fitness of the new type is lowered, and on the allelic diversity of the SI loci and the recombination between the two SI loci in the starting population. Moreover, under scenario 1, it also depends on the frequency of the SI alleles that became linked. We demonstrate that, following invasion, complete transitions in the reproductive system occurs under scenario 2 and is predicted only for small populations under scenario 1. Interestingly, such events are associated with a drastic reduction in mating type number.

Although dispersal is recognized as a key issue in several fields of population biology (such as behavioral ecology, population genetics, metapopulation dynamics or evolutionary modeling), these disciplines focus on different aspects of the concept and often make different implicit assumptions regarding migration models. Using simulations, we investigate how such assumptions translate into effective gene flow and fixation probability of selected alleles. Assumptions regarding migration type (e.g. source-sink, resident pre-emption, or balanced dispersal) and patterns (e.g. stepping-stone versus island dispersal) have large impacts when demes differ in sizes or selective pressures. The effects of fragmentation, as well as the spatial localization of newly arising mutations, also strongly depend on migration type and patterns. Migration rate also matters: depending on the migration type, fixation probabilities at an intermediate migration rate may lie outside the range defined by the low- and high-migration limits when demes differ in sizes. Given the extreme sensitivity of fixation probability to characteristics of dispersal, we underline the importance of making explicit (and documenting empirically) the crucial ecological/ behavioral assumptions underlying migration models.

International audience; We simulated a meta-population with random dispersal among demes but local mating within demes to investigate conditions under which a dominant female-determining gene W, with no individual selection advantage, can invade and become fixed in females, changing the population from male to female heterogamety. Starting with one mutant W in a single deme, the interaction of sex ratio selection and random genetic drift causes W to be fixed among females more often than a comparable neutral mutation with no influence on sex determination, even when YY males have slightly reduced viability. Meta-population structure and interdeme selection can also favour the fixation of W. The reverse transition from female to male heterogamety can also occur with higher probability than for a comparable neutral mutation. These results help to explain the involvement of sex-determining genes in the evolution of sex chromosomes and in sexual selection and speciation.

Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g., bottleneck and expansion) and spatial structure (e.g., migration, number, and size of populations) are known to shape the patterns of the genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species’ lifetime, repeated isolation and reconnection of populations occur. Geological and climatic events alternately isolate and reconnect habitats. We analytically document the dynamics of genetic diversity after an abrupt change in migration given the mutation rate and the number and sizes of the populations. We demonstrate that during transient dynamics, genetic diversity can reach unexpectedly high values that can be maintained over thousands of generations. We discuss the consequences of such processes for the evolution of species based on standing genetic variation and how they can affect the reconstruction of a population’s demographic and evolutionary history from genetic data. Our results also provide guidelines for the use of genetic data for the conservation of natural populations.

International audience; Mating systems, that is, whether organisms give rise to progeny by selfing, inbreeding or outcrossing, strongly affect important ecological and evolutionary processes. Large variations in mating systems exist in fungi, allowing the study of their origin and consequences. In fungi, sexual incompatibility is determined by molecular recognition mechanisms, controlled by a single mating-type locus in most unifactorial fungi. In Basidiomycete fungi, however, which include rusts, smuts and mushrooms, a system has evolved in which incompatibility is controlled by two unlinked loci. This bifactorial system probably evolved from a unifactorial system. Multiple independent transitions back to a unifactorial system occurred. It is still unclear what force drove evolution and maintenance of these contrasting inheritance patterns that determine mating compatibility. Here, we give an overview of the evolutionary factors that might have driven the evolution of bifactoriality from a unifactorial system and the transitions back to unifactoriality. Bifactoriality most likely evolved for selfing avoidance. Subsequently, multiallelism at mating-type loci evolved through negative frequency-dependent selection by increasing the chance to find a compatible mate. Unifactoriality then evolved back in some species, possibly because either selfing was favoured or for increasing the chance to find a compatible mate in species with few alleles. Owing to the existence of closely related unifactorial and bifactorial species and the increasing knowledge of the genetic systems of the different mechanisms, Basidiomycetes provide an excellent model for studying the different forces that shape breeding systems.

Host shifts can cause novel infectious diseases and is a key process in diversification. Disentangling the effects of host shift versus those of cospeciation is non trivial as both can result in phylogenic congruence. We develop a new framework based on network analysis and Approximate Bayesian Computation to quantify host shift and cospeciation rates in host parasite systems. Our method enables estimation of the expected time to the next host shift or cospeciation event. We then apply it to avian haemosporidian parasite systems and to the pocket gophers chewing lice system and demonstrate that both host shift and co speciation can be reliably estimated by our method. We confirm that host shifts have shaped the evolutionary history of avian haemosporidian parasites and have played a minor role in the gopher–chewing lice system. Our method is promising for predicting the rate of potential host shifts and thus the emergence of novel infectious diseases.

International audience; Over the past two decades, an increasing amount of phylogeographic work has sub- stantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial–drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi-aquatic animals, which faced tre- mendous challenges imposed by unpredictable availability of water resources. In this study, we investigate the Late Pleistocene history of the common hippopotamus (Hip- popotamus amphibius), using mitochondrial and nuclear DNA sequence variation and range-wide sampling. We documented a global demographic and spatial expansion approximately 0.1–0.3 Myr ago, most likely associated with an episode of massive drainage overflow. These events presumably enabled a historical continent-wide gene flow among hippopotamus populations, and hence, no clear continental-scale genetic structuring remains. Nevertheless, present-day hippopotamus populations are geneti- cally disconnected, probably as a result of the mid-Holocene aridification and contem- porary anthropogenic pressures. This unique pattern contrasts with the biogeographic paradigms established for savannah-adapted ungulate mammals and should be further investigated in other water-associated taxa. Our study has important consequences for the conservation of the hippo, an emblematic but threatened species that requires specific protection to curtail its long-term decline.

Occurrence of bacteria belonging to the order Chlamydiales was investigated for the first time in common toad ( Bufo bufo ) tadpole populations collected from 41 ponds in the Geneva metropolitan area, Switzerland. A Chlamydiales -specific real-time PCR was used to detect and amplify the Chlamydiales 16S ribosomal RNA-encoding gene from the tails of 375 tadpoles. We found the studied amphibian populations to host Chlamydia -like organisms (CLOs) attributable to the genera Similichlamydia, Neochlamydia, Protochlamydia and Parachlamydia (all belonging to the family Parachlamydiaceae ), Simkania (family Simkaniaceae ) and Estrella (family Criblamydiaceae ); additionally, DNA from the genus Thermoanaerobacter (family Thermoanaerobacteriaceae ) was detected. Global autocorrelation analysis did not reveal a spatial structure in the observed CLOs occurrence rates, and association tests involving land cover characteristics did not evidence any clear effect on CLOs occurrence rates in B. bufo. Although preliminary, these results suggest a random and ubiquitous distribution of CLOs in the environment, which would support the biogeographical expectation 'everything is everywhere' for the concerned microorganisms.