Directional genetic differentiation and asymmetric migration

Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly used to gather this information. One potential caveat is that these measures assume gene flow to be symmetric. However, asymmetric gene flow is common in nature, especially in systems driven by physical processes such as wind or water currents. Since information about levels of asymmetric gene flow among populations is essential for the correct interpretation of the distribution of contemporary genetic diversity within species, this should not be overlooked. To obtain information on asymmetric migration patterns from genetic data, complex models based on maximum likelihood or Bayesian approaches generally need to be employed, often at great computational cost. Here, a new simpler and more efficient approach for understanding gene flow patterns is presented. This approach allows the estimation of directional components of genetic divergence between pairs of populations at low computational effort, using any of the classical or modern measures of genetic differentiation. These directional measures of genetic differentiation can further be used to calculate directional relative migration and to detect asymmetries in gene flow patterns. This can be done in a user-friendly web application called divMigrate-online introduced in this paper. Using simulated data sets with known gene flow regimes, we demonstrate that the method is capable of resolving complex migration patterns under a range of study designs.Comment: 25 pages, 8 (+3) figures, 1 tabl

Safety, the Preface Paradox and Possible Worlds Semantics

This paper contains an argument to the effect that possible worlds semantics renders semantic knowledge impossible, no matter what ontological interpretation is given to possible worlds. The essential contention made is that possible worlds semantic knowledge is unsafe and this is shown by a parallel with the preface paradox

A genome-wide investigation of the worldwide invader Sargassum muticum shows high success albeit (almost) no genetic diversity

Twenty years of genetic studies of marine invaders have shown that successful invaders are often characterized by native and introduced populations displaying similar levels of genetic diversity. This pattern is presumably due to high propagule pressure and repeated introductions. The opposite pattern is reported in this study of the brown seaweed, Sargassum muticum, an emblematic species for circumglobal invasions. Albeit demonstrating polymorphism in the native range, microsatellites failed to detect any genetic variation over 1,269 individuals sampled from 46 locations over the Pacific-Atlantic introduction range. Single-nucleotide polymorphisms (SNPs) obtained from ddRAD sequencing revealed some genetic variation, but confirmed severe founder events in both the Pacific and Atlantic introduction ranges. Our study thus exemplifies the need for extreme caution in interpreting neutral genetic diversity as a proxy for invasive potential. Our results confirm a previously hypothesized transoceanic secondary introduction from NE Pacific to Europe. However, the SNP panel unexpectedly revealed two additional distinct genetic origins of introductions. Also, conversely to scenarios based on historical records, southern rather than northern NE Pacific populations could have seeded most of the European populations. Finally, the most recently introduced populations showed the lowest selfing rates, suggesting higher levels of recombination might be beneficial at the early stage of the introduction process (i.e., facilitating evolutionary novelties), whereas uniparental reproduction might be favored later in sustainably established populations (i.e., sustaining local adaptation).Agence Nationale de la Recherche - ANR-10-BTBR-04; European Regional Development Fund; Fundacao para a Ciencia e a Tecnologia - SFRH/BPD/107878/2015, UID/Multi/04326/2016, UID/Multi/04326/2019; Brittany Region;info:eu-repo/semantics/publishedVersio

Increasing the intensity and comprehensiveness of aphasia services: identification of key factors influencing implementation across six countries

Background: Aphasia services are currently faced by increasing evidence for therapy of greater intensity and comprehensiveness. Intensive Comprehensive Aphasia Programs (ICAPs) combine these elements in an evidence-based, time-limited group program. The incorporation of new service delivery models in routine clinical practice is, however, likely to pose challenges for both the service provider and administering clinicians. This program of research aims to identify these challenges from the perspective of aphasia clinicians from six countries and will seek to trial potential solutions. Continual advancements in global communication technologies suggest that solutions will be easily shared and accessed across multiple countries. Aims: To identify the perceived and experienced barriers and facilitators to the implementation of 1) intensive aphasia services, 2) comprehensive aphasia services, and 3) ICAPs, from aphasia clinicians across six countries. Methods and procedures: A qualitative enquiry approach included data from six focus groups (n = 34 participants) in Australia, New Zealand, Canada, United States of America (USA), United Kingdom (UK), and Ireland. A thematic analysis of focus group data was informed by the Theoretical Domains Framework (TDF). Outcomes and results: Five prominent theoretical domains from the TDF influenced the implementation of all three aphasia service types across participating countries: environmental context and resources, beliefs about consequences, social/professional role and identity, skills, and knowledge. Four overarching themes assisted the identification and explanation of the key barriers and facilitators: 1. Collaboration, joint initiatives and partnerships, 2. Advocacy, the promotion of aphasia services and evidence-based practice, 3. Innovation, the ability to problem solve challenges, and 4. Culture, the influence of underlying values. Conclusions: The results of this study will inform the development of a theoretically informed intervention to improve health services’ adherence to aphasia best practice recommendations

Incidence of childhood renal tumours: An international population-based study

Malignant renal tumours represent 5% of childhood cancers and include types with likely different aetiology: Wilms tumour (WT), rhabdoid renal tumour, kidney sarcomas and renal carcinomas. WT is the most common renal tumour in children, previously shown to vary internationally and with ethnicity. Using the comprehensive database of the International Incidence of Childhood Cancer study (IICC), we analysed global variations and time trends in incidence of renal tumour types in children (age 0‐14 years) and adolescents (age 15‐19 years). The results were presented by 14 world regions, and five ethnic groups in the United States. We included 15 320 renal tumours in children and 800 in adolescents reported to the 163 contributing registries during 2001‐2010. In children, age‐standardised incidence rate (ASR) of renal tumours was 8.3 per million (95% confidence interval, CI = 8.1, 8.4); it was the highest in North America and Europe (9‐10 per million) and the lowest in most Asian regions (4‐5 per million). In the United States, Blacks had the highest ASR (10.9 per million, 95% CI = 10.2, 11.6) and Asian and Pacific Islanders the lowest (4.4 per million, 95% CI = 3.6, 5.1). In adolescents, age‐specific incidence rate of renal tumours was 1.4 per million (95% CI = 1.3, 1.5). WT accounted for over 90% of all renal tumours in each age from 1 to 7 years and the proportion of renal carcinomas increased gradually with age. From 1996 to 2010, incidence remained mostly stable for WT (average annual percent change, AAPC = 0.1) and increased for renal carcinomas in children (AAPC = 3.7) and adolescents (AAPC = 3.2). Our findings warrant further monitoring

European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation?

Extant populations of the European wildcat are fragmented across the continent, the likely consequence of recent extirpations due to habitat loss and over-hunting. However, their underlying phylogeographic history has never been reconstructed. For testing the hypothesis that the European wildcat survived the Ice Age fragmented in Mediterranean refuges, we assayed the genetic variation at 31 microsatellites in 668 presumptive European wildcats sampled in 15 European countries. Moreover, to evaluate the extent of subspecies/population divergence and identify eventual wild × domestic cat hybrids, we genotyped 26 African wildcats from Sardinia and North Africa and 294 random-bred domestic cats. Results of multivariate analyses and Bayesian clustering confirmed that the European wild and the domestic cats (plus the African wildcats) belong to two well-differentiated clusters (average Ф ST = 0.159, r st = 0.392, P > 0.001; Analysis of molecular variance [AMOVA]). We identified from c. 5% to 10% cryptic hybrids in southern and central European populations. In contrast, wild-living cats in Hungary and Scotland showed deep signatures of genetic admixture and introgression with domestic cats. The European wildcats are subdivided into five main genetic clusters (average Ф ST = 0.103, r st = 0.143, P > 0.001; AMOVA) corresponding to five biogeographic groups, respectively, distributed in the Iberian Peninsula, central Europe, central Germany, Italian Peninsula and the island of Sicily, and in north-eastern Italy and northern Balkan regions (Dinaric Alps). Approximate Bayesian Computation simulations supported late Pleistocene-early Holocene population splittings (from c. 60 k to 10 k years ago), contemporary to the last Ice Age climatic changes. These results provide evidences for wildcat Mediterranean refuges in southwestern Europe, but the evolution history of eastern wildcat populations remains to be clarified. Historical genetic subdivisions suggest conservation strategies aimed at enhancing gene flow through the restoration of ecological corridors within each biogeographic units. Concomitantly, the risk of hybridization with free-ranging domestic cats along corridor edges should be carefully monitored

Environmental factors influence both abundance and genetic diversity in a widespread bird species.

Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations

Museum DNA reveals the demographic history of the endangered Seychelles warbler

The importance of evolutionary conservation – how understanding evolutionary forces can help guide conservation decisions – is widely recognized. However, the historical demography of many endangered species is unknown, despite the fact that this can have important implications for contemporary ecological processes and for extinction risk. Here, we reconstruct the population history of the Seychelles warbler (Acrocephalus sechellensis) – an ecological model species. By the 1960s, this species was on the brink of extinction, but its previous history is unknown. We used DNA samples from contemporary and museum specimens spanning 140 years to reconstruct bottleneck history. We found a 25% reduction in genetic diversity between museum and contemporary populations, and strong genetic structure. Simulations indicate that the Seychelles warbler was bottlenecked from a large population, with an ancestral Ne of several thousands falling to <50 within the last century. Such a rapid decline, due to anthropogenic factors, has important implications for extinction risk in the Seychelles warbler, and our results will inform conservation practices. Reconstructing the population history of this species also allows us to better understand patterns of genetic diversity, inbreeding and promiscuity in the contemporary populations. Our approaches can be applied across species to test ecological hypotheses and inform conservation

The role of imaging in the initial investigation of paediatric renal tumours.

Imaging has a key role in the assessment of paediatric renal tumours, especially when the initial treatment approach is to proceed to standard chemotherapy without histological confirmation. In Europe, according to the International Society of Paediatric Oncology guidelines, core needle biopsy is not routinely done unless the child is older than 10 years. Between age 6 months and 9 years, the child is treated with a standard regimen of preoperative chemotherapy unless there are concerns about non-Wilms' tumour pathology. Atypical imaging findings could therefore stratify a child into a different treatment protocol, and can prompt the need for pretreatment histology. This review details the latest protocols and techniques used in the assessment of paediatric renal tumours. Important imaging findings are discussed, especially the features that might prompt the need for a pretreatment biopsy. Local radiology practices vary, but both MRI and CT are widely used as routine imaging tests for the assessment of paediatric renal tumours in Europe. Advances in imaging technology and MRI sequences are facilitating the development of new techniques, which might increase the utility of imaging in terms of predicting tumour histology and clinical behaviour. Several of these new imaging techniques are outlined here