Graham Stone results 27
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Germline copy number variants and endometrial cancer riskNARA Subscribed
Known risk loci for endometrial cancer explain approximately one third of familial endometrial cancer. However, the association of germline copy number variants (CNVs) with endometrial cancer risk remains relatively unknown. We conducted a genome-wide analysis of rare CNVs overlapping gene regions in 4115 endometrial cancer cases and 17,818 controls to identify functionally relevant variants associated with disease. We identif...
Defining an ageing-related pathology, disease or syndrome: International Consensus StatementNARA Subscribed
Around the world, individuals are living longer, but an increased average lifespan does not always equate to an increased health span. With advancing age, the increased prevalence of ageing-related diseases can have a significant impact on health status, functional capacity and quality of life. It is therefore vital to develop comprehensive classification and staging systems for ageing-related pathologies, diseases and syndrom...
Delimiting the cryptic diversity and host preferences of Sycophila parasitoid wasps associated with oak galls using phylogenomic dataNARA Subscribed
Cryptic species diversity is a major challenge regarding the species‐rich community of parasitoids attacking oak gall wasps due to a high degree of sexual dimorphism, morphological plasticity, small size and poorly known biology. As such, we know very little about the number of species present, nor the evolutionary forces responsible for generating this diversity. One hypothesis is that trait diversity in the gall wasps, inclu...
Plant galls are novel and sometimes dramatic plant organs whose development is initiated and controlled by parasitic microbes, nematodes, insects and mites. For arthropods, galls provide relative safety from enemies and abiotic stresses while providing nutrition. Galls are formed entirely by the plant, whose transcriptional pathways are modified and coopted to produce a structure specific to the galler species; they comprise a...
Discordant Pleistocene population size histories in a guild of hymenopteran parasitoidsNARA Subscribed
Signatures of past changes in population size have been detected in genome‐wide variation in many species. However, the causes of such demographic changes and the extent to which they are shared across co‐distributed species remain poorly understood. During Pleistocene glacial maxima, many temperate European species were confined to southern refugia. While vicariance and range expansion processes associated with glacial cycles...
Sharing and reporting benefits from biodiversity researchNARA Subscribed
Low‐coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig waspNARA Subscribed
Population divergence and gene flow are key processes in evolution and ecology. Model‐based analysis of genome‐wide data sets allows discrimination between alternative scenarios for these processes even in nonmodel taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum [bSFS], the second on the pairwise sequentially Markovian coalescent [PSMC]) to infer the divergence history of a fig wa...
Rather little is known about the dietary richness and variation of generalist insectivorous species, including birds, due primarily to difficulties in prey identification. Using faecal metabarcoding, we provide the most comprehensive analysis of a passerine's diet to date, identifying the relative magnitudes of biogeographic, habitat and temporal trends in the richness and turnover in diet of Cyanistes caeruleus (blue tit) alo...
Tournament ABC analysis of the western Palaearctic population history of an oak gall wasp, Synergus umbraculusNARA Subscribed
Approximate Bayesian computation ( ABC ) is a powerful and widely used approach in inference of population history. However, the computational effort required to discriminate among alternative historical scenarios often limits the set that is compared to those considered more likely a priori. While often justifiable, this approach will fail to consider unexpected but well‐supported population histories. We used a hierarchical...
The city as a refuge for insect pollinatorsNARA Subscribed
Research on urban insect pollinators is changing views on the biological value and ecological importance of cities. The abundance and diversity of native bee species in urban landscapes that are absent in nearby rural lands evidence the biological value and ecological importance of cities and have implications for biodiversity conservation. Lagging behind this revised image of the city are urban conservation programs that hist...
ABC inference of multi‐population divergence with admixture from unphased population genomic dataNARA Subscribed
Rapidly developing sequencing technologies and declining costs have made it possible to collect genome‐scale data from population‐level samples in nonmodel systems. Inferential tools for historical demography given these data sets are, at present, underdeveloped. In particular, approximate Bayesian computation ( ABC ) has yet to be widely embraced by researchers generating these data. Here, we demonstrate the promise of ABC fo...
Likelihood‐based inference of population history from low‐coverage de novo genome assembliesNARA Subscribed
Short‐read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate between recent, nonequilibrium histories. We address both the assembly and inference challenges. We develop a bioinf...
A road map for molecular ecologyNARA Subscribed
The discipline of molecular ecology has undergone enormous changes since the journal bearing its name was launched approximately two decades ago. The field has seen great strides in analytical methods development, made groundbreaking discoveries and experienced a revolution in genotyping technology. Here, we provide brief perspectives on the main subdisciplines of molecular ecology, describe key questions and goals, discuss co...
Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids ( Cecidostiba fungosa , Cecidostiba semifascia , Hobbya stenonota and Mesopolobus...
Mitochondrial barcodes are diagnostic of shared refugia but not species in hybridizing oak gallwaspsNARA Subscribed
Mitochondrial DNA barcodes provide a simple taxonomic tool for systematic and ecological research, with particular benefit for poorly studied or species‐rich taxa. Barcoding assumes genetic diversity follows species boundaries; however, many processes disrupt species‐level monophyly of barcodes leading to incorrect classifications. Spatial population structure, particularly when shared across closely related and potentially hy...
Evidence for widespread cryptic sexual generations in apparently purely asexual Andricus gallwaspsNARA Subscribed
Oak gallwasps (Hymenoptera, Cynipidae, Cynipini) are one of seven major animal taxa that commonly reproduce by cyclical parthenogenesis (CP). A major question in research on CP taxa is the frequency with which lineages lose their sexual generations, and diversify as purely asexual radiations. Most oak gallwasp species are only known from an asexual generation, and secondary loss of sex has been conclusively demonstrated in sev...
Plant–pollinator interactions in a Mexican Acacia communityNARA Subscribed
Human dispersal of organisms is an important process modifying natural patterns of biodiversity. Such dispersal generates new patterns of genetic diversity that overlie natural phylogeographical signatures, allowing discrimination between alternative dispersal mechanisms. Here we use allele frequency and DNA sequence data to distinguish between alternative scenarios (unassisted range expansion and long range introduction) for...
Longitudinal range expansion and cryptic eastern species in the western Palaearctic oak gallwasp, Andricus coriariusNARA Subscribed
The oak gallwasp Andricus coriarius is distributed across the Western Palaearctic from Morocco to Iran. It belongs to a clade of host‐alternating Andricus species that requires host oaks in two sections of Quercus subgenus Quercus to complete its lifecycle, a requirement that has restricted the historic distribution and dispersal of members of this clade. Here we present nuclear and mitochondrial sequence evidence from the ent...
Insect parasitoids are important components of many terrestrial ecosystems. However, relatively little is known about the mechanisms responsible for structuring their populations. Here we investigate the ability of Megastigmus stigmatizans , an oak gall wasp parasitoid, to track its host Andricus kollari over two different timescales, and examine its current population structure across a divide in host population structure. Th...
Many studies have addressed the latitudinal gradients in intraspecific genetic diversity of European taxa generated during postglacial range expansion from southern refugia. Although Asia Minor is known to be a centre of diversity for many taxa, relatively few studies have considered its potential role as a Pleistocene refugium or a potential source for more ancient westward range expansion into Europe. Here we address these i...