Genetic differentiation in Scottish populations of the pine beauty moth Panolis flammea (Lepidoptera: Noctuidae)

Pine beauty moth, Panolis flammea (Denis & Schiffermüller), is a recent but persistent pest of lodgepole pine plantations in Scotland, but exists naturally at low levels within remnants and plantations of Scots pine. To test whether separate host races occur in lodgepole and Scots pine stands and to examine colonization dynamics, allozyme, randomly amplified polymorphic DNA (RAPD) and mitochondrial variation were screened within a range of Scottish samples. RAPD analysis indicated limited long distance dispersal (FST = 0.099), and significant isolation by distance (P < 0.05); but that colonization between more proximate populations was often variable, from extensive to limited exchange. When compared with material from Germany, Scottish samples were found to be more diverse and significantly differentiated for all markers. For mtDNA, two highly divergent groups of haplotypes were evident, one group contained both German and Scottish samples and the other was predominantly Scottish. No genetic differentiation was evident between P. flammea populations sampled from different hosts, and no diversity bottleneck was observed in the lodgepole group. Indeed, lodgepole stands appear to have been colonized on multiple occasions from Scots pine sources and neighbouring populations on different hosts are close to panmixia.A.J. Lowe, B.J. Hicks, K. Worley, R.A. Ennos, J.D. Morman, G. Stone and A.D. Wat

Assessment of caecal parameters in layer hens fed on diets containing wheat distillers dried grains with solubles

There is much interest in quantifying the nutritional value of UK wheat distillers dried grains with solubles (W-DDGS) for livestock species. A study was designed to evaluate caecal parameters (pH, short chain fatty acids (SCFAs) and bacterial diversity) in layer hens fed on balanced diets containing graded concentrations of W-DDGS. A total of 32 layer hens (Bovans Brown strain at 27 weeks of age) were randomly allocated to one of 4 dietary treatments containing W-DDGS at 0, 60, 120 or 180 g/kg. Each treatment was fed to 8 replicate individually housed layer hens over a 5-d acclimatisation period, followed by a 4-week trial. Individual feed intakes were monitored and all eggs were collected daily for weeks 2, 3 and 4 of the trial, weighed and an assessment of eggshell “dirtiness” made. All hens were culled on d 29 and caecal pH and SCFAs measured. Polymerase chain reaction denaturing gradient gel electrophoresis of the bacterial 16 S rDNA gene was used to assess total bacterial diversity of luminal caecal content from hens fed the 0 and 180 g W-DDGS/kg diets. Unweighted pair group method with arithmetic mean (UPGMA) dendrograms were generated from DGGE banding patterns. Increasing W-DDGS dietary concentrations resulted in a more acidic caecal environment. Caecal SCFAs were unaffected by diet aside from a quadratic effect for molar proportions of isobutyric acid. Diversity profiles of the bacterial 16S rRNA gene from luminal caecal contents were unaffected by W-DDGS inclusion. The results of the current study suggest that W-DDGS can be successfully formulated into nutritionally balanced layer diets (supplemented with xylanase and phytase) at up to 180 g/kg with no detrimental effects to the caecal environment

Investigating mitochondrial DNA relationships in Neolithic Western Europe through serial coalescent simulations

Recent ancient DNA studies on European Neolithic human populations have provided persuasive evidence of a major migration of farmers originating from the Aegean, accompanied by sporadic hunter-gatherer admixture into early Neolithic populations, but increasing toward the Late Neolithic. In this context, ancient mitochondrial DNA data collected from the Neolithic necropolis of Gurgy (Paris Basin, France), the largest mitochondrial DNA sample obtained from a single archeological site for the Early/Middle Neolithic period, indicate little differentiation from farmers associated to both the Danubian and Mediterranean Neolithic migration routes, as well as from Western European hunter-gatherers. To test whether this pattern of differentiation could arise in a single unstructured population by genetic drift alone, we used serial coalescent simulations. We explore female effective population size parameter combinations at the time of the colonization of Europe 45000 years ago and the most recent of the Neolithic samples analyzed in this study 5900 years ago, and identify conditions under which population panmixia between hunter-gatherers/Early-Middle Neolithic farmers and Gurgy cannot be rejected. In relation to other studies on the current debate of the origins of Europeans, these results suggest increasing hunter-gatherer admixture into farmers' group migrating farther west in Europe.European Journal of Human Genetics advance online publication, 28 December 2016; doi:10.1038/ejhg.2016.180

ABCtoolbox: a versatile toolkit for approximate Bayesian computations

BACKGROUND: The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations. RESULTS: Here we present ABCtoolbox, a series of open source programs to perform Approximate Bayesian Computations (ABC). It implements various ABC algorithms including rejection sampling, MCMC without likelihood, a Particle-based sampler and ABC-GLM. ABCtoolbox is bundled with, but not limited to, a program that allows parameter inference in a population genetics context and the simultaneous use of different types of markers with different ploidy levels. In addition, ABCtoolbox can also interact with most simulation and summary statistics computation programs. The usability of the ABCtoolbox is demonstrated by inferring the evolutionary history of two evolutionary lineages of Microtus arvalis. Using nuclear microsatellites and mitochondrial sequence data in the same estimation procedure enabled us to infer sex-specific population sizes and migration rates and to find that males show smaller population sizes but much higher levels of migration than females. CONCLUSION: ABCtoolbox allows a user to perform all the necessary steps of a full ABC analysis, from parameter sampling from prior distributions, data simulations, computation of summary statistics, estimation of posterior distributions, model choice, validation of the estimation procedure, and visualization of the results

Sexual selection protects against extinction

Reproduction through sex carries substantial costs, mainly because only half of sexual adults produce offspring. It has been theorised that these costs could be countered if sex allows sexual selection to clear the universal fitness constraint of mutation load. Under sexual selection, competition between (usually) males, and mate choice by (usually) females create important intraspecific filters for reproductive success, so that only a subset of males gains paternity. If reproductive success under sexual selection is dependent on individual condition, which depends on mutation load, then sexually selected filtering through ‘genic capture’ could offset the costs of sex because it provides genetic benefits to populations. Here, we test this theory experimentally by comparing whether populations with histories of strong versus weak sexual selection purge mutation load and resist extinction differently. After evolving replicate populations of the flour beetle Tribolium castaneum for ~7 years under conditions that differed solely in the strengths of sexual selection, we revealed mutation load using inbreeding. Lineages from populations that had previously experienced strong sexual selection were resilient to extinction and maintained fitness under inbreeding, with some families continuing to survive after 20 generations of sib × sib mating. By contrast, lineages derived from populations that experienced weak or non-existent sexual selection showed rapid fitness declines under inbreeding, and all were extinct after generation 10. Multiple mutations across the genome with individually small effects can be difficult to clear, yet sum to a significant fitness load; our findings reveal that sexual selection reduces this load, improving population viability in the face of genetic stress

Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection

SELECTOR is a software package for studying the evolution of multiallelic genes under balancing or positive selection while simulating complex evolutionary scenarios that integrate demographic growth and migration in a spatially explicit population framework. Parameters can be varied both in space and time to account for geographical, environmental, and cultural heterogeneity. SELECTOR can be used within an approximate Bayesian computation estimation framework. We first describe the principles of SELECTOR and validate the algorithms by comparing its outputs for simple models with theoretical expectations. Then, we show how it can be used to investigate genetic differentiation of loci under balancing selection in interconnected demes with spatially heterogeneous gene flow. We identify situations in which balancing selection reduces genetic differentiation between population groups compared with neutrality and explain conflicting outcomes observed for human leukocyte antigen loci. These results and three previously published applications demonstrate that SELECTOR is efficient and robust for building insight into human settlement history and evolution

Population genetic evidence for sex-specific dispersal in an inbred social spider

A grant from the One-University Open Access Fund at the University of Kansas was used to defray the author's publication fees in this Open Access journal. The Open Access Fund, administered by librarians from the KU, KU Law, and KUMC libraries, is made possible by contributions from the offices of KU Provost, KU Vice Chancellor for Research & Graduate Studies, and KUMC Vice Chancellor for Research. For more information about the Open Access Fund, please see http://library.kumc.edu/authors-fund.xml.Dispersal in most group-living species ensures gene flow among groups, but in cooperative social spiders, juvenile dispersal is suppressed and colonies are highly inbred. It has been suggested that such inbred sociality is advantageous in the short term, but likely to lead to extinction or reduced speciation rates in the long run. In this situation, very low levels of dispersal and gene flow among colonies may have unusually important impacts on fitness and persistence of social spiders. We investigated sex-specific differences in dispersal and gene flow among colonies, as reflected in the genetic structure within colonies and populations of the African social spider Stegodyphus dumicola Pocock, 1898 (Eresidae). We used DNA fingerprinting and mtDNA sequence data along with spatial mapping of colonies to compare male and female patterns of relatedness within and among colonies at three study sites. Samples were collected during and shortly after the mating season to detect sex-specific dispersal. Distribution of mtDNA haplotypes was consistent with proliferation of social nests by budding and medium- to long-distance dispersal by ballooning females. Analysis of molecular variance and spatial autocorrelation analyses of AFLPs showed high levels of genetic similarity within colonies, and STRUCTURE analyses revealed that the number of source populations contributing to colonies ranged from one to three. We also showed significant evidence of male dispersal among colonies at one site. These results support the hypothesis that in social spiders, genetic cohesion among populations is maintained by long-distance dispersal of female colony founders. Genetic diversity within colonies is maintained by colony initiation by multiple dispersing females, and adult male dispersal over short distances. Male dispersal may be particularly important in maintaining gene flow among colonies in local populations

High levels of genetic variability and differentiation in hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes) populations revealed by PCR-RFLP analysis of the mitochondrial DNA D-loop region

The hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes) is an important anadromous clupeid species from the Western division of the Indo-Pacific region. It constitutes the largest single fishable species in Bangladesh. Information on genetic variability and population structure is very important for both management and conservation purposes. Past reports on the population structure of T. ilisha involving morphometric, allozyme and RAPD analyses are contradictory. We examined genetic variability and divergence in two riverine (the Jamuna and the Meghna), two estuarine (Kuakata and Sundarbans) and one marine (Cox's Bazar) populations of T. ilisha by applying PCR-RFLP analysis of the mtDNA D-loop region. The amplified PCR products were restricted with four restriction enzymes namely, XbaI, EcoRI, EcoRV, and HaeIII. High levels of haplotype and gene diversity within and significant differentiations among, populations of T. ilisha were observed in this study. Significant FST values indicated differentiation among the river, estuary and marine populations. The UPGMA dendrogram based on genetic distance resulted in two major clusters, although, these were subsequently divided into three, corresponding to the riverine, estuarine and marine populations. The study underlines the usefulness of RFLP of mtDNA D-loop region as molecular markers, and detected at least two differentiated populations of T. ilisha in Bangladesh waters

Molecular techniques reveal cryptic life history and demographic processes of a critically endangered marine turtle

The concept of ‘effective population size’ (Ne), which quantifies how quickly a population will lose genetic variability, is one of the most important contributions of theoretical evolutionary biology to practical conservation management. Ne is often much lower than actual population size: how much so depends on key life history and demographic parameters, such as mating systems and population connectivity, that often remain unknown for species of conservation concern. Molecular techniques allow the indirect study of these parameters, as well as the estimation of current and historical Ne. Here, we use genotyping to assess the genetic health of an important population of the critically endangered hawksbill turtle (Eretmochelys imbricata), a slow-to-mature, difficult-to-observe species with a long history of severe overhunting. Our results were surprisingly positive: we found that the study population, located in the Republic of Seychelles, Indian Ocean, has a relatively large Ne, estimated to exceed 1000, and showed no evidence of a recent reduction in Ne (i.e. no genetic bottleneck). Furthermore, molecular inferences suggest the species' mating system is conducive to maintaining a large Ne, with a relatively large and widely distributed male population promoting considerable gene flow amongst nesting sites across the Seychelles area. This may also be reinforced by the movement of females between nesting sites. Our study underlines how molecular techniques can help to inform conservation biology. In this case our results suggest that this important hawksbill population is starting from a relatively strong position as it faces new challenges, such as global climate change

Mitochondrial DNA Regionalism and Historical Demography in the Extant Populations of Chirocephalus kerkyrensis (Branchiopoda: Anostraca)

Background: Mediterranean temporary water bodies are important reservoirs of biodiversity and host a unique assemblage of diapausing aquatic invertebrates. These environments are currently vanishing because of increasing human pressure. Chirocephalus kerkyrensis is a fairy shrimp typical of temporary water bodies in Mediterranean plain forests and has undergone a substantial decline in number of populations in recent years due to habitat loss. We assessed patterns of genetic connectivity and phylogeographic history in the seven extant populations of the species from Albania, Corfu Is. (Greece), Southern and Central Italy. Methodology/Principal Findings: We analyzed sequence variation at two mitochondrial DNA genes (Cytochrome Oxidase I and 16s rRNA) in all the known populations of C. kerkyrensis. We used multiple phylogenetic, phylogeographic and coalescence-based approaches to assess connectivity and historical demography across the whole distribution range of the species. C. kerkyrensis is genetically subdivided into three main mitochondrial lineages; two of them are geographically localized (Corfu Is. and Central Italy) and one encompasses a wide geographic area (Albania and Southern Italy). Most of the detected genetic variation (<81%) is apportioned among the aforementioned lineages. Conclusions/Significance: Multiple analyses of mismatch distributions consistently supported both past demographic and spatial expansions with the former predating the latter; demographic expansions were consistently placed during interglacial warm phases of the Pleistocene while spatial expansions were restricted to cold periods. Coalescence methods revealed a scenario of past isolation with low levels of gene flow in line with what is already known for other co-distributed fairy shrimps and suggest drift as the prevailing force in promoting local divergence. We recommend that these evolutionary trajectories should be taken in proper consideration in any effort aimed at protecting Mediterranean temporary water bodies