Genetic evidence for the origin of Aedes aegypti,the yellow fever mosquito,in the southwestern Indian Ocean

Aedes aegypti is among the best‐studied mosquitoes due to its critical role as a vector of human pathogens and ease of laboratory rearing. Until now, this species was thought to have originated in continental Africa, and subsequently colonized much of the world following the establishment of global trade routes. However, populations of this mosquito on the islands in the southwestern Indian Ocean (SWIO), where the species occurs with its nearest relatives referred to as the Aegypti Group, have received little study. We re‐evaluated the evolutionary history of Ae. aegypti and these relatives, using three data sets: nucleotide sequence data, 18,489 SNPs and 12 microsatellites. We found that: (a) the Aegypti Group diverged 16 MYA (95% HPD: 7–28 MYA) from its nearest African/Asian ancestor; (b) SWIO populations of Ae. aegypti are basal to continental African populations; (c) after diverging 7 MYA (95% HPD: 4–15 MYA) from its nearest formally described relative (Ae. mascarensis), Ae. aegypti moved to continental Africa less than 85,000 years ago, where it recently (<1,000 years ago) split into two recognized subspecies Ae. aegypti formosus and a human commensal, Ae. aegypti aegypti; (d) the Madagascar samples form a clade more distant from all other Ae. aegypti than the named species Ae. mascarensis, implying that Madagascar may harbour a new cryptic species; and (e) there is evidence of introgression between Ae. mascarensis and Ae. aegypti on Réunion, and between the two subspecies elsewhere in the SWIO, a likely consequence of recent introductions of domestic Ae. aegypti aegypti from Asia.     

Geography is more important than host plant use for the population genetic structure of a generalist insect herbivore

Population divergence can occur due to mechanisms associated with geographic isolation and/or due to selection associated with different ecological niches. Much of the evidence for selection‐driven speciation has come from studies of specialist insect herbivores that use different host plant species; however, the influence of host plant use on population divergence of generalist herbivores remains poorly understood. We tested how diet breadth, host plant species and geographic distance influence population divergence of the fall webworm (Hyphantria cunea; FW). FW is a broadly distributed, extreme generalist herbivore consisting of two morphotypes that have been argued to represent two different species: black‐headed and red‐headed. We characterized the differentiation of FW populations at two geographic scales. We first analysed the influence of host plant and geographic distance on genetic divergence across a broad continental scale for both colour types. We further analysed the influence of host plant, diet breadth and geographic distance on divergence at a finer geographic scale focusing on red‐headed FW in Colorado. We found clear genetic and morphological distinction between red‐ and black‐headed FW, and Colorado FW formed a genetic cluster distinct from other locations. Although both geographic distance and host plant use were correlated with genetic distance, geographic distance accounted for up to 3× more variation in genetic distance than did host plant use. As a rare study investigating the genetic structure of a widespread generalist herbivore over a broad geographic range (up to 3,000 km), our study supports a strong role for geographic isolation in divergence in this system.     

Pollen,wind and fire: how to investigate genetic effects of disturbance‐induced change in forest trees

Understanding the consequences of habitat disturbance on mating patterns although pollen and seed dispersal in forest trees has been a long‐standing theme of forest and conservation genetics. Forest ecosystems face global environmental pressures from timber exploitation to genetic pollution and climate change, and it is therefore essential to comprehend how disturbances may alter the dispersal of genes and their establishment in tree populations in order to formulate relevant recommendations for sustainable resource management practices and realistic predictions of potential adaptation to climate change by means of range shift or expansion (Kremer et al. 2012 ). However, obtaining reliable evidence of disturbance‐induced effects on gene dispersal processes from empirical evaluation of forest tree populations is difficult. Indeed, tree species share characteristics such as high longevity, long generation time and large reproductive population size, which may impede the experimenter's ability to assess parameters at the spatial and time scales at which any change may occur (Petit and Hampe 2006 ). It has been suggested that appropriate study designs should encompass comparison of populations before and after disturbance as well as account for demonstrated variation in conspecific density, that is, the spatial distribution of mates, and forest density, including all species and relating to alteration in landscape openness (Bacles & Jump 2011 ). However, more often than not, empirical studies aiming to assess the consequences of habitat disturbance on genetic processes in tree populations assume rather than quantify a change in tree densities in forests under disturbance and generally fail to account for population history, which may lead to inappropriate interpretation of a causal relationship between population genetic structure and habitat disturbance due to effects of unmonitored confounding variables (Gauzere et al. 2013). In this issue, Shohami and Nathan ( 2014 ) take advantage of the distinctive features of the fire‐adapted wind‐pollinated Aleppo pine Pinus halepensis (Fig. 1) to provide an elegant example of best practice. Thanks to long‐term monitoring of the study site, a natural stand in Israel, Shohami and Nathan witnessed the direct impact of habitat disturbance, here taking the shape of fire, on conspecific and forest densities and compared pre‐ and postdisturbance mating patterns estimated from cones of different ages sampled on the same surviving maternal individuals (Fig. 2). This excellent study design is all the more strong that Shohami and Nathan took further analytical steps to account for confounding variables, such as historical population genetic structure and possible interannual variation in wind conditions, thus giving high credibility to their findings of unequivocal fire‐induced alteration of mating patterns in P. halepensis. Most notably, the authors found, at the pollen pool level, a disruption of local genetic structure which, furthermore, they were able to attribute explicitly to enhanced pollen‐mediated gene immigration into the low‐density fire‐disturbed stand. This cleverly designed research provides a model approach to be followed if we are to advance our understanding of disturbance‐induced dispersal and genetic change in forest trees.     

These aren’t the loci you’e looking for: Principles of effective SNP filtering for molecular ecologists

Sequencing reduced‐representation libraries of restriction site‐associated DNA (RADseq) to identify single nucleotide polymorphisms (SNPs) is quickly becoming a standard methodology for molecular ecologists. Because of the scale of RADseq data sets, putative loci cannot be assessed individually, making the process of filtering noise and correctly identifying biologically meaningful signal more difficult. Artefacts introduced during library preparation and/or bioinformatic processing of SNP data can create patterns that are incorrectly interpreted as indicative of population structure or natural selection. Therefore, it is crucial to carefully consider types of errors that may be introduced during laboratory work and data processing, and how to minimize, detect and remove these errors. Here, we discuss issues inherent to RADseq methodologies that can result in artefacts during library preparation and locus reconstruction resulting in erroneous SNP calls and, ultimately, genotyping error. Further, we describe steps that can be implemented to create a rigorously filtered data set consisting of markers accurately representing independent loci and compare the effect of different combinations of filters on four RAD data sets. At last, we stress the importance of publishing raw sequence data along with final filtered data sets in addition to detailed documentation of filtering steps and quality control measures.     

Modelling the introduction and spread of non‐native species: international trade and climate change drive ragweed invasion

Biological invasions are a major driver of global change, for which models can attribute causes, assess impacts and guide management. However, invasion models typically focus on spread from known introduction points or non‐native distributions and ignore the transport processes by which species arrive. Here, we developed a simulation model to understand and describe plant invasion at a continental scale, integrating repeated transport through trade pathways, unintentional release events and the population dynamics and local anthropogenic dispersal that drive subsequent spread. We used the model to simulate the invasion of Europe by common ragweed (Ambrosia artemisiifolia), a globally invasive plant that causes serious harm as an aeroallergen and crop weed. Simulations starting in 1950 accurately reproduced ragweed's current distribution, including the presence of records in climatically unsuitable areas as a result of repeated introduction. Furthermore, the model outputs were strongly correlated with spatial and temporal patterns of ragweed pollen concentrations, which are fully independent of the calibration data. The model suggests that recent trends for warmer summers and increased volumes of international trade have accelerated the ragweed invasion. For the latter, long distance dispersal because of trade within the invaded continent is highlighted as a key invasion process, in addition to import from the native range. Biosecurity simulations, whereby transport through trade pathways is halted, showed that effective control is only achieved by early action targeting all relevant pathways. We conclude that invasion models would benefit from integrating introduction processes (transport and release) with spread dynamics, to better represent propagule pressure from native sources as well as mechanisms for long‐distance dispersal within invaded continents. Ultimately, such integration may facilitate better prediction of spatial and temporal variation in invasion risk and provide useful guidance for management strategies to reduce the impacts of invasion.     

First molecular identification of the vertebrate hosts of Culicoides imicola in Europe and a review of its blood‐feeding patterns worldwide: implications for the transmission of bluetongue disease and African horse sickness

Culicoides (Diptera: Ceratopogonidae) are vectors of pathogens that affect wildlife, livestock and, occasionally, humans. Culicoides imicola (Kieffer, 1913) is considered to be the main vector of the pathogens that cause bluetongue disease (BT) and African horse sickness (AHS) in southern Europe. The study of blood‐feeding patterns in Culicoides is an essential step towards understanding the epidemiology of these pathogens. Molecular tools that increase the accuracy and sensitivity of traditional methods have been developed to identify the hosts of potential insect vectors. However, to the present group's knowledge, molecular studies that identify the hosts of C. imicola in Europe are lacking. The present study genetically characterizes the barcoding region of C. imicola trapped on farms in southern Spain and identifies its vertebrate hosts in the area. The report also reviews available information on the blood‐feeding patterns of C. imicola worldwide. Culicoides imicola from Spain feed on blood of six mammals that include species known to be hosts of the BT and AHS viruses. This study provides evidence of the importance of livestock as sources of bloodmeals for C. imicola and the relevance of this species in the transmission of BT and AHS viruses in Europe.     

Knowing the past to predict the future: land‐use change and the distribution of invasive bullfrogs

Biological invasions and land‐use changes are two major causes of the global modifications of biodiversity. Habitat suitability models are the tools of choice to predict potential distributions of invasive species. Although land‐use is a key driver of alien species invasions, it is often assumed that land‐use is constant in time. Here we combine historical and present day information, to evaluate whether land‐use changes could explain the dynamic of invasion of the American bullfrog Rana catesbeiana (=Lithobathes catesbeianus) in Northern Italy, from the 1950s to present‐day. We used maxent to build habitat suitability models, on the basis of past (1960s, 1980s) and present‐day data on land‐uses and species distribution. For example, we used models built using the 1960s data to predict distribution in the 1980s, and so on. Furthermore, we used land‐use scenarios to project suitability in the future. Habitat suitability models predicted well the spread of bullfrogs in the subsequent temporal step. Models considering land‐use changes predicted invasion dynamics better than models assuming constant land‐use over the last 50 years. Scenarios of future land‐use suggest that suitability will remain similar in the next years. Habitat suitability models can help to understand and predict the dynamics of invasions; however, land‐use is not constant in time: land‐use modifications can strongly affect invasions; furthermore, both land management and the suitability of a given land‐use class may vary in time. An integration of land‐use changes in studies of biological invasions can help to improve management strategies.     

metapop2: Re‐implementation of software for the analysis and management of subdivided populations using gene and allelic diversity

Management programmes often have to make decisions based on the analysis of the genetic properties and diversity of populations. Expected heterozygosity (or gene diversity) and population structure parameters are often used to make recommendations for conservation, such as avoidance of inbreeding or migration across subpopulations. Allelic diversity, however, can also provide complementary and useful information for conservation programmes, as it is highly sensitive to population bottlenecks, and is more related to long‐term selection response than heterozygosity. Here we present a completely revised and updated re‐implementation of the software metapop for the analysis of diversity in subdivided populations, as well as a tool for the management and dynamic estimation of optimal contributions in conservation programmes. This new update includes computation of allelic diversity for population analysis and management, as well as a simulation mode to forecast the consequences of taking different management strategies over time. Furthermore, the new implementation in C++ includes code optimization and improved memory usage, allowing for fast analysis of large data sets including single nucleotide polymorphism markers, as well as enhanced cross‐software and cross‐platform compatibility.     

Geographical gradients of species richness: a test of the water‐energy conjecture of Hawkins et al. (2003) using European data for five taxa

Aims We present an analysis of grid‐based species‐richness data for European plants, mammals, birds, amphibians and reptiles, designed to test the proposition of Hawkins et al. (2003a ) that the single best factor describing richness variation switches from the water regime to the energy regime in the mid‐latitudes and that the ‘breakpoint’ is related to the physiological character of the taxa. We go on to develop subregional models showing the extent to which regional model fits vary as a function of the extent of the study system, and compare the relative performance of ‘water’, ‘energy’ and ‘water–energy’ models of richness for southern, northern and pan‐European models. Location Western Europe. Methods We use atlas data comprising species range data for 187 species of mammals, 445 species of breeding birds, 58 amphibians, 91 reptiles and 2362 plant species, inserted into a c. 50 × 50 km grid cell system. We used 11 modelled climate variables, averaged for the period 1961–90. Statistical analyses were carried out using generalized additive models (GAMs), with splines simplified to a maximum of four degrees of freedom, and we tested for spatial autocorrelation using Moran's I values obtained at 10 different distance intervals. We selected favoured models on the grounds of deviance explained combined with a simple parsimony criterion, such that we selected either: (1) the best two‐variable energy, water or water–energy model, or (2) a four‐variable water–energy model, where the latter improved on the best two‐variable model by a minimum of 5% deviance explained. Results Threshold energy values, at which richness shows a transition from an increasing to a decreasing function of annual solar radiation, were identified for all taxa apart from reptiles. We found conditional support for the switch from dominance of water variables (southern models) to energy variables (northern models). Our favoured models switched between ‘water’ and ‘energy’ for mammals, and between ‘energy’ and ‘water–energy’ for birds, depending on whether we used data of pan‐European extent, southern or northern subsets. Deviance explained in our favoured models varied from 15% (birds, southern Europe) to 72% (amphibians, northern Europe), i.e. ranging from very poor to good fits with the data. Comparison with previous work indicates that our models are generally consistent with (if sometimes weaker than) previous findings. Main conclusions Our models are incomplete representations of factors influencing macro‐scale richness patterns across Europe, taking no explicit account of, for example, topographic variation, human influences or long‐term climatic variation. However, with the exception of birds, for which only the northern model attains over one‐third deviance explained, the models show that climate can account for meaningful proportions of the deviance. We find general support for considering water and energy regimes together in modelling species richness, and for the proposition that water is more limiting in southern Europe and energy in the north. Our analyses demonstrate the sensitivity of model outcomes to the geographical location and extent of the study system, illustrating that simple curve‐fitting exercises like these, particularly if based on regions with the complex history and geography characteristic of Europe, are unlikely to provide the basis for global, predictive models. However, such exercises may be of value in detecting which aspects of water and energy regimes may be of most importance in refining independently generated global models for regional application.