Landscape Genetics and Species Delimitation in the Andean Palm Rocket Frog (Aromobatidae, Rheobates)

The complex topography of the species-rich northern Andes creates heterogeneous environmental landscapes that are hypothesized to have promoted population fragmentation and diversification by processes such as vicariance or local adaptation. Previous phylogenetic work on the palm rocket frog (Anura: Aromobatidae: Rheobates spp.), endemic to midelevation forests of Colombia, suggested that valleys were important in promoting divergence between lineages. In this study, we first evaluated previous hypotheses of species-level diversity, then fitted an isolation-with-migration (IM) historical demographic model, and tested two landscape genetic models to explain genetic divergence within Rheobates: isolation by distance and isolation by environment. The data consisted of two mitochondrial and four nuclear genes from 24 samples covering most of the geographic range of the genus. Species delimitation by Bayesian Phylogenetics and Phylogeography recovered five highly divergent genetic lineages within Rheobates, among which few to no migrants are exchanged according to IM. We found that isolation by environment provided the only variable significantly correlated with genetic distances for both mitochondrial and nuclear genes, suggesting that local adaptation may have a role in driving the genetic divergence within this frog genus. Thus, genetic divergence in Rheobates may be driven more by variation among the local environments where these frogs live rather than by geographic distance.

Species delimitation and mitonuclear discordance within a species complex of biting midges

The inability to distinguish between species can be a serious problem in groups responsible for pathogen transmission. Culicoides biting midges transmit many pathogenic agents infecting wildlife and livestock. In North America, the C. variipennis species complex contains three currently recognized species, only one of which is a known vector, but limited species-specific characters have hindered vector surveillance. Here, genomic data were used to investigate population structure and genetic differentiation within this species complex. Single nucleotide polymorphism data were generated for 206 individuals originating from 17 locations throughout the United States and Canada. Clustering analyses suggest the occurrence of two additional cryptic species within this complex. All five species were significantly differentiated in both sympatry and allopatry. Evidence of hybridization was detected in three different species pairings indicating incomplete reproductive isolation. Additionally, COI sequences were used to identify the hybrid parentage of these individuals, which illuminated discordance between the divergence of the mitochondrial and nuclear datasets.

High dispersal capacity of Culicoides obsoletus (Diptera: Ceratopogonidae), vector of bluetongue and Schmallenberg viruses, revealed by landscape genetic analyses

BACKGROUND

In the last two decades, recurrent epizootics of bluetongue virus and Schmallenberg virus have been reported in the western Palearctic region. These viruses affect domestic cattle, sheep, goats and wild ruminants and are transmitted by native hematophagous midges of the genus Culicoides (Diptera: Ceratopogonidae). Culicoides dispersal is known to be stratified, i.e. due to a combination of dispersal processes occurring actively at short distances and passively or semi-actively at long distances, allowing individuals to jump hundreds of kilometers.

METHODS

Here, we aim to identify the environmental factors that promote or limit gene flow of Culicoides obsoletus, an abundant and widespread vector species in Europe, using an innovative framework integrating spatial, population genetics and statistical approaches. A total of 348 individuals were sampled in 46 sites in France and were genotyped using 13 newly designed microsatellite markers.

RESULTS

We found low genetic differentiation and a weak population structure for C. obsoletus across the country. Using three complementary inter-individual genetic distances, we did not detect any significant isolation by distance, but did detect significant anisotropic isolation by distance on a north-south axis. We employed a multiple regression on distance matrices approach to investigate the correlation between genetic and environmental distances. Among all the environmental factors that were tested, only cattle density seems to have an impact on C. obsoletus gene flow.

CONCLUSIONS

The high dispersal capacity of C. obsoletus over land found in the present study calls for a re-evaluation of the impact of Culicoides on virus dispersal, and highlights the urgent need to better integrate molecular, spatial and statistical information to guide vector-borne disease control.

Harnessing landscape genomics to identify future climate resilient genotypes in a desert annual

Local adaptation features critically in shaping species responses to changing environments, complicating efforts to revegetate degraded areas. Rapid climate change poses an additional challenge that could reduce fitness of even locally sourced seeds in restoration. Predictive restoration strategies that apply seeds with favourable adaptations to future climate may promote long-term resilience. Landscape genomics is increasingly used to assess spatial patterns in local adaption and may represent a cost-efficient approach for identifying future-adapted genotypes. To demonstrate such an approach, we genotyped 760 plants from 64 Mojave Desert populations of the desert annual Plantago ovata. Genome scans on 5,960 SNPs identified 184 potentially adaptive loci related to climate and satellite vegetation metrics. Causal modelling indicated that variation in potentially adaptive loci was not confounded by isolation by distance or isolation by habitat resistance. A generalized dissimilarity model (GDM) attributed spatial turnover in potentially adaptive loci to temperature, precipitation and NDVI amplitude, a measure of vegetation green-up potential. By integrating a species distribution model (SDM), we find evidence that summer maximum temperature may both constrain the range of P. ovata and drive adaptive divergence in populations exposed to higher temperatures. Within the species' current range, warm-adapted genotypes are predicted to experience a fivefold expansion in climate niche by midcentury and could harbour key adaptations to cope with future climate. We recommend eight seed transfer zones and project each zone into its relative position in future climate. Prioritizing seed collection efforts on genotypes with expanding future habitat represents a promising strategy for restoration practitioners to address rapidly changing climates.

Niche specificity influences gene flow across fine-scale habitat mosaics in Succulent Karoo plants

While the tempo of diversification in biodiversity hotspots has received much attention, the spatial scale of diversification has often been overlooked. Addressing this deficiency requires understanding the drivers of population divergence and the spatial scales at which they operate in species-rich clades and ecosystems. South Africa's Succulent Karoo (SK) hotspot provides an excellent system for such research, being both compact (ca. 110,000 km² ) and home to spectacular in-situ radiations, such as the ruschioid Aizoaceae. Here we use GBS to document genetic structure in two co-occurring ruschioid species, at both coarse (>10 km) and fine (<500 m) spatial scales. Where Ruschia burtoniae shows strong between-population genetic differentiation and no gene flow, Conophytum calculus shows weak differentiation, with high levels of admixture suggesting recent or ongoing gene flow. Community analysis and transplant experiments reveal that R. burtoniae occupies a narrow, low-pH edaphic niche, and at scales of a few hundred metres, areas of elevated genetic turnover correspond to patches of edaphically unsuitable habitat. In contrast, C. calculus occupies a broader niche and exhibits isolation-by-distance without a habitat effect. We suggest that edaphic specialisation, coupled with highly restricted seed and pollen dispersal in heterogeneous landscapes, has played a major role in driving rapid diversification at small spatial scales in this system. However, the contrasting patterns in our study species show that these factors do not influence all organisms uniformly, being strongly modulated by lineage-specific traits that influence both the spatial scale of gene flow and habitat specificity.

The Andaman day gecko paradox: an ancient endemic without pronounced phylogeographic structure

The Andaman day gecko (Phelsuma andamanensis) is endemic to the Andaman Archipelago, located ~ 6000 km away from Madagascar where the genus Phelsuma likely evolved. We complemented existing phylogenetic data with additional markers to show that this species consistently branches off early in the evolution of the genus Phelsuma, and this early origin led us to hypothesize that island populations within the Andaman Archipelago could have further diversified. We sampled the Andaman day gecko from all major islands in the Andamans, developed new microsatellite markers and amplified mitochondrial markers to study population diversification. We detected high allelic diversity in microsatellites, but surprisingly poor geographical structuring. This study demonstrates that the Andaman day gecko has a panmictic population (K = 1), but with weak signals for two clusters that we name ‘North’ (North Andaman, Middle Andaman, Interview, Baratang, Neil, and Long Islands) and ‘South’ (Havelock, South Andaman, Little Andaman Islands). The mitochondrial COI gene uncovered wide haplotype sharing across islands with the presence of several private haplotypes (except for the Little Andaman Island, which only had an exclusive private haplotype) signalling ongoing admixture. This species differs from two other Andaman endemic geckos for which we provide comparative mitochondrial data, where haplotypes show a distinct phylogeographic structure. Testing population history scenarios for the Andaman day gecko using Approximate Bayesian Computation (ABC) supports two possible scenarios but fails to tease apart whether admixture or divergence produced the two weak clusters. Both scenarios agree that admixture and/or divergence prior to the onset of the last glacial maximum shaped the genetic diversity and structure detected in this study. ABC supports population expansion, possibly explained by anthropogenic food subsidies via plantations of cash crops, potentially coupled with human mediated dispersal resulting in the observed panmictic population. The Andaman day gecko may thus be a rare example of an island endemic reptile benefiting from habitat modification and increased movement in its native range.

Distribution and evolution of the major viruses infecting cucurbitaceous and solanaceous crops in the French Mediterranean area

Plant viral diseases represent a significant burden to plant health, and their highest impact in Mediterranean agriculture is on vegetables grown under intensive horticultural practices. In order to understand better virus evolution and emergence, the most prevalent viruses were mapped in the main cucurbitaceous (melon, squashes) and solanaceous (tomato, pepper) crops and in some wild hosts in the French Mediterranean area, and virus diversity, evolution and population structure were studied through molecular epidemiology approaches. Surveys were performed in summer 2016 and 2017, representing a total of 1530 crop samples and 280 weed samples. The plant samples were analysed using serological and molecular approaches, including high-throughput sequencing (HTS). The viral species and their frequency in crops were quite similar to those of surveys conducted ten years before in the same areas. Contrary to other Mediterranean countries, aphid-transmitted viruses remain the most prevalent in France whereas whitefly-transmitted ones have not yet emerged. However, HTS analysis of viral evolution revealed the appearance of undescribed viral variants, especially for watermelon mosaic virus (WMV) in cucurbits, or variants not present in France before, as for cucumber mosaic virus (CMV) in solanaceous crops. Deep sequencing also revealed complex virus populations within individual plants with frequent recombination or reassortment. The spatial genetic structure of cucurbit aphid-borne yellows virus (CABYV) was related to the landscape structure, whereas in the case of WMV, the recurrence of introduction events and probable human exchanges of plant material resulted in complex spatial pattern of genetic variation.

Combining genetic and demographic monitoring better informs conservation of an endangered urban snake

Conversion and fragmentation of wildlife habitat often leads to smaller and isolated populations and can reduce a species' ability to disperse across the landscape. As a consequence, genetic drift can quickly lower genetic variation and increase vulnerability to extirpation. For species of conservation concern, quantification of population size and connectivity can clarify the influence of genetic drift in local populations and provides important information for conservation management and recovery strategies. Here, we used genome-wide single nucleotide polymorphism (SNP) data and capture-mark-recapture methods to evaluate the genetic diversity and demography within seven focal sites of the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia), a species affected by alteration and isolation of wetland habitats throughout its distribution. The primary goals were to determine the population structure and degree of genetic isolation among T. s. tetrataenia populations and estimate effective size and population abundance within sites to better understand the present and future importance of genetic drift. We also used temporally sampled datasets to examine the magnitude of genetic change over time. We found moderate population genetic structure throughout the San Francisco Peninsula that partitions sites into northern and southern regional clusters. Point estimates of both effective size and population abundance were generally small (≤ 100) for a majority of the sites, and estimates were particularly low in the northern populations. Genetic analyses of temporal datasets indicated an increase in genetic differentiation, especially for the most geographically isolated sites, and decreased genetic diversity over time in at least one site (Pacifica). Our results suggest that drift-mediated processes as a function of small population size and reduced connectivity from neighboring populations may decrease diversity and increase differentiation. Improving genetic diversity and connectivity among T. s. tetrataenia populations could promote persistence of this endangered snake.

ResDisMapper: An r package for fine-scale mapping of resistance to dispersal

Management of biological invasions and conservation activity in the fight against habitat fragmentation both require information on how ongoing dispersal of organisms is affected by the environment. However, there are few landscape genetic computer programs that map resistance to dispersal at small spatiotemporal scales. To facilitate such analyses, we present an r package named ResDisMapper for the mapping of resistance to dispersal at small spatiotemporal scales, without the need for prior knowledge on environmental features or intensive computation. Based on the concept of isolation by distance (IBD), ResDisMapper calculates resistance using deviations of each pair of samples from the general IBD trend (IBD residuals). The IBD residuals are projected onto the studied area, which allows construction and visualization of a fine-scale map of resistance based on spatial accumulation of positive or negative IBD residuals. In this study, we tested ResDisMapper with both simulated and empirical data sets and compared its performance with two other popular landscape genetic programs. Overall, we found that ResDisMapper can map resistance with relatively high accuracy. The latest version of the package and associated documentation are available on Github (https://github.com/takfung/ResDisMapper).

Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range

The greater horseshoe bat (Rhinolophus ferrumequinum) is among the most widespread bat species in Europe but it has experienced severe declines, especially in Northern Europe. This species is listed Near Threatened in the European IUCN Red List of Threatened Animals, and it is considered to be highly sensitive to human activities and particularly to habitat fragmentation. Therefore, understanding the population boundaries and demographic history of populations of this species is of primary importance to assess relevant conservation strategies. In this study, we used 17 microsatellite markers to assess the genetic diversity, the genetic structure, and the demographic history of R. ferrumequinum colonies in the western part of its distribution. We identified one large population showing high levels of genetic diversity and large population size. Lower estimates were found in England and northern France. Analyses of clustering and isolation by distance suggested that the Channel and the Mediterranean seas could impede R. ferrumequinum gene flow. These results provide important information to improve the delineation of R. ferrumequinum management units. We suggest that a large management unit corresponding to the population ranging from Spanish Basque Country to northern France must be considered. Particular attention should be given to mating territories as they seem to play a key role in maintaining high levels of genetic mixing between colonies. Smaller management units corresponding to English and northern France colonies must also be implemented. These insular or peripheral colonies could be at higher risk of extinction in the near future.

Landscape genetic analyses of Cervus elaphus and Sus scrofa: comparative study and analytical developments

Red deer and wild boar are two major game species whose populations are managed and live in areas impacted by human activities. Measuring and understanding the impact of landscape features on individual movements and spatial patterns of genetic variability in these species is thus of importance for managers. A large number of individuals sampled across Wallonia (Belgium) for both species have been genotyped using microsatellite markers (respectively > 1700 and > 1200 genotyped individuals) and some individuals have also been followed using a capture-mark-recapture (CMR) protocol. The combined data set represents an unprecedented opportunity to study and compare the environmental factors impacting the interconnectivity of these large mammals. The present study describes and uses a landscape genetic workflow to compare spatial patterns of genetic variability and the impact of environmental factors on genetic differentiation. For the latter analyses, we investigate the correlation between genetic and environmental distances (pairwise approach) and also between local genetic dissimilarity and environmental conditions (point approach). Preliminary analyses of CMR data confirm that motorways act as significant barriers to dispersal. However, analyses performed with the pairwise approach do not highlight any evidence of an impact of motorways on genetic differentiation, which is presumably due to their recent establishment. Complementary analyses performed with the point approach reveal that low altitude tends to be associated with higher genetic dissimilarity. From a methodological point of view, the present workflow illustrates the complementary application of both pairwise and point approaches, as well as univariate and multivariate analyses.

Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics

Landscape genetics has provided many insights into how heterogeneous landscape features drive processes influencing spatial genetic variation in free-living organisms. This rapidly developing field has focused heavily on vertebrates, and expansion of this scope to the study of infectious diseases holds great potential for landscape geneticists and disease ecologists alike. The potential application of landscape genetics to infectious agents has garnered attention at formative stages in the development of landscape genetics, but systematic examination is lacking. We comprehensively review how landscape genetics is being used to better understand pathogen dynamics. We characterize the field and evaluate the types of questions addressed, approaches used and systems studied. We also review the now established landscape genetic methods and their realized and potential applications to disease ecology. Lastly, we identify emerging frontiers in the landscape genetic study of infectious agents, including recent phylogeographic approaches and frameworks for studying complex multihost and host-vector systems. Our review emphasizes the expanding utility of landscape genetic methods available for elucidating key pathogen dynamics (particularly transmission and spread) and also how landscape genetic studies of pathogens can provide insight into host population dynamics. Through this review, we convey how increasing awareness of the complementarity of landscape genetics and disease ecology among practitioners of each field promises to drive important cross-disciplinary advances.

Plasmodium falciparum genetic variation of var2csa in the Democratic Republic of the Congo

BACKGROUND

The Democratic Republic of the Congo (DRC) bears a high burden of malaria, which is exacerbated in pregnant women. The VAR2CSA protein plays a crucial role in pregnancy-associated malaria (PAM), and hence quantifying diversity at the var2csa locus in the DRC is important in understanding the basic epidemiology of PAM, and in developing a robust vaccine against PAM.

METHODS

Samples were taken from the 2013-14 Demographic and Health Survey conducted in the DRC, focusing on children under 5 years of age. A short subregion of the var2csa gene was sequenced in 115 spatial clusters, giving country-wide estimates of sequence polymorphism and spatial population structure.

RESULTS

Results indicate that var2csa is highly polymorphic, and that diversity is being maintained through balancing selection, however, there is no clear signal of phylogenetic or geographic structure to this diversity. Linear modelling demonstrates that the number of var2csa variants in a cluster correlates directly with cluster prevalence, but not with other epidemiological factors such as urbanicity.

CONCLUSIONS

Results suggest that the DRC fits within the global pattern of high var2csa diversity and little genetic differentiation between regions. A broad multivalent VAR2CSA vaccine candidate could benefit from targeting stable regions and common variants to address the substantial genetic diversity.

Evaluating methods to visualize patterns of genetic differentiation on a landscape

With advances in sequencing technology, research in the field of landscape genetics can now be conducted at unprecedented spatial and genomic scales. This has been especially evident when using sequence data to visualize patterns of genetic differentiation across a landscape due to demographic history, including changes in migration. Two recent model-based visualization methods that can highlight unusual patterns of genetic differentiation across a landscape, SpaceMix and EEMS, are increasingly used. While SpaceMix's model can infer long-distance migration, EEMS' model is more sensitive to short-distance changes in genetic differentiation, and it is unclear how these differences may affect their results in various situations. Here, we compare SpaceMix and EEMS side by side using landscape genetics simulations representing different migration scenarios. While both methods excel when patterns of simulated migration closely match their underlying models, they can produce either un-intuitive or misleading results when the simulated migration patterns match their models less well, and this may be difficult to assess in empirical data sets. We also introduce unbundled principal components (un-PC), a fast, model-free method to visualize patterns of genetic differentiation by combining principal components analysis (PCA), which is already used in many landscape genetics studies, with the locations of sampled individuals. Un-PC has characteristics of both SpaceMix and EEMS and works well with simulated and empirical data. Finally, we introduce msLandscape, a collection of tools that streamline the creation of customizable landscape-scale simulations using the popular coalescent simulator ms and conversion of the simulated data for use with un-PC, SpaceMix and EEMS.

Exploiting Genetic Information to Trace Plant Virus Dispersal in Landscapes

During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.