Adaptive landscape genetics and malaria across divergent island bird populations

Environmental conditions play a major role in shaping the spatial distributions of pathogens, which in turn can drive local adaptation and divergence in host genetic diversity. Haemosporidians, such as Plasmodium (malaria), are a strong selective force, impacting survival and fitness of hosts, with geographic distributions largely determined by habitat suitability for their insect vectors. Here, we have tested whether patterns of fine‐scale local adaptation to malaria are replicated across discrete, ecologically differing island populations of Berthelot's pipits Anthus berthelotii . We sequenced TLR4, an innate immunity gene that is potentially under positive selection in Berthelot's pipits, and two SNPs previously identified as being associated with malaria infection in a genome‐wide association study (GWAS) in Berthelot's pipits in the Canary Islands. We determined the environmental predictors of malaria infection, using these to estimate variation in malaria risk on Porto Santo, and found some congruence with previously identified environmental risk factors on Tenerife. We also found a negative association between malaria infection and a TLR4 variant in Tenerife. In contrast, one of the GWAS SNPs showed an association with malaria risk in Porto Santo, but in the opposite direction to that found in the Canary Islands GWAS. Together, these findings suggest that disease‐driven local adaptation may be an important factor in shaping variation among island populations

Recording fine‐scale movement of ground beetles by two methods: Potentials and methodological pitfalls

Movement trajectories are usually recorded as a sequence of discrete movement events described by two parameters: step length (distance) and turning angle (bearing). One of the most widespread methods to record the geocoordinates of each step is by a GPS device. Such devices have limited suitability for recording fine movements of species with low dispersal ability including flightless carabid beetles at small spatio‐temporal scales. As an alternative, the distance‐bearing approach can avoid the measurement error of GPS units since it uses directly measured distances and compass azimuths. As no quantification of measurement error between distance‐bearing and GPS approaches exists so far, we generated artificial fine‐scale trajectories and in addition radio‐tracked living carabids in a temperate forest and recorded each movement step by both methods. Trajectories obtained from distance‐bearing were compared to those obtained by a GPS device in terms of movement parameters. Consequently, both types of trajectories were segmented by state‐switching modeling into two distinct movement stages typical for carabids: random walk and directed movement. We found that the measurement error of GPS compared to distance‐bearing was 1.878 m (SEM = 0.181 m) for distances and 31.330° (SEM = 2.066°) for bearings. Moreover, these errors increased under dense forest canopy and rainy weather. Distance error did not change with increasing distance recorded by distance‐bearing but bearings were significantly more sensitive to error at short distances. State‐switching models showed only slight, not significant, differences in movement states between the two methods in favor of the random walk in the distance‐bearing approach. However, the shape of the GPS‐measured trajectories considerably differed from those recorded by distance‐bearing caused especially by bearing error at short distances. Our study showed that distance‐bearing could be more appropriate for recording movement steps not only of ground‐dwelling beetles but also other small animals at fine spatio‐temporal scales

Lack of genetic structure in greylag goose (Anser anser) populations along the European Atlantic flyway

Greylag goose populations are steadily increasing in north-western Europe. Although individuals breeding in the Netherlands have been considered mainly sedentary birds, those fromScandinavia or northern Germany fly towards their winter quarters, namely over France as far as Spain. This study aimed to determine the genetic structure of these birds, and to evaluate how goose populations mix. We used mitochondrial DNA and microsatellites from individuals distributed throughout the European Atlantic flyway, from breeding sites in Norway and the Netherlands to stopover and wintering sites in northern and south-western France. The mtDNA marker (CR1 D-Loop, 288 bp sequence, 144 ind.) showed 23 different haplotypes. The genetic distances amongst individuals sampled in Norway, northern France and the Netherlands were low (range 0.012–0.013). Individuals in south-western France showed a slightly higher genetic distance compared to all other sampling areas (ranges 0.018–0.022). The NJ tree does not show evidence of any single clades grouping together all individuals fromthe same geographic area. Besides, individuals from each site are found in different branches. Bayesian clustering procedures on 14 microsatellites (169 individuals) did not detect any geographically distinct cluster, and a high genetic admixture was recorded in all studied areas except for the individuals from the breeding sites in Norway, which were genetically very close. Estimation of migration rates through Bayesian inference confirms the scenario for the current mixing of goose populations. Subjects Biodiversity, Zoology Keywords mtDNA, Microsatellites, Greylag goose, Genetic structure, France and Norwa

Human Appropriation of Net Primary Productivity and Rural Livelihoods: Findings From Six Villages in Zimbabwe

The African land system is undergoing rapid change, and novel approaches are needed to understand the drivers and consequences of land use intensification. Human Appropriation of Net Primary Productivity (HANPP) is a powerful indicator of land use intensity, but has rarely been calculated at high spatial resolutions. Based on data from six villages in Zimbabwe, we present a novel method of calculating HANPP at community and household scales, and explore to what extent household wealth is related to NPP appropriation. HANPP at the village scale was higher than expected from previous studies, ranging from 48% to 113% of potential NPP. Loss of NPP through land use change accounted for the greater proportion of HANPP in four of the six villages, but NPP embodied in livestock feed, firewood and construction materials also contributed significantly to total appropriation. Increasing household wealth was associated with increasing appropriation of NPP in harvested resources, but not with loss of potential NPP through land use change. Our results indicate that land use intensity is currently underestimated in smallholder farming areas of southern Africa. High-resolution HANPP calculations based on field data offer an effective new approach to improving understanding of land use intensification in complex socioecological system

Influence of life-history traits on the occurrence of carnivores within exotic Eucalyptus plantations

Aim The world's forested area has been declining, especially in developing countries. In contrast, forest plantations are increasing, particularly exotic Eucalyptus plantations, which cover nowadays over 20 million ha worldwide. This global landscape change affects native communities, especially those at higher trophic levels that are affected by bottom–up cascading effects, such as carnivores. We seek to identify the general life‐history traits of mammalian carnivore species that use exotic Eucalyptus plantations. Location We reviewed 55 studies reporting carnivore presence in Eucalyptus plantations worldwide. Methods We consider seven species life‐history traits (generation length, social behaviour, body mass, energetic trophic level, diet diversity, habitat generalist/specialist and locomotion mode) as candidate drivers. We used generalized linear mixed models, with life‐history traits as fixed factors, and study as well as carnivore species as random factors. We obtained the carnivore occurrence data from the literature (detection of 42 different species, from seven families). We considered non‐detected species those with an IUCN Red List of Threatened Species estimated distribution range overlapping with the study areas, but not recorded by the studies. Results While we found no evidence of an effect of any of the other life‐history traits tested, our modelling procedure indicated that habitat generalist species are more likely to use Eucalyptus forests than specialist species. Main conclusions Our results, therefore, confirm an impoverishment of predator communities in disturbed environments, with the exclusion of the most specialist predators, leading to fragmentation of their populations and, ultimately contributing to their local extinction. The local extinction of specialist carnivores may lead to “functional homogenization” of communities within plantations, modifying ecosystem functioning with a negative impact on plantations’ productivity, profitability and services.info:eu-repo/semantics/publishedVersio

Prey availability and intraguild competition regulate the spatiotemporal dynamics of a modified large carnivore guild

Effective conservation management requires an understanding of the spatiotemporal dynamics driving large carnivore density and resource partitioning. In African ecosystems, reduced prey populations and the loss of competing guild members, most notably lion (Panthera leo), are expected to increase the levels of competition between remaining carnivores. Consequently, intraguild relationships can be altered, potentially increasing the risk of further population decline. Kasungu National Park (KNP), Malawi, is an example of a conservation area that has experienced large‐scale reductions in both carnivore and prey populations, leaving a resident large carnivore guild consisting of only leopard (Panthera pardus) and spotted hyena (Crocuta crocuta). Here, we quantify the spatiotemporal dynamics of these two species and their degree of association, using a combination of co‐detection modeling, time‐to‐event analyses, and temporal activity patterns from camera trap data. The detection of leopard and spotted hyena was significantly associated with the detection of preferred prey and competing carnivores, increasing the likelihood of species interaction. Temporal analyses revealed sex‐specific differences in temporal activity, with female leopard activity patterns significantly different to those of spotted hyena and male conspecifics. Heightened risk of interaction with interspecific competitors and male conspecifics may have resulted in female leopards adopting temporal avoidance strategies to facilitate coexistence. Female leopard behavioral adaptations increased overall activity levels and diurnal activity rates, with potential consequences for overall fitness and exposure to sources of mortality. As both species are currently found at low densities in KNP, increased risk of competitive interactions, which infer a reduction in fitness, could have significant implications for large carnivore demographics. The protection of remaining prey populations is necessary to mitigate interspecific competition and avoid further alterations to the large carnivore guild

Unravelling the evolution of Africa's drainage basins through a widespread freshwater fish, the African sharptooth catfish Clarias gariepinus

Aim The formation history of Africa's current river basins remains largely unknown. In order to date changes in landscape and climate, we studied the biogeography of the African freshwater fish with the largest natural distribution. We also validated biogeographical units. Location Continental Africa. Taxon Clarias gariepinus sl. Methods We investigated mitochondrial cytb sequences of 443 individuals from 97 localities, using a haplotype network and a genetic landscape analysis. We inferred a dated phylogeny using maximum likelihood and Bayesian inference approaches and reconstructed ancestral areas with S-DEC and S-DIVA models. Microsatellite genotyping complemented the mitochondrial approach in the Congo basin, where the latter revealed complex patterns. Results Limited differentiation is found in northern and south-western Africa, and sharp genetic differentiation in the continent's east and centre. Populations with affinities to neighbouring basins occur at the edges of the Congo province. High diversity exists in the south of the Congo basin. The Zambezi province is partitioned into eastern, central and western sectors. In the east, specimens were related to those from the Congo. In the west, they were similar to Southern representatives. Phylogenetic inference placed the origin of C. gariepinus in the East Coast, with intraspecific diversification starting around the Great Lakes. These events occurred ca. 4.8-1.65 and 2.3-0.8 MYA respectively. Main conclusions Clades of C. gariepinus sl. show a clear geographical signature. The origin of C. gariepinus in the East Coast and diversification around the Great Lakes coincided with the periods of increased aridity. Low genetic differentiation in northern and southern Africa may result from connectivity during recent periods of higher rainfall. In contrast to other widespread African freshwater fish, colonization rather than extinction seemed to mediate distribution patterns. This can be explained by a high ecological tolerance. We highlight the species' suitability to study landscape and climate evolution at various scales.Peer reviewe

Supplemental Information 1: Sequence data

Episodic sea level changes that repeatedly exposed and inundated the Sunda Shelf characterize the Pleistocene. Available evidence points to a more xeric central Sunda Shelf during periods of low sea levels, and despite the broad land connections that persisted during this time, some organisms are assumed to have faced barriers to dispersal between land-masses on the Sunda Shelf. Eutropis rugifera is a secretive, forest adapted scincid lizard that ranges across the Sunda Shelf. In this study, we sequenced one mitochondrial (ND2) and four nuclear (BRCA1, BRCA2, RAG1, and MC1R) markers and generated a time-calibrated phylogeny in BEAST to test whether divergence times between Sundaic populations of E. rugifera occurred during Pleistocene sea-level changes, or if they predate the Pleistocene. We find that E. rugifera shows pre-Pleistocene divergences between populations on different Sundaic land-masses. The earliest divergence within E. rugifera separates the Philippine samples from the Sundaic samples approximately 16 Ma; the Philippine populations thus cannot be considered conspecific with Sundaic congeners. Sundaic populations diverged approximately 6 Ma, and populations within Borneo from Sabah and Sarawak separated approximately 4.5 Ma in the early Pliocene, followed by further cladogenesis in Sarawak through the Pleistocene. Divergence of peninsular Malaysian populations from the Mentawai Archipelago occurred approximately 5 Ma. Separation among island populations from the Mentawai Archipelago likely dates to the Pliocene/Pleistocene boundary approximately 3.5 Ma, and our samples from peninsular Malaysia appear to coalesce in the middle Pleistocene, about 1 Ma. Coupled with the monophyly of these populations, these divergence times suggest that despite consistent land-connections between these regions throughout the Pleistocene E. rugifera still faced barriers to dispersal, which may be a result of environmental shifts that accompanied the sea-level changes

Drivers of plant diversity in Bulgarian dry grasslands vary across spatial scales and functional-taxonomic groups

Questions: Studying dry grasslands in a previously unexplored region, we asked: (a) which environmental factors drive the diversity patterns in vegetation; (b) are taxonomic groups (vascular plants, bryophytes, lichens) and functional vascular plant groups differently affected; and (c) how is fine-grain beta diversity affected by environmental drivers? Location: Northwestern and Central Bulgaria. Methods: We sampled environmental data and vascular plant, terricolous bryophyte and lichen species in 97 10-m2 plots and 15 nested-plot series with seven grain sizes (0.0001–100 m2) of ten grassland sites within the two regions. We used species richness as measure of alpha-diversity and the z-value of the power-law species–area relationship as measure of beta-diversity. We analysed effects of landscape, topographic, soil and land-use variables on the species richness of the different taxonomic and functional groups. We applied generalised linear models (GLMs) or, in the presence of spatial autocorrelation, generalised linear mixed-effect models (GLMMs) in a multi-model inference framework. Results: The main factors affecting total and vascular plant species richness in 10-m2 plots were soil pH (unimodal) and inclination (negative). Species richness of bryophytes was positively affected by rock cover, sand proportion and negatively by inclination. Inclination and litter cover were also negative predictors of lichen species richness. Elevation negatively affected phanerophyte and therophyte richness, but positively that of cryptophytes. A major part of unexplained variance in species richness was associated with the grassland site. The z-values for total richness showed a positive relationship with elevation and inclination. Conclusions: Environmental factors shaping richness patterns strongly differed among taxonomic groups, functional vascular plant groups and spatial scales. The disparities between our and previous findings suggest that many drivers of biodiversity cannot be generalised but rather depend on the regional context. The large unexplained variance at the site level calls for considering more site-related factors such as land-use history