Dispersal in [i]Mastomys natalensis[/i] mice: use of fine-scale genetic analyses for pest management

Mastomys natalensis is the major pest rodent in sub-Saharan Africa. In this study, population genetic techniques were used to gain new insights into its dispersal behaviour, a critical parameter in pest management. Using 11 microsatellites, 272 individuals from a 300 ha area in Tanzania were genotyped. Genetic diversity was high, with no isolation by distance and little differentiation between field plots far apart, indicating a large effective population size and high dispersal rates in agreement with ecological observations. On the other hand, genetic differentiation between nearby field plots, isolation by distance within a single field plot and kin clustering were also observed. This apparent contradiction may be explained by yearly founder effects of a small number of breeding individuals per square area, which is consistent with the presence of linkage disequilibrium. An alternative, not mutually exclusive explanation is that there are both dispersing and sedentary animals in the population. The low-density field plots were characterized by low relatedness and small genetic distances to other field plots, indicating a high turnover rate and negative density-dependent dispersal. In one field plot female-biased dispersal was observed, which may be related to inbreeding avoidance or female competition for resources. Most juveniles appeared to be local recruits, but they did not seem to stay in their native area for more than two months. Finally, possible implications for pest management are discussed

Breeding den selection by Arctic foxes (Vulpes lagopus) in southern Yamal Peninsula, Russia

Selecting the right location for a den during the breeding season is a type of habitat selection in the Arctic fox (Vulpes lagopus) that is likely to affect its reproductive success. A den’s suitability likely depends on its ability to provide shelter, as well as its proximity to prey resources. Depending on the different relative risks that Arctic foxes may face across their broad circumpolar range, Arctic foxes may place different emphases on selection for shelter and prey resources in different ecosystems. Understanding the different requirements for reproduction under different ecological conditions is highly relevant to conservation efforts in areas where Arctic foxes are threatened by rapid environmental changes. Here, we investigated the relative selection for shelter and prey resources in southern Yamal Peninsula (Russia) using data from 45 dens collected over a 13-year period. Arctic foxes preferred to breed in dens with more den entrances; an indicator of shelter quality. Arctic foxes also preferred dens surrounded by more prey resources (quantified by the amount of river valley habitat), but this result was less conclusive. These results complement the findings reported from other study areas, illustrating that Arctic foxes in ecosystems with diverse predator communities may put emphasis on selection for shelter quality. In less productive ecosystems, Arctic foxes may rather put emphasis on selection for prey resources. As tundra ecosystems become more productive and generalist predators move north, the reproductive requirements and habitat selection of Arctic foxes may change accordingly, depending on the species’ ability to adapt

Avian Influenza Surveillance with FTA Cards: Field Methods, Biosafety, and Transportation Issues Solved

Avian Influenza Viruses (AIVs) infect many mammals, including humans1. These AIVs are diverse in their natural hosts, harboring almost all possible viral subtypes2. Human pandemics of flu originally stem from AIVs3. Many fatal human cases during the H5N1 outbreaks in recent years were reported. Lately, a new AIV related strain swept through the human population, causing the 'swine flu epidemic'4. Although human trading and transportation activity seems to be responsible for the spread of highly pathogenic strains5, dispersal can also partly be attributed to wild birds6, 7. However, the actual reservoir of all AIV strains is wild birds

A natural gene drive system influences bovine tuberculosis susceptibility in African buffalo : possible implications for disease management

Bovine tuberculosis (BTB) is endemic to the African buffalo (Syncerus caffer) of HluhluweiMfolozi Park (HiP) and Kruger National Park, South Africa. In HiP, the disease has been actively managed since 1999 through a test-and-cull procedure targeting BTB-positive buffalo. Prior studies in Kruger showed associations between microsatellite alleles, BTB and body condition. A sex chromosomal meiotic drive, a form of natural gene drive, was hypothesized to be ultimately responsible. These associations indicate high-frequency occurrence of two types of male-deleterious alleles (or multiple-allele haplotypes). One type negatively affects body condition and BTB resistance in both sexes. The other type has sexually antagonistic effects: negative in males but positive in females. Here, we investigate whether a similar gene drive system is present in HiP buffalo, using 17 autosomal microsatellites and microsatellite-derived Y-chromosomal haplotypes from 401 individuals, culled in 2002– 2004. We show that the association between autosomal microsatellite alleles and BTB susceptibility detected in Kruger, is also present in HiP. Further, Y-haplotype frequency dynamics indicated that a sex chromosomal meiotic drive also occurred in HiP. BTB was associated with negative selection of male-deleterious alleles in HiP, unlike positive selection in Kruger. Birth sex ratios were female-biased. We attribute negative selection and female-biased sex ratios in HiP to the absence of a Y-chromosomal sex-ratio distorter. This distorter has been hypothesized to contribute to positive selection of male-deleterious alleles and male-biased birth sex ratios in Kruger. As previously shown in Kruger, microsatellite alleles were only associated with male-deleterious effects in individuals born after wet pre-birth years; a phenomenon attributed to epigenetic modification. We identified two additional allele types: male-specific deleterious and beneficial alleles, with no discernible effect on females. Finally, we discuss how our findings may be used for breeding disease-free buffalo and implementing BTB test-and-cull programs.S1 Text. Sex chromosomal meiotic drive can explain genome-wide high-frequency occurrence of male-deleterious alleles.S2 Text. Frequency differences of DEmajority and SAEpooled alleles between HiP and Kruger.S1 Fig. Map with sampling localities.S2 Fig. Monthly rainfall in HiP.S3 Fig. Annual rainfall in HiP in the period 1979–2004.S4 Fig. Frequencies of DEmajority and SAEpooled alleles in HiP compared with Kruger.S5 Fig. Difference in Amale-spec between SAEindvN alleles from Kruger observed and not observed in HIP.S6 Fig. Allele frequency differences between northern Kruger and HiP per SAE allele type.S1 Table. List of SAEpooled and DEmajority alleles.S2 Table. List of individual alleles at the DE microsatellite loci.S3 Table. List of individual alleles at the SAE microsatellite loci.S4 Table. List of individual alleles at the SAE microsatellite loci with unknown linkage.S5 Table. Logistic regression of BTB-infection risk for each sex separately.S6 Table. Logistic regression of BTB-infection risk for dry and wet pre-birth years separately.S7 Table. Logistic regression between sex (dependent) and age and 3yr-pre-birth rainfall.The US NSF Division of Environmental Biology (Grant number 0090323 awarded to Dr Wayne M. Getz) and the M3B2 DST/NRF SARChI Chair, University of Pretoria.http://www.plosone.orgam2019Mammal Research InstituteZoology and Entomolog

Evolution and connectivity in the world-wide migration system of the mallard: Inferences from mitochondrial DNA

<p>Abstract</p> <p>Background</p> <p>Main waterfowl migration systems are well understood through ringing activities. However, in mallards (<it>Anas platyrhynchos</it>) ringing studies suggest deviations from general migratory trends and traditions in waterfowl. Furthermore, surprisingly little is known about the population genetic structure of mallards, and studying it may yield insight into the spread of diseases such as Avian Influenza, and in management and conservation of wetlands. The study of evolution of genetic diversity and subsequent partitioning thereof during the last glaciation adds to ongoing discussions on the general evolution of waterfowl populations and flyway evolution. Hypothesised mallard flyways are tested explicitly by analysing mitochondrial mallard DNA from the whole northern hemisphere.</p> <p>Results</p> <p>Phylogenetic analyses confirm two mitochondrial mallard clades. Genetic differentiation within Eurasia and North-America is low, on a continental scale, but large differences occur between these two land masses (<it>F</it>_ST= 0.51). Half the genetic variance lies within sampling locations, and a negligible portion between currently recognised waterfowl flyways, within Eurasia and North-America. Analysis of molecular variance (AMOVA) at continent scale, incorporating sampling localities as smallest units, also shows the absence of population structure on the flyway level. Finally, demographic modelling by coalescence simulation proposes a split between Eurasia and North-America 43,000 to 74,000 years ago and strong population growth (~100fold) since then and little migration (not statistically different from zero).</p> <p>Conclusions</p> <p>Based on this first complete assessment of the mallard's world-wide population genetic structure we confirm that no more than two mtDNA clades exist. Clade A is characteristic for Eurasia, and clade B for North-America although some representatives of clade A are also found in North-America. We explain this pattern by evaluating competing hypotheses and conclude that a complex mix of historical, recent and anthropogenic factors shaped the current mallard populations. We refute population classification based on flyways proposed by ornithologists and managers, because they seem to have little biological meaning. Our results have implications for wetland management and conservation, with special regard to the release of farmed mallards for hunting, as well as for the possible transmission of Avian Influenza by mallards due to migration.</p

Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in South Africa

Background: South Africa's long and extensive trade activity has ensured ample opportunities for exotic species introduction. Whereas the rich biodiversity of endemic southern African fauna has been the focus of many studies, invasive vertebrates are generally overlooked despite potential impacts on biodiversity, health and agriculture. Genetic monitoring of commensal rodents in South Africa which uncovered the presence of Rattus tanezumi, a South-East Asian endemic not previously known to occur in Africa, provided the impetus for expanded studies on all invasive Rattus species present. Results: To this end, intensified sampling at 28 South African localities and at one site in Swaziland, identified 149 Rattus specimens. Cytochrome b gene sequencing revealed the presence of two R. tanezumi, seven R. rattus and five R. norvegicus haplotypes in south Africa. Phylogenetic results were consistent with a single, recent R. tanezumi introduction and indicated that R. norvegicus and R. rattus probably became established following at least two and three independent introductions, respectively. Intra- and inter-specific diversity was highest in informal human settlements, with all three species occurring at a single metropolitan township site. Rattus norvegicus and R. rattus each occurred sympatrically with R. tanezumi at one and five sites, respectively. Karyotyping of selected R. rattus and R. tanezumi individuals identified diploid numbers consistent with those reported previously for these cryptic species. Ordination of bioclimatic variables and MaxEnt ecological niche modelling confirmed that the bioclimatic niche occupied by R. tanezumi in south Africa was distinct from that occupied in its naturalised range in south-east Asia suggesting that factors other than climate may influence the distribution of this species. Conclusions: This study has highlighted the value of genetic typing for detecting cryptic invasive species, providing historical insights into introductions and for directing future sampling. The apparent ease with which a cryptic species can become established signals the need for broader implementation of genetic monitoring programmes. In addition to providing baseline data and potentially identifying high-risk introduction routes, the predictive power of ecological niche modelling is enhanced when species records are genetically verified

Rainfall-driven sex-ratio genes in African buffalo suggested by correlations between Y-chromosomal haplotype frequencies and foetal sex ratio

Background - The Y-chromosomal diversity in the African buffalo (Syncerus caffer) population of Kruger National Park (KNP) is characterized by rainfall-driven haplotype frequency shifts between year cohorts. Stable Y-chromosomal polymorphism is difficult to reconcile with haplotype frequency variations without assuming frequency-dependent selection or specific interactions in the population dynamics of X- and Y-chromosomal genes, since otherwise the fittest haplotype would inevitably sweep to fixation. Stable Y-chromosomal polymorphism due one of these factors only seems possible when there are Y-chromosomal distorters of an equal sex ratio, which act by negatively affecting X-gametes, or Y-chromosomal suppressors of a female-biased sex ratio. These sex-ratio (SR) genes modify (suppress) gamete transmission in their own favour at a fitness cost, allowing for stable polymorphism. Results - Here we show temporal correlations between Y-chromosomal haplotype frequencies and foetal sex ratios in the KNP buffalo population, suggesting SR genes. Frequencies varied by a factor of five; too high to be alternatively explained by Y-chromosomal effects on pregnancy loss. Sex ratios were male-biased during wet and female-biased during dry periods (male proportion: 0.47-0.53), seasonally and annually. Both wet and dry periods were associated with a specific haplotype indicating a SR distorter and SR suppressor, respectively. Conclusions - The distinctive properties suggested for explaining Y-chromosomal polymorphism in African buffalo may not be restricted to this species alone. SR genes may play a broader and largely overlooked role in mammalian sex-ratio variatio

A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium

A high genetic load can negatively affect population viability and increase susceptibility to diseases and other environmental stressors. Prior microsatellite studies of two African buffalo (Syncerus caffer) populations in South Africa indicated substantial genome-wide genetic load due to high-frequency occurrence of deleterious alleles. The occurrence of these alleles, which negatively affect male body condition and bovine tuberculosis resistance, throughout most of the buffalo’s range were evaluated in this study. Using available microsatellite data (2–17 microsatellite loci) for 1676 animals from 34 localities (from 25˚S to 5˚N), we uncovered continent-wide frequency clines of microsatellite alleles associated with the aforementioned male traits. Frequencies decreased over a south-to-north latitude range (average per-locus Pearson r = -0.22). The frequency clines coincided with a multilocus-heterozygosity cline (adjusted R2 = 0.84), showing up to a 16% decrease in southern Africa compared to East Africa. Furthermore, continent-wide linkage disequilibrium (LD) at five linked locus pairs was detected, characterized by a high fraction of positive interlocus associations (0.66, 95% CI: 0.53, 0.77) between male-deleterious-trait-associated alleles. Our findings suggest continent-wide and genome-wide selection of male-deleterious alleles driven by an earlier observed sex-chromosomal meiotic drive system, resulting in frequency clines, reduced heterozygosity due to hitchhiking effects and extensive LD due to male-deleterious alleles co-occurring in haplotypes. The selection pressures involved must be high to prevent destruction of allele-frequency clines and haplotypes by LD decay. Since most buffalo populations are stable, these results indicate that natural mammal populations, depending on their genetic background, can withstand a high genetic load.S1 Text. Allele size standardization.S1 Table. Earlier reported associations of microsatellite alleles with low body condition and bovine tuberculosis (BTB) infection risk.S2 Table. Allele size standardization.S3 Table. Overview of alleles selected for analysis.S4 Table. p-MDTA allele frequencies per population.S5 Table. Per-locus Pearson correlation between ‘p-MDTA minus p-wildtype’ allele frequency difference and latitude, and between He and latitude.S6 Table. He per locus per population.S7 Table. Linkage disequilibrium per population.S8 Table. He per locus in KNP, HiP and Addo NP.S1 Fig. Increase of pairwise FST with geographic distance.S2 Fig. Multilocus-He cline based on twelve microsatellites per locality.S3 Fig. Multilocus-He cline based on seven microsatellites analysed in both East and southern Africa (microsatellite sets A, B and D) plus ABS010 and AGLA293.S4 Fig. Correlation between per-locus southern/northern KNP He ratio and He-latitude Pearson correlation, based on 19 microsatellites.http://www.plosone.orgam2022Zoology and Entomolog