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

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

Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos)

<p>Abstract</p> <p>Background</p> <p>Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl.</p> <p>Results</p> <p>More than one billion base pairs of sequence information were generated resulting in a 16× coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72.</p> <p>Conclusion</p> <p>We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, ~101,000 SNPs were detected within our wild mallard sequences and ~49,000 were detected between wild and domesticated duck data. In the ~101,000 SNPs we found a subset of ~20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (~150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e.g. disentangling migratory connectivity) and industrial breeding programs.</p

Fine-Scale Tracking of Ambient Temperature and Movement Reveals Shuttling Behavior of Elephants to Water

Movement strategies of animals have been well studied as a function of ecological drivers (e.g., forage selection and avoiding predation) rather than physiological requirements (e.g., thermoregulation). Thermal stress is a major concern for large mammals, especially for savanna elephants (Loxodonta africana), which have amongst the greatest challenge for heat dissipation in hot and arid environments. Therefore, elephants must make decisions about where and how fast to move to reduce thermal stress. We tracked 14 herds of elephant in Kruger National Park (KNP), South Africa, for 2 years, using GPS collars with inbuilt temperature sensors to examine the influence of temperature on movement strategies, particularly when accessing water. We first confirmed that collar-mounted temperature loggers captured hourly variation in relative ambient temperatures across the landscape, and, thus, could be used to predict elephant movement strategies at fine spatio-temporal scales. We found that elephants moved slower in more densely wooded areas, but, unexpectedly, moved faster at higher temperatures, especially in the wet season compared to the dry season. Notably, this speed of movement was highest when elephants were approaching and leaving water sources. Visits to water showed a periodic shuttling pattern, with a peak return rate of 10-30 h, wherein elephants were closest to water during the hotter times of the day, and spent longer at water sources in the dry season compared to the wet season. When elephants left water, they showed low fidelity to the same water source, and traveled farther in the dry season than in the wet season. In KNP, where water is easily accessible, and the risk of poaching is low, we found that elephants use short, high-speed bursts of movement to get to water at hotter times of day. This strategy not only provides the benefit of predation risk avoidance, but also allows them to use water to thermoregulate. We demonstrate that ambient temperature is an important predictor of movement and water use across the landscape, with elephants responding facultatively to a ``landscape of thermal stress.'

Selection at the Y chromosome of the African buffalo driven by rainfall.

Selection coefficients at the mammalian Y chromosome typically do not deviate strongly from neutrality. Here we show that strong balancing selection, maintaining intermediate frequencies of DNA sequence variants, acts on the Y chromosome in two populations of African buffalo (Syncerus caffer). Significant correlations exist between sequence variant frequencies and annual rainfall in the years before conception, with five- to eightfold frequency changes over short time periods. Annual rainfall variation drives the balancing of sequence variant frequencies, probably by affecting parental condition. We conclude that sequence variants confer improved male reproductive success after either dry or wet years, making the population composition and dynamics very sensitive to climate change. The mammalian Y chromosome, interacting with ecological processes, may affect male reproductive success much more strongly than previously thought

Host body size and the diversity of tick assemblages on Neotropical vertebrates.

Identifying the factors that influence the species diversity and distribution of ticks (Acari: Ixodida) across vertebrate host taxa is of fundamental ecological and medical importance. Host body size is considered one of the most important determinants of tick abundance, with larger hosts having higher tick burdens. The species diversity of tick assemblages should also be greater on larger-bodied host species, but empirical studies testing this hypothesis are lacking. Here, we evaluate this relationship using a comparative dataset of feeding associations from Panama between 45 tick species and 171 host species that range in body size by three orders of magnitude. We found that tick species diversity increased with host body size for adult ticks but not for immature ticks. We also found that closely related host species tended to have similar tick species diversity, but correcting for host phylogeny did not alter the relationships between host body size and tick species diversity. The distribution of tick species was highly aggregated, with approximately 20% of the host species harboring 80% of all tick species, following the Pareto principle or 20/80 Rule. Thus, the aggregated pattern commonly observed for tick burdens and disease transmission also holds for patterns of tick species richness. Our finding that the adult ticks in this system preferentially parasitize large-bodied host species suggests that the ongoing anthropogenic loss of large-bodied vertebrates is likely to result in host-tick coextinction events, even when immature stages feed opportunistically. As parasites play critical roles in ecological and evolutionary processes, such losses may profoundly affect ecosystem functioning and services

Private Bag X54001

other individuals familiar from earlier in life when foraging, but select for partners that are 38 unfamiliar during mate choice. We found no effect of either personality or dominance on 39 foraging associations or mate choice. Our study shows how using social network analysis can 40 increase our understanding of the drivers behind population structure (in our case kin 41 selection and inbreeding avoidance). Moreover, our study demonstrates that social networks 42 can be largely determined by long-term processes, in particular early-life familiarity. Flack et al. 2006; Lusseau et al. 2011; Hirsch et al. 2012; Madden et al. 2012 based on earlier findings in this species (Choudhury &amp; Black 1994; Black &amp; Owen 1995). 90 We had no a priori expectations in respect of dominance or boldness (Schuett et al. 2010). and Sons, &apos;t Zand, the Netherlands) and after the experiments geese were returned to the 115 breeding farm. were circa two years of age. Two weeks before, the geese were separated into two single-sex 120 flocks, allowing the study of sex-specific factors that may contribute to association 121 preferences while avoiding any confounding inter-sexual interactions. We thus performed our 122 observations on one group consisting of all males, and one group consisting of all females. were seen together out of the total number of times those individuals were observed, thereby 141 controlling for inter-individual differences in the total number of sightings. SRI tends to be a and males similarly from 1 to 23. From these ranks, we derived a dominance distance matrix, RESULTS 274 Genetic relatedness 275 The average pairwise relatedness among all of the dyads was 0.035 ± 0.094 SD (range: 0 - females having relatively few strong and many weak connections 286 Female geese associated significantly more with individuals from the same familiarity group 287 (MRMPA: P &lt; 0.0001, 292 Average SRI within the male group was 0.034 ± 0.057 SD (range 0 -0.50), with most 293 individuals again having relatively few strong association