Characterization of genome-wide SNPs for the water flea Daphnia pulicaria generated by genotyping-by-sequencing (GBS)

The keystone aquatic herbivore Daphnia has been studied for more than 150 years in the context of evolution, ecology and ecotoxicology. Although it is rapidly becoming an emergent model for environmental and population genomics, there have been limited genome-wide level studies in natural populations. We report a unique resource of novel Single Nucleotide Polymorphic (SNP) markers for Daphnia pulicaria using the reduction in genomic complexity with the restriction enzymes approach, genotyping-by-sequencing. Using the genome of D. pulex as a reference, SNPs were scored for 53 clones from five natural populations that varied in lake trophic status. Our analyses resulted in 32,313 highly confident and bi-allelic SNP markers. 1,364 outlier SNPs were mapped on the annotated D. pulex genome, which identified 2,335 genes, including 565 within functional genes. Out of 885 EuKaryotic Orthologous Groups that we found from outlier SNPs, 294 were involved in three metabolic and four regulatory pathways. Bayesian-clustering analyses showed two distinct population clusters representing the possible combined effects of geography and lake trophic status. Our results provide an invaluable tool for future population genomics surveys in Daphnia targeting informative regions related to physiological processes that can be linked to the ecology of this emerging eco-responsive taxon.We thank the European Union (EU) Marie-Curie International Outgoing Fellowship Program (FP7-PEOPLE-2010, ADAPT-ENVGENOME, project code #271485) to J.M., A.J. Green and L.J.W., and the U.S. National Science Foundation (NSF-IOS-OEI) collaborative grants #0924289 and #1256881 to L.J.W. and grant #09244019 to P.D. Jeyasingh for funding this project. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the U.S. National Science Foundation. J.M. was also supported by the European Science Foundation (ConGenOmics, project code #4810) to develop the bioinformatics part of this study. L.J.W. also acknowledges the support of the KU Leuven Research Fund (fellowship SF/12/009), which allowed him to visit KU Leuven during the course of this project. A.C. was financed by the KU Leuven Research Fund excellence center financing PF/2010/07 during this project.EUR 1,165 APC fee funded by the EC FP7 Post-Grant Open Access PilotPeer reviewe

The invasion history of the exotic freshwater zooplankter Daphnia lumholtzi (Cladocera, Crustacea) in North America: A genetic analysis

Daphnia lumholtzi is a planktonic crustacean native to subtropical regions in Africa, Asia and Australia. Since its invasion to the southern USA in ~1990 it has spread across North America as far north as the Laurentian Great Lakes. We assessed invasion history using microsatellite makers and to explore the influence of mean annual temperature on the genetic structure along a latitudinal gradient in North America. Genotypic data were obtained from 9 microsatellite markers for 178 individuals from 13 populations (eight populations introduced to North America and five populations in the native range). Pairwise Fst values as well as Bayesian clustering showed a strong subdivision between native and introduced populations. Bayesian clustering identified multiple genetic clusters in recently invaded locations, suggestive of multiple invasions from various sources, including Asia and Africa. Using variation partitioning, we determined the amount of variation for genetic clusters of populations in the invaded range due to mean annual air temperature and the year of first detection. The results point to a primary introduction into the southern range of North America, with a subsequent northward expansion, and multiple introductions possibly from both the native range and by secondary spread from previously-invaded locations. Separate analysis of genetic clusters within the invaded range suggests additional effects of temperature conditions on geographic genetic structure, possibly as a consequence of D. lumholtzi's tropical origin. © 2012 Springer Science+Business Media B.V.Peer Reviewe

Temporal dynamics of genotypic diversity reveal strong clonal selection in the aphid Myzus persicae

Parthenogenetic organisms often harbour substantial genotypic diversity. This diversity may be the result of recurrent formations of new clones, or it may be maintained by environmental heterogeneity acting on ecological differences among clones. In aphids, both processes may be important because obligate and cyclical parthenogens can form mixed populations. Using microsatellites, I analysed the temporal dynamics of clonal diversity in such a population of the aphid Myzus persicae over a 1-year period. The frequency distribution of clonal genotypes was very skewed, with many rare and few common clones. The relative frequencies of common clones underwent strong and rapid changes indicative of intense clonal selection. Differences in their host associations suggest that these shifts may partly be caused by changes in the abundance of annual host plants. Other selective factors of potential importance are also discussed. New, sexually produced genotypes made a minor contribution to clonal diversity, consistent with the observed heterozygote excess characteristic of predominantly asexual populations in M. persicae

Ecological and evolutionary significance of dispersal by freshwater invertebrates

Traditional expectations for how widely and how often freshwater invertebrates disperse differ from empirical data. Freshwater invertebrates have been characterized as frequent, widespread dispersers, particularly those that are transported passively. Our review finds that this characterization may describe the potential for dispersal in some taxa, but it is not an accurate generalization for actual dispersal rates. High variance among habitats and taxonomic groups is a consistent theme. Advances in population genetics may help resolve these issues, but underlying assumptions should be carefully tested. Further, even unbiased estimates of gene flow may not equate with individual movement, because not all dispersers survive and reproduce. Some freshwater invertebrates may exist in classic Levins metapopulations. However, other species fit into a broader metapopulation definition, where temporal dispersal via diapause is functionally equivalent to spatial dispersal. In the latter case, local extinctions and rescue effects may be rare or absent. Finally, limited dispersal rates in many taxa suggest that theories of freshwater community assembly and structure can be made more robust by integrating dispersal and local processes as joint, contingent regulators. Recent research on freshwater invertebrate dispersal has substantially advanced our basic and applied understanding of freshwaters, as well as evolutionary ecology in general

Patterns and determinants of shorebird species richness in the circumpolar Arctic

Aim The intention with this study was first to investigate and describe the broad-scale geographical patterns of species richness of breeding shorebirds (Charadriiformes; families: Charadriidae, Scolopacidae and Haematopodidae) throughout the arctic tundra biome. Secondly, after compensating for the positive relationship between net primary productivity (NPP) and species richness, the relative importance of additional ecological and historical variables for species richness was investigated. The main variables considered are NPP, length of snow- and ice-free season, accessibility of regions depending on migratory flyway systems, tundra area at Pleistocene (120 and 20-18 ka bp) and Holocene (8 ka bp) times, and tundra area at present. Methods Information on shorebird species breeding distributions was compiled from distribution atlases and species accounts. The breeding distributions of shorebirds with ranges partly or completely in the Arctic (a total of 50 species) were mapped in ArcView 3.2 to create a raster grid layer of shorebird species richness at a 1degrees latitude x longitude resolution. The total and mean species richness value was calculated per each 10degrees of longitude sector of the Arctic. The relationships between species richness and the different climatic and environmental variables were analysed on the basis of this sector-wise division of the arctic tundra. The influence of each variable on species richness was investigated using univariate and multivariate analyses (multivariate linear regression and general linear model). Results We found that patterns of breeding shorebird species richness in the Arctic tundra biome are to a large degree determined by the NPP, the length of the snow- or ice-free season, the diversity of migratory flyways, as well as the historical extent of tundra habitat area during the maximum cooling of the last glacial period. Essentially, two main regions are distinguishable in the circumpolar Arctic regarding shorebird community richness. These are a species-rich Beringia-centred region and a species-poor Atlantic-centred region. Main conclusions The underlying explanations to these major trends may primarily be attributed to factors that operate at present through accessibility of areas from contemporary migration flyways, as well as processes that operated in the past during and after the last glacial cycle. The most prominent influence on the shorebird diversity was found for NPP in combination with the diversity of migratory flyways. These flyways provide the links between breeding and wintering resources, often separated by huge distances, and the geographical and ecological conditions associated with the shorebirds' migration seem to be of particular importance for their breeding diversity in different sectors of circumpolar tundra