Inconsistent genetic structure among members of a multitrophic system: did bruchid parasitoids (Horismenus spp.) escape the effects of bean domestication?

Anthropogenic range expansion and cultural practices have modified the distribution, abundance and genetic diversity of domesticated organisms, thereby altering multitrophic assemblages through space and time. The putative Mesoamerican domestication centre of the common bean, Phaseolus vulgaris L., in Mexico allows investigating the effects of plant domestication on the genetic structure of members of a multitrophic system. The aim of this study was to compare the evolutionary history of Horismenus parasitoids (Hymenoptera: Eulophidae) to those of their bruchid beetle hosts (Coleoptera: Bruchidae) and their domesticated host plant (P. vulgaris), in the context of traditional agriculture in Mexico. We analyzed the population genetic structure of four Horismenus species in Mexico using mitochondrial COI haplotype data. The two most abundant parasitoid species were Horismenus depressus and Horismenus missouriensis. Horismenus missouriensis were infected by Wolbachia endosymbionts and had little to no population differentiation (F ST=0.06). We suspect the mitochondrial history of H. missouriensis to be blurred by Wolbachia, because differentiation among infected vs. non-infected individuals exists (F ST=0.11). Populations of H. depressus were found to be highly differentiated (F ST=0.34), but the genetic structuring could not be explained by tested spatial components. We then compared the genetic structure observed in this parasitoid species to previously published studies on bruchid beetles and their host plants. Despite extensive human-mediated migration and likely population homogenization of its two Acanthoscelides bruchid beetle hosts, H. depressus populations are structured like its host plant, by a recent dispersal from a diverse ancestral gene pool. Distinct evolutionary dynamics may explain inconsistent patterns among trophic levels. Parasitoids likely migrate from wild bean populations and are poorly adapted to bean storage conditions similar to their bruchid beetle hosts. Integrating several trophic levels to the study of evolutionary history has proven to be fruitful in detecting different ecological responses to human-mediated disturbances and host parasite interaction

Exploring Pandora's Box: potential and pitfalls of low coverage genome surveys for evolutionary biology

High throughput sequencing technologies are revolutionizing genetic research. With this ‘‘rise of the machines’’, genomic sequences can be obtained even for unknown genomes within a short time and for reasonable costs. This has enabled evolutionary biologists studying genetically unexplored species to identify molecular markers or genomic regions of interest (e.g. micro- and minisatellites, mitochondrial and nuclear genes) by sequencing only a fraction of the genome. However, when using such datasets from non-model species, it is possible that DNA from non-target contaminant species such as bacteria, viruses, fungi, or other eukaryotic organisms may complicate the interpretation of the results. In this study we analysed 14 genomic pyrosequencing libraries of aquatic non-model taxa from four major evolutionary lineages. We quantified the amount of suitable micro- and minisatellites, mitochondrial genomes, known nuclear genes and transposable elements and searched for contamination from various sources using bioinformatic approaches. Our results show that in all sequence libraries with estimated coverage of about 0.02–25%, many appropriate micro- and minisatellites, mitochondrial gene sequences and nuclear genes from different KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways could be identified and characterized. These can serve as markers for phylogenetic and population genetic analyses. A central finding of our study is that several genomic libraries suffered from different biases owing to non-target DNA or mobile elements. In particular, viruses, bacteria or eukaryote endosymbionts contributed significantly (up to 10%) to some of the libraries analysed. If not identified as such, genetic markers developed from high-throughput sequencing data for non-model organisms may bias evolutionary studies or fail completely in experimental tests. In conclusion, our study demonstrates the enormous potential of low-coverage genome survey sequences and suggests bioinformatic analysis workflows. The results also advise a more sophisticated filtering for problematic sequences and non-target genome sequences prior to developing markers

A software tool ‘CroCo’ detects pervasive cross-species contamination in next generation sequencing data

International audienceBackground: Multiple RNA samples are frequently processed together and often mixed before multiplex sequencing in the same sequencing run. While different samples can be separated post sequencing using sample barcodes, the possibility of cross contamination between biological samples from different species that have been processed or sequenced in parallel has the potential to be extremely deleterious for downstream analyses