Blanco-Pastor, J. L. | Search bioRxiv

bioRxiv2018

Pleistocene climate changes explain large-scale genetic variation in a dominant grassland species, Lolium perenne L.

AimGrasslands have been pivotal in the development of herbivore breeding since the Neolithic and are still nowadays the most widespread agricultural land-use across Europe. However, it remains unclear whether the current large-scale genetic variation of plant species found in natural grasslands of Europe is the result of human activities or natural processes.\n\nLocationEurope.\n\nTaxonLolium perenne L (perennial ryegrass).\n\nMethodsWe reconstructed the phylogeographic history of L. perenne, a dominant grassland species, using 481 natural populations including 11 populations from closely related taxa. We combined the Genotyping-by-Sequencing (GBS) and Pool-sequencing (Pool-seq) methods to obtain high-quality allele frequency calls of ~ 500 k SNP loci. We performed genetic structure analyses and demographic reconstructions based on the site frequency spectrum (SFS). We additionally used the same genotyping protocol to assess the genomic diversity of a set of 32 cultivars representative of the L. perenne cultivars widely used for forage purposes.\n\nResultsExpansion across Europe took place during the Wurm glaciation (12-110 kya), a cooling period that decreased the dominance of trees in favour of grasses. Splits and admixtures in L. perenne fit historical sea level changes in the Mediterranean basin. The development of agriculture in Europe (7-3.5 kya), that caused an increase in the abundance of grasslands, did not have an effect on the demographic patterns of L. perenne. We found little differentiation between modern cultivars and certain natural variants. However, modern cultivars do not represent the wide genetic variation found in natural populations.\n\nMain conclusionsDemographic events in L. perenne can be explained by the changing climatic conditions during the Pleistocene. Natural populations maintain a wide genomic variability at continental scale that has been underused by recent breeding activities. This variability constitutes valuable standing genetic variation for future adaptation of grasslands to climate change, safeguarding the agricultural services they provide.

evolutionary biology↗

bioRxiv2018

Robustness of RADseq for evolutionary network reconstruction from gene trees

Although hybridization has played an important role in the evolution of many species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. Recently, the combined development of high-throughput sequencing and evolutionary network models offer new opportunities for phylogenetic inference under complex patterns of hybridization in the context of incomplete lineage sorting. Restriction site associated DNA sequencing (RADseq) has been a popular sequencing technique for evolutionary reconstructions of close relatives in the Next Generation Sequencing (NGS) era. However, the utility of RADseq data for the reconstruction of complex evolutionary networks has not been thoroughly discussed. Here, we used new molecular data collected from diploid perennial Medicago species using single-digest RADseq to reconstruct evolutionary networks from gene trees, an approach that is computationally tractable with datasets that include several species and complex patterns of hybridization. Our analyses revealed that complex network reconstructions from RADseq-derived gene trees were not robust under variations of the assembly parameters and filters. Filters to exclusively select loci with high phylogenetic information created datasets that retrieved the most anomalous topologies. Conversely, alternative clustering thresholds or filters on the number of samples per locus affected the level of missing data but had a lower impact on networks. When most anomalous networks were discarded, all remaining network analyses consistently supported a hybrid origin for M. carstiensis and M. cretacea.

genetics↗