Conclusion
The presented pipeline showed a good match with a complementary dataset (Sanger sequenced cloned fragments) and high potential for geno-taxonomy and evolutive inferences in oaks. Pure samples can be used to identify unknown individuals and inspect their genetic background. Mixed samples demonstrated a good ability to reveal presence/absence of taxa or specific lineages without missing any target in the sample. In addition, the pipeline has the potentiality to identify processes such as hybridization and introgression. At the same time, complex patterns resulting from multiplexed samples can be compared among different areas to evaluate genetic connectivity, discover local hotspots of genetic diversity, map the overall per-section diversity and possibly retrieve specific phylogeographic patterns. The only limitation is that the 5S IGS marker has different geno-taxonomic resolution in oak lineages. This problem applies mainly to members of section Quercus , but it could be partly overcome by expanding the benchmark reference.
Gaining better knowledge and evidence of the genetic resources of natural ecosystems, evolutionary dynamics and community assemblages is fundamental to improve our understanding of the natural processes shaping past and future biodiversity trends. HTS approaches are an innovative and important tool at this regard. They can provide new fundamental insights on species identity, history and natural evolution of communities. Adequately generating and interpreting data remain challenging but can be of utmost importance to reverse biodiversity decline, one of the fundamental targets of the 2030 Agenda for Sustainable Development (www.sustainabledevelopment.un.org). In oaks, the quest for a speedy and reliable marker for species identification and detection of introgression is on the way (Lepoittevin et al. 2015; Fitzek et al. 2018). However, transferability of the recently developed SNP toolkits to all taxa distributed across western Eurasia and other parts of the world, and even among distant populations within the same species, remains to be addressed. Our method is more flexible, as it can be used independently of the set-up of large genomic species-specific SNP surveys or genotype-by-sequencing approaches that for the western Eurasian oaks rely on just two species of one section (Q. robur and Q. petraea ).