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 ).