Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genusQuercus(oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilexL.,Q. cocciferaL.,Q. aucheriJaub. & Spach.,Q. alnifoliaPoech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing allQuercussubgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members ofQuercusGroup Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split withinQuercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.

Oaks (Quercus) comprise more than 400 species worldwide and centres of diversity for most sections lie in the Americas and East/Southeast Asia. The only exception is the Eurasian sect.Cerristhat comprises about 15 species, most of which are confined to western Eurasia. This section has not been comprehensively studied using molecular tools. Here, we assess species diversity and provide a first comprehensive taxonomic and phylogeographic scheme of western Eurasian members of sect.Cerrisusing plastid (trnH-psbA) and nuclear (5S-IGS) DNA variation with a dense intra-specific and geographic sampling. Chloroplast haplotypes primarily reflected phylogeographic patterns originating from interspecific cytoplasmic gene flow within sect.Cerrisand its sister sectionIlex. We identified two widespread and ancestral haplotypes, and locally restricted derived variants. Signatures shared with Mediterranean species of sect.Ilex, but not with the East AsianCerrisoaks,suggest that the western Eurasian lineage came into contact withIlexonly after the first (early Oligocene) members of sect.Cerrisin Northeast Asia had begun to radiate and move westwards. Nuclear 5S-IGS diversification patterns were more useful for establishing a molecular-taxonomic framework and to reveal hybridization and reticulation. Four main evolutionary lineages were identified. The first lineage is comprised ofQ. libani,Q. trojanaandQ. afaresand appears to be closest to the root of sect.Cerris. These taxa are morphologically most similar to the East Asian species ofCerris, and to both Oligocene and Miocene fossils of East Asia and Miocene fossils of western Eurasia. The second lineage is mainly composed of the widespreadQ. cerrisand the narrow endemic speciesQ. castaneifolia, Q. look, andQ. euboica. The third lineage comprises three Near East species (Q. brantii,Q. ithaburensisandQ. macrolepis), well adapted to continental climates with cold winters. The forth lineage appears to be the most derived and comprisesQ. suberandQ. crenata.Q. cerrisandQ.  trojanadisplayed high levels of variation;Q. macrolepisandQ. euboica,previously treated as subspecies ofQ. ithaburensisandQ. trojana,likely deserve independent species status. A trend towards inter-specific crosses was detected in several taxa; however, we found no clear evidence of a hybrid origin ofQ.afaresandQ. crenata, as currently assumed.

Mayfly (Ephemeroptera) systematics has considerably changed over the years, but many questions have yet to be answered. The synergistic connection between traditional knowledge and new data sources, producing increasingly complex information, has become a compelling issue for modern taxonomy. Molecular tests and the use of reliable reference sequence libraries may constitute effective complements to the traditional method in guiding recognition of species and giving information about taxonomic incongruences which require further examination. In the present study, we sought to verify the current Italian mayfly nomenclatural system through DNA barcoding and relevant points to reliably manage the available amount of morpho-ecological and molecular data are discussed. We investigated COI (Cytochrome oxidase I) sequence variation in 163 individuals of Italian mayflies, 126 of which were previously assigned to 24 morphologically recognised species, and 37 could be attributed only to generic taxonomic entities (“sp.”, “cf.” or “gr.”). DNA barcoding statistical tests for species delimitation hypotheses based on genetic distances and inferred gene trees were integrated with GenBank searches and surveys of the historical literature to better understand the knowledge acquired on the status and diversity of the investigated taxa. Combined criteria to define three categories of reliability were then assessed. Concurrent data allowing unambiguous identification were attained for only eight species. High intraspecific genetic distances (> 3%) and a lack of reliable reference material or convincing taxonomic information evidenced 29 critical states, deserving further investigation. Solid species names, potential cryptic species and entities about which little is known are pointed out for a future upgrade/reorganisation of the taxonomy of Italian Ephemeroptera.

Available knowledge on the European white oaks (Quercus, sect. Quercus) plastome still exhibits large gaps, mostly in respect of detailed phylogeny and information from southern Europe and adjacent Near East. We investigated DNA sequence polymorphism at two plastid loci on 270 individuals representing 13 white oak species/taxa and retrieved several hundred sequences of the same two DNA regions from GenBank to fill the above gaps, and contribute to a better understanding of white oak diversity and evolution. The modern European sect. Quercus species exhibits a poorly differentiated plastid DNA, despite its current highly diversified taxonomy. Twenty-nine haplotypes were identified across the Euro-Mediterranean and Near East regions, including two ancestral variants that are westerly and south-easterly partitioned. Other high- and low-frequency haplotypes also showed a well-structured geographic distribution consistent with the current phytogeographic framework of the European continent. The climatic and geological events that characterized the end of the Tertiary and Quaternary periods played a crucial role in triggering haplotype mixing, isolation, and in offering niche opportunities for more recent diversification. Euro-Mediterranean southern territories host a high and as yet poorly studied genetic variation; the role of the Italian Peninsula as a crossroad and threshold for haplotype diversity and distribution clearly emerges from this study.