The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny.We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny of the world's oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity.The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.

Combining molecular analyses with geological and palaeontological data may reveal timing and modes for the divergence of lineages within species. The Mediterranean Basin is particularly appropriate for this kind of multidisciplinary studies, because of its complex geological history and biological diversity. Here, we investigated chloroplast DNA of Quercus suber populations in order to detect possible relationships between their geographical distribution and the palaeogeographical history of the western Mediterranean domain. We analysed 110 cork oak populations, covering the whole distribution range of the species, by 14 chloroplast microsatellite markers, among which eight displayed variation among populations. We identified five haplotypes whose distribution is clearly geographically structured. Results demonstrated that cork oak populations have undergone a genetic drift geographically consistent with the Oligocene and Miocene break-up events of the European-Iberian continental margin and suggested that they have persisted in a number of separate microplates, currently found in Tunisia, Sardinia, Corsica, and Provence, without detectable chloroplast DNA modifications for a time span of over 15 million years. A similar distribution pattern of mitochondrial DNA of Pinus pinaster supports the hypothesis of such long-term persistence, in spite of Quaternary climate oscillations and of isolation due to insularity, and suggests that part of the modern geographical structure of Mediterranean populations may be traced back to the Tertiary history of taxa.

Grain hardness (“hard” or “soft” kernel texture) is the single most important trait in determining the utilization and marketing of wheat (Triticum aestivum L.). Puroindoline a and b proteins represent the molecular basis for this trait. This study surveyed the prevalence of puroindoline hardness mutations (alleles) among North American spring and winter wheat varieties with emphasis on those that are historically important. Each variety was assessed for kernel texture using the Single Kernel Characterization System; Hardness alleles were defined by puroindoline gene sequence and the presence or absence of puroindoline a protein on polyacrylamide gels. A total of 90 spring wheats were examined: nine were soft and possessed wild‐type (“soft”) puroindoline sequences, 10 were mixed hardness, and the remaining 71 were uniformly hard. Of these hard spring wheats, 18 carried the Pina‐D1b hardness allele (null for puroindoline a protein), 47 the Pinb‐D1b allele (Gly‐46–Ser‐46), and four the Pinb‐D1c allele (Leu‐60–Pro‐60). Two hard spring wheats possessed a new allele, designated Pinb‐D1e, which involves a single nucleotide change in Trp‐39 to a “stop” codon. Lastly, among the spring wheats, a new hardness allele was found in the hard component of the variety ‘Utac’ which was mixed. This allele, Pinb‐D1f, also involved a single nucleotide change such that Trp‐44 became a “stop” codon. A total of 62 winter wheat varieties were examined, of which five were soft and three were of mixed hardness. Of interest, the three mixed hardness wheats were ‘Turkey’, ‘Kharkof’, and ‘Weston’. The hard component of each carried the Pinb‐D1b allele. Of the 54 remaining wheats, all of which were hard, all but two carried this same Pinb‐D1b allele. ‘Chiefkan’ winter wheat carried the same Pinb‐D1e allele as ‘Canadian Red’ and ‘Gehun’ spring wheats. ‘Andrews’ hard red winter wheat possessed a new allele, designated Pinb‐D1g, which was a single nucleotide change in Cys‐56 to a “stop” codon. In conclusion, hard grain phenotype results from one of various mutations in either of the puroindoline proteins. To‐date, seven hardness alleles have been discovered and characterized in hexapoid wheat. All but one occur in the puroindoline b gene coding sequence and result from single nucleotide changes. These molecular markers are useful in characterizing lineages and analyzing ancestral relationships.

41• The tree of life is highly reticulate, with the history of population divergence buried amongst 42 phylogenies deriving from introgression and lineage sorting. In this study, we test the 43 hypothesis that there are regions of the oak (Quercus, Fagaceae) genome that are broadly 44 informative about phylogeny and investigate global patterns of oak diversity. 45• We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 46 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the world's 47• The support we find for the phylogeny contrasts with high genomic heterogeneity in 56 phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may 57 in fact depend on the gene flow that shapes the oak genome. 58 59

Durum wheat (Triticum turgidum ssp. durum) is a leading cereal grain whose primary use is the production of semolina and pasta. Its rich culinary relationship to humans is related, in part, to its very hard kernel texture. This very hard texture is due to the loss of the Puroindoline genes that were eliminated during the allopolyploid formation of T. turgidum approximately 0.5 million years ago. In the present report, we describe the transfer of the Puroindoline genes through ph1b‐mediated homoeologous recombination. Puroindoline a and Puroindoline b were successfully recombined (translocated) from chromosome 5D of the soft wheat (T. aestivum) variety Chinese Spring into cv. Langdon durum using a Langdon 5D(5B) disomic substitution line. Although initial recombination lines were highly unstable, recurrent backcrossing into Svevo durum cultivar produced stable lines that segregated in a normal 1:2:1 soft:heterozygous:very hard ratio. The final backcross (BC3) Svevo line produced uniformly soft grain (Single Kernel Characterization System hardness of 24 ±14). The transfer of this fundamental grain property to durum wheat will undoubtedly have an expansive and profound effect on the way that durum grain is milled and on the products that are made from it. As such, our interaction with this important food species will continue to evolve.

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 genus Quercus (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 ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric 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 of Quercus Group 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 within Quercus. 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.

DNA barcoding may be particularly important in influencing ecology, economic issues, and the fundamental crisis facing biodiversity as a standardized, species-level identification tool for taxonomy assessment. Trees play important roles in the conservation of many land ecosystems, the wood trade, and the definition of biogeographical processes; nevertheless, peculiar biological, evolutionary and taxonomical features will probably constitute an intriguing challenge to barcoders. We examined whether four marker regions (trnh-psba, rbcL, rpoc1, matK) proposed by the Consortium for the Barcode of Life (CBOL) matched species taxonomy in a preliminary tree biodiversity survey of Italian forested land. Our objective was to provide a test of future in situ applications of DNA barcodes by evaluating the efficacy of species discrimination under the criteria of uniformity of methods and natural co-occurrence of the species in the main forest ecosystems. Fifty-two species were included in a floristic study. We obtained 73% total discrimination success, with trnH-psbA as the best performing marker and oaks as the least responsive plants to the markers used. A further taxon-based study of Quercus (thirty specimens, 12 species) revealed that this genus is refractory to barcoding (0% discrimination success), a probable consequence of low variation rate at the plastid genome level, hybridization, and the incidence of biogeography. We conclude that some species-rich tree genera in small geographical regions may prove exceptionally difficult to barcode. Until more efficient markers are developed, we recommend that improved and diversified sampling (multiple locations of sympatric and co-occurring congenerics) be embraced as a timely and important goal for the precise assessment of haplotype specificity to facilitate the productive application of barcoding in practice.

DNA barcoding, a species identification system based on sequences from a short, standardized DNA region, has emerged recently as a new tool for taxonomists. We investigated the discriminatory power of a subset of highly variable proposed plant barcoding loci (matK, trnH‐psbA, ITS2) in Quercus, a taxonomically complex tree genus of global importance. The research included all currently recognized species and some major variants of the Mediterranean region and Europe (32 taxa) and 17 East Asian and North American species used for comparison. Based on sequence character state, we assigned unique plastid haplotypes to 40.8% of the investigated species; ITS2 increased the resolution up to 87.8% of total taxa. Nevertheless, unsuccessful genetic distance‐based discrimination questioned the potential efficiency of correct species identification for future studies. Most species appeared to be nonmonophyletic in parallel phylogenetic tests. Three subgeneric groups were outlined, with different rates of within‐group variability and geographical differentiation. Members of one of these groups (corresponding to the Eurasian Group Ilex) were paraphyletic to Group Quercus from the New and Old World and the Eurasian Group Cerris. The data gathered indicate that barcoding markers may help to identify closely related species clusters and contribute to the inference of major diversification and evolutionary patterns in oaks, but the methodology per se appears to be of limited efficacy in defining species limits, unless we make a profound revision of traditional Quercus taxonomic categories. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172, 478–499.