@article {156, title = {Using phylogenomics to infer the evolutionary history of oaks}, journal = {International Oak JournalInternational Oak Journal}, volume = {24}, year = {2013}, pages = {61-71}, abstract = {One of the most basic questions about oaks has long vexed botanists, systematists, and oak enthusiasts of all stripes: what is the shape and timing of the oak tree of life? In this paper, we present new data from a genomic study of 20 oak individuals representing a broad swath of the oaks of the Americas. The paper explains how we are using next-generation sequencing methods to analyze millions of base pairs of DNA data for all individuals studied, and what we have learned to date from this work about the oak tree of life.}, keywords = {Phylogenetics, Quercus, restriction-site associated DNA (RAD) tags, systematics}, author = {Hipp, Andrew L. and Manos, Paul S. and Cavender-Bares, Jeannine and Eaton, Deren A. R. and Nipper, Rick} } @article {161, title = {A framework phylogeny of the American oak clade based on sequenced RAD data}, journal = {PLoS ONEPLoS ONE}, volume = {9}, year = {2014}, pages = {e93975}, abstract = {Oaks (Quercus, Fagaceae) are notorious in plant systematics for the problems they pose at the species level and for higher-level phylogenetics. Previous studies based on nuclear and chloroplast DNA sequences have failed to resolve the backbone phylogeny of the genus with strong support. In this study, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23{\textendash}33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.39E06 aligned nucleotides, constituting 27,727 sequence clusters or {\textquoteleft}loci.{\textquoteright} We reran a subset of seven individuals as technical replicates and found that RAD-Seq data are readily combined across runs, with no difference in phylogenetic placement between replicates, despite the fact that a change in sequencing platforms between replicate runs resulted in data overlap between technical replicates of only 43{\textendash}64\%. 17\% (4,715) of the loci we analyzed could be matched with high confidence (BLASTN E-value < 1E{\textendash}15) to one or more expressed sequence tags (ESTs) in NCBI Genbank. A concatenated matrix of the loci that BLAST to at least one EST sequence provides approximately half as many variable or parsimony-informative characters as same-sized datasets from the non-EST loci. The EST-associated matrix is more complete (fewer missing loci) and has slightly lower homoplasy than non-EST subsampled matrices of the same size, but there is no difference in phylogenetic support or relative attribution of base substitutions to internal versus terminal branches of the phylogeny. The phylogeny we recover provides a robust estimate of the framework phylogeny for the American oak clade and demonstrates the utility of RAD-Seq data for inferring phylogeny in a 23{\textendash}33 million year-old vascular plant clade.}, keywords = {Expressed sequence tags (EST), Fagaceae, next-generation sequencing, phylogenomics, plant systematics, Quercus, restriction-site associated DNA}, author = {Hipp, Andrew L. and Eaton, Deren A. R. and Cavender-Bares, Jeannine and Fitzek, Elisabeth and Nipper, Rick and Manos, Paul S.} } @article {138, title = {Prospects of barcoding the Italian wild dendroflora: oaks reveal severe limitations to tracking species identity}, journal = {Molecular Ecology ResourcesMolecular Ecology Resources}, volume = {11}, number = {1}, year = {2011}, pages = {72-83}, publisher = {Blackwell Publishing Ltd}, abstract = {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.}, keywords = {DNA barcoding, forest trees, Italy, Quercus, regional sampling}, isbn = {1755-0998}, author = {Piredda, Roberta and Simeone, Marco C. and Attimonelli, Marcella and Bellarosa, Rosanna and Schirone, Bartolomeo} } @article {141, title = {Phytophagy on phylogenetically isolated trees: why hosts should escape their relatives}, journal = {Ecology LettersEcology Letters}, year = {2011}, pages = {no-no}, publisher = {Blackwell Publishing Ltd}, abstract = {Hosts belonging to the same species suffer dramatically different impacts from their natural enemies. This has been explained by host neighbourhood, that is, by surrounding host-species diversity or spatial separation between hosts. However, even spatially neighbouring hosts may be separated by many million years of evolutionary history, potentially reducing the establishment of natural enemies and their impact. We tested whether phylogenetic isolation of oak hosts from neighbouring trees within a forest canopy reduces phytophagy. We found that an increase in phylogenetic isolation by 100 million years corresponded to a 10-fold decline in phytophagy. This was not due to poorer living conditions for phytophages on phylogenetically isolated oaks. Neither species diversity of neighbouring trees nor spatial distance to the closest oak affected phytophagy. We suggest that reduced pressure by natural enemies is a major advantage for individuals within a host species that leave their ancestral niche and grow among distantly related species.}, keywords = {Community phylogeny, forest canopy, insect herbivory, intraspecific variation, Lepidoptera, macroevolution, plant{\textendash}insect interactions, Quercus, temperate forest}, isbn = {1461-0248}, author = {Yguel, Benjamin and Bailey, Richard and Tosh, N. Denise and Vialatte, Aude and Vasseur, Chlo{\'e} and Vitrac, Xavier and Jean, Frederic and Prinzing, Andreas} } @article {134, title = {Cytogenetic studies on Quercus L. (Fagaceae) species belonging to Ilex and Cerris section in Turkey}, journal = {CaryologiaCaryologia}, volume = {64}, number = {3}, year = {2011}, pages = {297-301}, abstract = {A detailed karyotype analyses of the five species of Quercus L. (Q. coccifera L., Q. ilex L., Q. aucheriJaub. \& Spach, Q. cerris L. and Q. ithaburensis Decne subsp. macrolepsis (Kotschy) Hedge \& Yalt.) belonging toIlex and Cerris section were examined. The somatic chromosome number of all studied taxa 2n = 24 was found.The karyotypes of investigated species showed the great similarity with the chromosome length and the positionof centromere. Chromosome number and detailed karyotype of these species were first time counted from Turkey.}, keywords = {cerris, ilex, Karyotype analyses, Quercus, Turkey}, author = {Yilmaz Aykut and Emel Uslu and M. Tekin Baba{\c c}} } @article {146, title = {Gene flow and hybridisation in a mixed oak forest (Quercus pyrenaica Willd. and Quercus petraea (Matts.) Liebl.) in central Spain}, journal = {Heredity}, volume = {95}, number = {6}, year = {2005}, pages = {457-465}, abstract = {Oaks are long-standing models for the study of gene flow and hybridisation. Temperate (Quercus petraea) and sub-Mediterranean (Quercus pyrenaica) oaks coexist in central Spain, showing remarkable differences in population size and structure. Q. petraea has a scattered distribution in central Spain, where it is at one of the southernmost limits of its range, and forms low-density stands; in contrast, Q. pyrenaica is widespread in the region. We selected a mixed population of the two species (approx13 ha, 176 adults and 96 saplings) to compare the patterns of gene flow within each species and the extent of introgression between them. Using five nuclear microsatellite markers, we performed a parentage analysis and found considerable immigration from outside the stand (approx38\% for Q. petraea and approx34\% for Q. pyrenaica), and estimated average seed-dispersal distances of 42 and 14 m for Q. petraea and Q. pyrenaica, respectively. Introgression between species was also estimated using our microsatellite battery. First, we developed a multivariate discriminant approach and, second, we compared our results with a widely used clustering method (STRUCTURE). Both analyses were consistent with a low level of introgression between Q. petraea and Q. pyrenaica. Indeed, only 15 adult trees, approx8.5\%, were identified as putative hybrids when both methods of analysis were combined. Hybrids may be most common in contact zones due merely to physical proximity.}, keywords = {gene flow, genetic differentiation, hybrid zones, introgression, microsatellites, Quercus}, author = {Valbuena-Carabana, M. and Gonzalez-Martinez, S. C. and Sork, V.L. and Collada, C. and SOTO, A. and Goicoechea, P.G. and Gil, L.} } @article {117, title = {Species relative abundance and direction of introgression in oaks}, journal = {Molecular Ecology}, volume = {18}, year = {2009}, month = {2009}, pages = {2228-2242}, abstract = {Successful hybridisation and subsequent introgression lead to the transfer of genetic material across species boundaries. In this process, species relative abundance can play a significant role. If one species is less abundant than the other, its females will receive many heterospecific gametes, increasing mate-recognition errors and thus hybridisation rate. Moreover, first-generation hybrids will also more likely mate with the more abundant species, leading to asymmetric introgression. These predictions have important fundamental consequences, especially during biological invasions or when a rare species threatened by extinction is surrounded by individuals from a related species. However, experimental tests in nature of the importance of the relative abundance of each species on hybridisation dynamics remain scarce. We assess here the impact of species relative abundance on hybridisation dynamics among four species from the European white oak species complex. A total of 2107 oak trees were genotyped at 10 microsatellite markers and Bayesian clustering methods were used to identify reference trees of each species. We then used these reference trees to simulate purebred and hybrid genotypes to determine optimal threshold for genetic assignment. With this approach, we found widespread evidence of hybridisation between all studied oak species, with high occurrence of hybrids, varying from 11\% to 31\% according to stand and sampling strategies. This finding suggests that hybridisation is a common phenomenon that plays a significant role in evolution of this oak species complex. In addition, we demonstrate a strong impact of species abundance on both hybridisation rate and introgression directionality.}, keywords = {Quercus}, url = {http://dx.doi.org/10.1111/j.1365-294X.2009.04137.x}, author = {Lepais, O. and Petit, R.J. and Guichoux, E. and Lavabre, J.E. and Alberto, F. and Kremer, A. and Gerber, S.} }