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  • 1.
    Denk, Thomas
    et al.
    Swedish Museum of Natural History.
    Hipp, Andrew L.
    Manos, Paul S.
    Hahn, Marlene
    Avishai, Michael
    Bodénès, Catherine
    Cavender-Bares, Jeannine
    Crowl, Andrew A.
    Deng, Min
    Fitz-Gibbon, Sorel
    Gailing, Oliver
    Gonzalez-Elizondo, Antonio
    Grimm, Guido W.
    Jiang, Xiao-Long
    Kremer, Antoine
    Lesur, Isabelle
    McVay, John D.
    Plomion, Christophe
    Rodriguez-Correa, Hernando
    Schulze, Ernst-Detlef
    Simeone, Marco C.
    Sork, Victoria L.
    Valencia-Avalos, Susana
    Genomic landscape of the global oak phylogeny2019In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, p. 1-15, article id doi: 10.1111/nph.16162Article in journal (Refereed)
    Abstract [en]

    The tree of life is highly reticulate, with the history of population divergence emerging frompopulations of gene phylogenies that reflect histories of introgression, lineage sorting anddivergence. In this study, we investigate global patterns of oak diversity and test the hypothesisthat 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 632individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny ofthe world’s oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstructshifts in lineage diversification rates, accounting for among-clade sampling biases. We thenmap the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomicdistribution of introgression and phylogenetic support across the phylogeny. Oak lineages have diversified among geographic regions, followed by ecological divergencewithin regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to fourclades that experienced increases in net diversification, probably in response to climatic transitionsor ecological opportunity. The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogeneticsignal and introgression. Oaks are phylogenomic mosaics, and their diversity may infact depend on the gene flow that shapes the oak genome.

  • 2. Divakar, Pradeep K.
    et al.
    Crespo, Ana
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi2015In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 208, p. 1217-1226Article in journal (Refereed)
  • 3.
    Friis, Else Marie
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Crane, Peter Robert
    Oak Spring Gardens.
    Pedersen, Kaj Raunsgaard
    University of Aarhus.
    The endothelium in seeds of early angiosperms2019In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 224, p. 1419-1424Article in journal (Refereed)
    Abstract [en]

    Studies of Cretaceous age mesofossil floras – assemblages of small carbonaceous plant fossils isolated from poorly consolidated sediments – have provided a wealth of new insights into the early fossil history of angiosperms (for references, see Friis et al., 2011). The fossils recovered from such mesofloras include well‐preserved flowers, fruits and seeds that can be compared in detail with those of living plants to provide an integrated picture of early angiosperm evolution. Data from mesofossil floras have also provided many of the fossil calibrations used to model the age of different angiosperm clades based on molecular data (Magallón & Sanderson, 2005; Beaulieu et al., 2015; Magallón et al., 2015). From the Early Cretaceous these kinds of fossils have so far only been discovered in deposits from Portugal and eastern North America, where they are sometimes abundant, and often have an exquisite preservation of cellular details.

  • 4. Yan, Hai-Fei
    et al.
    Zhang, Cai-Yun
    Anderberg, Arne Alfred
    Swedish Museum of Natural History, Department of Botany.
    Hao, Gang
    Ge, Xue-Jun
    Wiens, John J.
    What explains high plant richness in East Asia? Time anddiversification in the tribe Lysimachieae (Primulaceae)2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 219, p. 436-448Article in journal (Refereed)
    Abstract [en]

    What causes the disparity in biodiversity among regions is a fundamental question in bio-geography, ecology, and evolutionary biology. Evolutionary and biogeographic processes(speciation, extinction, dispersal) directly determine species richness patterns, and can bestudied using integrative phylogenetic approaches. However, the strikingly high richness ofEast Asia relative to other Northern Hemisphere regions remains poorly understood from thisperspective. Here, for the first time, we test two general hypotheses (older colonization time,faster diversification rate) to explain this pattern, using the plant tribe Lysimachieae (Primu-laceae) as a model system.We generated a new time-calibrated phylogeny for Lysimachieae (13 genes, 126 species),to estimate colonization times and diversification rates for each region and to test the relativeimportance of these two factors for explaining regional richness patterns.We find that neither time nor diversification rates alone explain richness patterns amongregions in Lysimachieae. Instead, a new index that combines both factors explains global rich-ness patterns in the group and their high East Asian biodiversity.Based on our results from Lysimachieae, we suggest that the high richness of plants in EastAsia may be explained by a combination of older colonization times and faster diversificationrates in this region

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