Angiosperms versus gymnosperms in the Cretaceous

Birks, H. J. B.

doi:10.1073/pnas.2021186117

Cited by 6 publications

(2 citation statements)

References 25 publications

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“…The ancient, widespread range and diversification of Torreya in the Jurassic and Cretaceous found in our study (Fig. 6) agree with previous inferences from the fossil record that gymnosperm lineages underwent considerable diversification during the Jurassic or early Cretaceous coupled with global range expansions (Crisp & Cook, 2011; Wang & Ran, 2014; Birks, 2020). However, it is widely believed that angiosperms later effectively outcompeted gymnosperms in many types of habitats and, thus, led to increasingly restrictive geographic ranges for gymnosperms (Biffin et al, 2012; Brodribb et al, 2012).…”

Section: Discussionsupporting

confidence: 92%

Phylogenomics and biogeography of Torreya (Taxaceae)—Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD‐seq

Zhou

Harris

Xiang

2022

J of Systematics Evolution

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Restriction site-associated DNA sequencing (RAD-seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD-seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RAD-seq Allele Dropout Remedy in our study of the gymnosperm genus, Torreya, to mitigate ADO in outgroups by recovering missing loci from previously published transcriptomes. By using RADADOR to supplement Rad-seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and tested hypotheses on anomalies of biodiversity of the eastern Asian-North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for Torreya. Using the fossilized birth-death model and divergence-extinction-cladogenesis method, we resolved a detailed biogeographic history of Torreya that suggested a Jurassic origin spanning Laurasia and differential speciation and extinction among continents accounting for modern diversity, which is biased toward eastern Asia (EA). The biogeographic results also supported a vicariance origin of modern Torreya from a widespread ancestor in EA and North America (NA) in the mid-Eocene, and cross Beringian exchange in the early Paleogene before the vicariant isolation, in contrast to the "out of NA" pattern common to gymnosperms and to the "out of EA" hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies for Torreya jackii, suggesting differential lineage sorting of plastid genomes among species of Torreya or plastid genome capture in T. jackii.

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Section: Discussionsupporting

confidence: 92%

Phylogenomics and biogeography of Torreya (Taxaceae)—Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD‐seq

Zhou

Harris

Xiang

2022

J of Systematics Evolution

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“…Gymnosperms, naked-seed plants, are phylogenetically sister to the flowering plants (angiosperms), of which the origin can be traced back to the Devonian period. Despite their flourishing diversity in the Mesozoic era, only ~1000 living species of gymnosperms exist in the modern flora (~0.4% of the number of angiosperms) [ 1 ]. However, they account for at least 39% of the world’s forests [ 2 ] and hold great economic and cultural importance in horticulture, medicine, and the timber industry [ 3 ].…”

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confidence: 99%