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Plants (Basel) 2022 Jun 7;11(12). Epub 2022 Jun 7.

Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China.

Phylogenetic conflicts limit our understanding of the evolution of terrestrial life under multiple whole genome duplication events, and the phylogeny of early terrestrial plants remains full of controversy. Although much incongruence has been solved with so-called robust topology based on single or lower copy genes, the evolutionary mechanisms behind phylogenetic conflicts such as polyploidization remain poorly understood. Here, through decreasing the effects of polyploidization and increasing the samples of species, which represent all four orders and eight families that comprise early leptosporangiate ferns, we have reconstructed a robust phylogenetic tree and network with 1125 1-to-1 orthologs based on both coalescent and concatenation methods. Read More

Curr Biol 2022 Jun 14. Epub 2022 Jun 14.

Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada. Electronic address:

Supervolcanoes are volcanoes capable of mega-colossal eruptions that emit more than 1,000 km of ash and other particles. The earth's most recent mega-colossal eruption was the Oruanui eruption of the Taupo supervolcano 25,580 years before present (YBP) on the central North Island of New Zealand. This eruption blanketed major swaths of the North Island in thick layers of ash and igneous rock, devastating habitats and likely causing widespread population extinctions. Read More

Syst Biol 2022 Jun 16. Epub 2022 Jun 16.

Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.

Contamination of a genetic sample with DNA from one or more non-target species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and Next-Generation Sequencing (NGS) studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on detection of bimodal distributions of patristic distances across gene trees. When the contamination occurs between samples within a dataset, comparisons between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. Read More

Mol Phylogenet Evol 2022 Jun 8;174:107543. Epub 2022 Jun 8.

Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT 84602, USA; M. L. Bean Life Science Museum, Brigham Young University, 1115 MLBM, Provo, UT 84602, USA.

While advances in sequencing technologies have been invaluable for understanding evolutionary relationships, increasingly large genomic data sets may result in conflicting evolutionary signals that are often caused by biological processes, including hybridization. Hybridization has been detected in a variety of organisms, influencing evolutionary processes such as generating reproductive barriers and mixing standing genetic variation. Here, we investigate the potential role of hybridization in the diversification of the most speciose genus of lichen-forming fungi, Xanthoparmelia. Read More

Mol Phylogenet Evol 2022 Jun 8;174:107545. Epub 2022 Jun 8.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China.

The utility of transcriptome data in plant phylogenetics has gained popularity in recent years. However, because RNA degrades much more easily than DNA, the logistics of obtaining fresh tissues has become a major limiting factor for widely applying this method. Here, we used Ranunculaceae to test whether silica-dried plant tissues could be used for RNA extraction and subsequent phylogenomic studies. Read More