Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict floraJialiang Li, Yujiao Zhang, Markus Ruhsam, Richard Ian Milne, Yi Wang, Dayu Wu, Shiyu Jia, Tongzhou Tao & Kangshan Mao
The eastern Asia (EA) – eastern North America (ENA) disjunction is a typical and well known biogeographic. Although its origin has been the topic of many studies, some new insights will arise when more complex evolutionary histories are revealed using phylogenomic methods. Here, we used targeted exon capture and sequenced >1,000 single copy nuclear, plus 73 chloroplast genes, to resolve interspecific relationships and the biogeographic history of an intercontinental disjunct genus Thuja. Two separate clades...
This case study provides an overview of the use of persistent identifiers (PIDs) at the Royal Botanic Garden Edinburgh (RBGE). RBGE delivers plant science, conservation and education programmes that are underpinned by the world-class RBGE Collections, comprising a Living Collection, a Herbarium collection and Library and Archive collections. Within the context of this case study, a persistent identifier is an identifier that is globally unique, actionable (it can be resolved to a resource or information...
Premise of the study: Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants....
Lowiaceae (order Zingiberales) is a small family of forest herbs in Southeast Asia. All species belong to the genus Orchidantha. They are known for possessing orchid-like flowers that are smelly, apparently mimicking dead animals, feces, or mushrooms. Little is known of the biogeographic patterns or character evolution of the family. We sampled the family extensively, including many recently discovered species, and reconstructed the phylogeny of the family using HybSeq with Lowiaceae-specific RNA baits. Our phylogenetic...
Variable tree cover characterizes tropical grassy biomes. Light availability in the ground layer becomes increasingly limited as tree cover increases while open canopy environments are associated with a flammable grassy ground layer. Grass species dominating the ground layer of these ecosystems have adopted strategies to persist and proliferate with frequent fire. However, there is limited understanding of how grass growth and flammability traits respond to changes in light availability. We experimentally grew 14 grass species...
Data from: Testing genome skimming for species discrimination in the large and taxonomically difficult genus RhododendronChao-Nan Fu, Zhi-Qiong Mo, Jun-Bo Yang, Jie Cai, Lin-Jiang Ye, Jia-Yun Zou, Han-Tao Qin, Wei Zheng, Peter M. Hollingsworth, De-Zhu Li & Lian-Ming Gao
Standard plant DNA barcodes based on 2-3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice. Of particular interest is whether adding substantially more plastid and nrDNA characters will lead...
TNT file for phylogenetic analysis of the moss class Polytrichopsida composed of morphological and sequence level charactersJaakko Hyvönen, Jorge Flores, Neil Bell, Alexander Bippus & Alexandru Tomescu
PREMISE OF THE STUDY: When fossils are sparse in morphologically divergent lineages, phylogenetic analyses based on morphology may support hypotheses of relationships incongruent with those supported by gene sequence data. Integration of morphological and sequence data from conservative gene regions may reconcile such situations by circumscribing the search space of combined analyses. METHODS: We revisited the phylogeny of Polytrichopsida, a highly divergent group of mosses, in parsimony analyses. We supplemented the existing morphological matrix with...
Some animals fashion tools and other constructions out of plant materials to aid foraging, reproduction, self-maintenance, and protection. The choice of raw materials can affect the structure and mechanical properties of the resulting artefacts, with significant fitness consequences. Documenting animals’ material preferences is challenging, however, as manufacture behaviour is often difficult to observe directly, and materials may be processed so heavily that they lack identifying features. Here, we use DNA barcoding techniques to identify, from...
Royal Botanic Garden Edinburgh11
Botanischer Garten und Botanisches Museum Berlin3
Meise Botanic Garden3
Natural History Museum3
University of Tartu3
Museum für Naturkunde3
Naturalis Biodiversity Center3
Senckenberg Nature Research Society2
University of Lisbon2
Royal Belgian Institute of Natural Sciences2