Sources of gene tree discordance and their implications for systematics and evolution of a megadiverse Australian plant radiation (subtribe Hakeinae, Proteaceae)

Resolving phylogenetic relationships in the presence of conflicting signal across genes is one of the major challenges of the phylogenomic era. Conflicting signals can emerge from biological processes, such as incomplete lineage sorting or introgression, or have technical origins, such as from misaligned sequences. As such, decisions made in the process of estimating species trees may result in alternative tree topologies and large variation in branch support values with important systematic consequences. Here we compare alternative strategies for alignment cleaning, loci filtering, and phylogenetic estimation in 551 taxa in the Proteaceae subtribe Hakeinae, to explore how these methodological choices affect the estimation of relationships. We found that node support values across gene trees were low and gene discordance was high in the Hakeinae, particularly in lineages from the Temperate Forests biome of southeastern Australia. Higher stringency of alignment cleaning tended to decreas..., In short, This study used 551 sequences for 482 Proteaceae taxa, of which 186 sequences were obtained from an earlier study (Cardillo et al. 2017). These 186 sequences include 151 species of Hakea, four species of Grevillea (G. dimorpha, G. evanescens, G. hookeriana, and G. batrachiodes), and Opisthiolepis heterophylla of the Hakeinae, together with eight Proteaceae outgroup taxa: Lomatia silaifolia, Stenocarpus davallioides, Alloxylon pinnatum, A. flammeum, Telopea speciosissima, Banksia paludosa, B. rufa, and Lambertia formosa. In addition, 368 samples were collected for novel DNA extraction and sequencing, sourced from fresh plant tissue obtained from wild or cultivated plants, or from dried herbarium specimens (see Table S1 for a list of samples). These included 320 species of Grevillea and Finschia chloroxantha from the Hakeinae, and additional Proteaceae outgroups: Stenocarpus milnei, Oreocallis mucronata, Macadamia integrifolia, Adenanthos glabrescens, Lambertia formosa, Isopogon..., , This README.txt file was generated 22.10.2024 by Alexander Skeels

## GENERAL INFORMATION

1\. Title of Dataset: Data from: 'Paleoenvironments shaped biotic exchange of terrestrial vertebrates across Wallace’s Line'

2\. Author Information

Corresponding Investigator
Name: Dr Alexander Skeels
Institution: Research School of Biology, Australian National University, 46 Sullivans Creek Rd, Acton, ACT 0200, Australia
Email: [[e-mail]](mailto:[e-mail])

Co-investigator 1
Name: Hervé Sauquet
Institution: National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, NSW, Australia / Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052 Australia

Co-investigator 2
Name: Austin Mast
Institution: Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee 32306, Florida, USA

Co-investigator 3
Name: Peter H. Weston
Institution: National...