Partitioned gene-tree analyses and gene-based topology testing help resolve incongruence in a phylogenomic study of host-specialist bees (Apidae: Eucerinae)

Main Authors: Freitas, Felipe V., Branstetter, Michael G., Griswold, Terry, Almeida, Eduardo A.B.
Format: Article eJournal
Bahasa: eng
Terbitan: , 2020
Subjects:
GGI
Online Access: https://zenodo.org/record/3996596
Daftar Isi:
  • Incongruence among results from different approaches analyzing genomic data has been an issue faced by almost every study using this kind of data. The incongruence comes from the uncertainty that permeates the phenomena generating this incongruence, and from the difficulties in determining the best model and strategy to be used in each situation according to the kind of data available. Here we present results of a phylogenomic study based on Ultraconserved Elements (UCEs) that investigate eucerine bees, a large subfamily of Apidae with more than 1200 species. We sampled representatives of all tribes of Eucerinae and more than 80% of the genera, including the first inclusion in a molecular phylogenetic study of two mysterious South American genera, Chilimalopsis and Teratognatha. These data were explored with some of the most up to date strategies, such as data filtering, locus partitioning for gene-trees search, and topological tests. We show that locus partitioning and topological tests can be useful for improving the gene-trees used as input for summary methods and to solve incongruence among competing results, respectively.