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

Authors: FREITAS, FELIPE - Universidade De Sao Paulo; Branstetter, Michael; Griswold, Terry; ALMEIDA, EDUARDO - Universidad De Sao Paulo

Submitted to: Molecular Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/19/2020
Publication Date: 11/12/2020
Citation: Freitas, F.V., Branstetter, M.G., Griswold, T.L., Almeida, E.A. 2020. Partitioned gene-tree analyses and gene-based topology testing help resolve incongruence in a phylogenomic study of host-specialist bees (Apidae: Eucerinae). Molecular Biology and Evolution. 38(3):1090-1100. https://doi.org/10.1093/molbev/msaa277.
DOI: https://doi.org/10.1093/molbev/msaa277

Interpretive Summary: Partitioned gene-tree analyses and gene-based topology testing help resolve incongruence in a phylogenomic study of host-specialist bees (Apidae: Eucerinae): An important group of bees for agriculture is the subfamily Eucerinae. This group is closely related to honey bees and bumble bees and includes the well-known squash bees, which are specialist pollinators of cucurbit plants throughout the Americas. Eucerinae comprises 1,200 species globally with most of the diversity found in the New World tropics. Despite the importance of this group, uncertainty exists regarding the phylogenetic relationships among species and higher-level groups, such as genera and tribes. Using genomic data from ultraconserved elements and a sample of over 190 species, a robust, global phylogeny of the group was inferred, resolving the placement of several enigmatic genera and tribes and solidifying the group’s classification and nomenclature. A practical approach to dealing with incongruent results from different types of genomic analyses is also demonstrated, providing useful guidelines for other researchers dealing with similar data. Overall, the results improve knowledge of a diverse group of pollinators with importance to agriculture and provide a useful evolutionary framework for future research.

Technical Abstract: Incongruence among phylogenetic results has become a common occurrence in analyses of genome-scale data sets. Incongruence originates from uncertainty in underlying evolutionary processes (e.g. incomplete lineage sorting, lateral gene transfer) and from difficulties in determining the best analytical approaches for each situation. To overcome these difficulties, more studies are needed that identify incongruences and demonstrate practical ways to confidently resolve them. Here we present results of a phylogenomic study based on the analysis 197 taxa and 2,526 Ultraconserved Element (UCE) loci. We investigate evolutionary relationships of Eucerinae, a diverse subfamily of apid bees (relatives of honey bees and bumble bees) with more than 1,200 species, many of which are host-plant specialists. We sampled representatives of all tribes within the group and more than 80% of genera, including two mysterious South American genera, Chilimalopsis and Teratognatha. Initial analysis of the UCE data revealed two conflicting hypotheses for relationships among tribes. To resolve the incongruence, we tested concatenation and species tree approaches and used a variety of additional strategies including locus filtering, partitioned gene-trees searches, and gene-based topological tests following the gene-genealogy interrogation (GGI) method. We show that within locus partitioning improves gene-tree and subsequently species-tree estimation, and that this approach, in combination with GGI topological testing, confidently resolves the incongruence observed in our data set. Our results provide a robust phylogenetic hypothesis for Eucerinae and demonstrate a practical strategy for resolving incongruence in other phylogenomic data sets.