Partitioned Gene-Tree Analyses and Gene-Based Topology Testing Help Resolve Incongruence in a Phylogenomic Study of Host-Specialist Bees (Apidae: Eucerinae)

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) 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 >1,200 species. We sampled representatives of all tribes within the group and >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. We show that within-locus partitioning improves gene tree and subsequent species-tree estimation, and that this approach, confidently resolves the incongruence observed in our data set. After exploring our proposed analytical strategy on eucerine bees, we validated its efficacy to resolve hard phylogenetic problems by implementing it on a published UCE data set of Adephaga (Insecta: Coleoptera). Our results provide a robust phylogenetic hypothesis for Eucerinae and demonstrate a practical strategy for resolving incongruence in other phylogenomic data sets.

A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation

“…Second, we need more and better summary statistics that will guide us in the development of more accurate phylogenetic substitution models. Third, we need to modify our standard phylogenetic pipelines to include more complex substitution models, for example, within-locus partitioning (Freitas et al 2021), site-heterogeneous substitution models (Lartillot et al 2007; Wu et al 2013) and Markov modulate Markov model (Baele et al 2021). Then, we should revisit both the gene tree accuracy as well as gene tree model adequacy.…”

Phylogenomic dating and Bayesian biogeography illuminate an antitropical pattern for eucerine bees

“…The box on the bottom left shows the four areas considered for the reconstructions and colours denoting combinations of two or more areas; the box on the bottom right shows a schematic legend for biogeographical reconstructions. For support values of phylogenetic results, see Freitas et al (2021)…”

Phylogenomic analyses clarify the pattern of evolution of Adephaga (Coleoptera) and highlight phylogenetic artefacts due to model misspecification and excessive data trimming

“…Recent SCA analyses that tentatively suggested monophyletic ‘Hydradephaga’ are very implausible from a morphological perspective. Moreover, strong clade support for this hypothesis was not provided (Freitas et al ., 2021). The reason why our quartet‐concordance analyses did not support a sister group relationship between Gyrinidae and the remaining Adephaga is unknown.…”

“…Heterogeneous composition of amino acids and nucleotides across taxa or across alignment sites, systematic bias resulting from hypervariable alignment sites, and deficient taxon sampling are among the potential factors affecting the internal phylogeny of the superfamily Dytiscoidea, including the monophyly of Aspidytidae (Baca et al ., 2017a; Vasilikopoulos et al ., 2019; Cai et al ., 2020; Gustafson et al ., 2020). Furthermore, it has been observed that summary coalescent and concatenation‐based phylogenetic analyses often deliver incongruent topologies within Adephaga (Baca et al ., 2017a; Gustafson et al ., 2020; Freitas et al ., 2021). However, the factors that contribute to this incongruence remain poorly understood (Baca et al ., 2017a; Freitas et al ., 2021).…”

“…Furthermore, it has been observed that summary coalescent and concatenation‐based phylogenetic analyses often deliver incongruent topologies within Adephaga (Baca et al ., 2017a; Gustafson et al ., 2020; Freitas et al ., 2021). However, the factors that contribute to this incongruence remain poorly understood (Baca et al ., 2017a; Freitas et al ., 2021). In particular, the extent of gene‐tree errors in previous summary coalescent analyses of Adephaga and their effect on species‐tree estimation remain uncertain (Baca et al ., 2017a; Vasilikopoulos et al ., 2019; Gustafson et al ., 2020).…”