Phylogenomics Controlling for Base Compositional Bias Reveals a Single Origin of Eusociality in Corbiculate Bees

Abstract

As increasingly large molecular data sets are collected for phylogenomics, the conflicting phylogenetic signal among gene trees poses challenges to resolve some difficult nodes of the Tree of Life. Among these nodes, the phylogenetic position of the honey bees (Apini) within the corbiculate bee group remains controversial, despite its considerable importance for understanding the emergence and maintenance of eusociality. Here, we show that this controversy stems in part from pervasive phylogenetic conflicts among GC-rich gene trees. GC-rich genes typically have a high nucleotidic heterogeneity among species, which can induce topological conflicts among gene trees. When retaining only the most GC-homogeneous genes or using a nonhomogeneous model of sequence evolution, our analyses reveal a monophyletic group of the three lineages with a eusocial lifestyle (honey bees, bumble bees, and stingless bees). These phylogenetic relationships strongly suggest a single origin of eusociality in the corbiculate bees, with no reversal to solitary living in this group. To accurately reconstruct other important evolutionary steps across the Tree of Life, we suggest removing GC-rich and GC-heterogeneous genes from large phylogenomic data sets. Interpreted as a consequence of genome-wide variations in recombination rates, this GC effect can affect all taxa featuring GC-biased gene conversion, which is common in eukaryotes.

Multiple Aggressions Among Nestmates Lead to Weak Dominance Hampering Primitively Eusocial Behaviour in an Orchid Bee

“…This behaviour leads to a weak dominance in E. annectans different from E. cordata whose dominant females performed oophagy and replaced all the eggs of the subordinate with her own (Freiria et al, 2017). Albeit E. annectans is in a close phylogenetic relationship to honey bees and other socially advanced Apid species, it shows a less advanced social organization (Romiguier et al, 2015). Our find showed the importance of long term nest observations, making E. annecatns an important system to study female totipotency and reproductive hierarchy formation in the Apidae.…”

A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference

“…For example, the average RCV of the 75 yeast gene trees that were topologically identical (RFD = 0) to the yeast eMRC phylogeny is about three quarters that of the remaining 2,757 yeast genes that topologically disagreed (RFD > 0) with the eMRC phylogeny (see supplementary table S2, Supplementary Material online). In general, models of sequence evolution assume that sequences are compositionally homogeneous, an assumption often violated in biological data sets, leading to systematic error and topological incongruence (e.g., Conant and Lewis 2001; Betancur et al 2013; Pisani et al 2015; Romiguier et al 2016). Thus, selection of genes that show high compositional homogeneity or inference using models that take into account compositional heterogeneity is likely to be advantageous.…”

Dynamic microbiome evolution in social bees

“…Although the species relationships within Apis and Bombu s and the reciprocal monophyly of Bombini and Meliponini are generally accepted, the relationships within the Meliponini, as well as the placement of the Euglossini with respect to the other three corbiculate tribes, are contentious ( 103 ). The host taxa relationships presented here (Figs.…”

“…The host taxa relationships presented here (Figs. 4 and 5) were obtained by joining the results of multigene phylogenies within Apis ( 104 ), Bombus ( 105 , 106 ), and the Meliponini ( 90 ), together in a supertree based on their most highly supported relations with each other and with the outgroups ( 94 , 103 , 107 ). For bee species that were not included in these previous studies, placement was based on that of their respective genera.…”