A Screen for Gene Paralogies Delineating Evolutionary Branching Order of Early Metazoa

Abstract

The evolutionary diversification of animals is one of Earth’s greatest marvels, yet its earliest steps are shrouded in mystery. Animals, the monophyletic clade known as Metazoa, evolved wildly divergent multicellular life strategies featuring ciliated sensory epithelia. In many lineages epithelial sensoria became coupled to increasingly complex nervous systems. Currently, different phylogenetic analyses of single-copy genes support mutually-exclusive possibilities that either Porifera or Ctenophora is sister to all other animals. Resolving this dilemma would advance the ecological and evolutionary understanding of the first animals and the evolution of nervous systems. Here we describe a comparative phylogenetic approach based on gene duplications. We computationally identify and analyze gene families with early metazoan duplications using an approach that mitigates apparent gene loss resulting from the miscalling of paralogs. In the transmembrane channel-like (TMC) family of mechano-transducing channels, we find ancient duplications that define separate clades for Eumetazoa (Placozoa + Cnidaria + Bilateria) vs. Ctenophora, and one duplication that is shared only by Eumetazoa and Porifera. In the Max-like protein X (MLX and MLXIP) family of bHLH-ZIP regulators of metabolism, we find that all major lineages from Eumetazoa and Porifera (sponges) share a duplicated gene pair that is sister to the single-copy gene maintained in Ctenophora. These results suggest a new avenue for deducing deep phylogeny by choosing rather than avoiding ancient gene paralogies.

Age-Related Hearing Loss: Sensory and Neural Etiology and Their Interdependence

“…Approximately 300 genes are identified and associated with ARHL (Bowl et al, 2017 ). TMC1/2 is vital for the normal formation of hearing function (Yoshimura et al, 2019 ; Erives and Fritzsch, 2020 ), as well as Cdh23 and Pcdh15 , which together form the tip links of stereocilia (Elliott et al, 2018 ; Qiu and Müller, 2018 ).…”

An Integrated Perspective of Evolution and Development: From Genes to Function to Ear, Lateral Line and Electroreception

“…Other interactions are known, but these interactions require additional work for the MET formation ( Figure 5 ). A unique formation of vertebrate hair cells is found in the Tmc1/2 single gene in cyclostomes [ 43 ]. Tmc1/2 is separated from the closely related gene, Tmc3 .…”

“…The next step involves the development of the tip links to allow the connections between CDH23 and PCDH15 to open up the channel to form a mechanosensory hair cell [37,38], with opposing polarity in most of the ear and lateral line [34,[39][40][41]. TMC1/2 provides a major function that seems to interact with additional channel proteins (TMHS, TMIE), forming a complex interaction [37,[42][43][44]. In contrast, while the electroreception forms next to lateral line hair cells [22,23,45], these hair cells lack any polarity organization, and certain ampullary hair cells are dependent on Ca v 1.3 [46].…”

Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis

“…While phylogenetic relationships at the base of the animal tree have been heavily debated for over ten years, Porifera (sponges) are frequently considered as one of the most basal branches in the metazoan tree [26,43,46,49,70,74,88,89,126,131]. Porifera therefore constitute an important group in which to trace the emergence of epithelia.…”