Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles

Abstract

Understanding the phylogenetic placement of crown turtles (Testudines) among amniotes has been a source of particular contention. Recent morphological analyses suggest that turtles are sister to all other reptiles, whereas virtually all analyses of gene sequences support turtles as being inside Diapsida, and usually as sister to crown Archosauria (birds and crocodylians). Previously, a study using microRNAs (miRNAs) placed turtles inside diapsids, but as sister to lepidosaurs (lizards and Sphenodon) rather than archosaurs. Here, we test this result with an expanded dataset, and employ proper criteria for miRNA annotation. Significantly, we find no support for a turtle + lepidosaur sister-relationship; intstead, we recover strong support for turtles sharing a more recent common ancestor with archosaurs as the living sister group to birds + crocodylians. These results are in accordance with most gene sequence studies, providing strong, consilient evidence from diverse independent datasets for the phylogenetic position of turtles.

The phylogenetic utility and functional constraint of microRNA flanking sequences

“…Conversely, further analysis of flanking sequences in widely distributed Drosophila melanogaster populations showed little intraspecific variation in these regions, even in geographically distant populations, underlining the constraints placed on them compared with the wider non-coding genomic landscape. This study establishes a new approach for resolving animal species relationships, building markedly on ideas first noted in Field et al [9], and suggests that the flanking sequences of miRNAs are under strong functional constraint after speciation events.…”

Bichir microRNA repertoire suggests a ray-finned fish affinity of Polypteriforme

“…As elaborated above, miRNAs possess unique properties such as continuous acquisition and low level of loss, which make them ideal candidates to resolve difficult phylogenetic problems. In order to be reliable phylogenetic markers, miRNA validation should be more rigor than the original miRNA validation criteria of Ambros et al (2003), such as the presence of a correctly-processed star sequence (Tarver et al, 2013;Field et al, 2014). On the other hand, there has also been some debate on the utility of miRNA-based phylogenetics, which claimed that miRNAs are often lost from metazoan genomes and many early miRNA-based phylogenetic studies had numerous 'false negatives' because of the incorporation of taxa into their data matrix with a genome but no RNA sequencing data, or RNA sequencing date but no genome (Thomson et al, 2014).…”

“…Phylogenetic analyses were performed using branch and bound Maximum Parsimony searches (Farris, 1977) implemented in PAUP* v.4.0b10 (Swofford, 2002). Bayesian analysis was performed using BEAST 1.8 (Drummond et al, 2006(Drummond et al, , 2012 with parameter settings following Field et al (2014).…”

A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome

“…These sequences represent the miRNA complement of the LCA of tetrapods (41). Then, we analyzed substitution patterns using the method of Wheeler et al (154), as explained in detail in Supplemental Figure 3b–d.…”