Bat molecular phylogenetics: Past, present, and future directions

Abstract

With the development of techniques for the isolation, amplification, and sequencing of DNA, studies addressing phylogenetic relationships among bats moved in the 1980s and early 1990s from restriction fragment length polymorphisms and DNA hybridization to examination of changes at the level of individual nucleotides via DNA sequence analysis. Coinciding with these molecular advances were increases in computational capacity and the development of sophisticated analytical models of the nucleotide and amino acid substitution processes. Thus, molecular phylogenetics moved primarily from distance-and parsimony-based algorithms to complex optimality criterion, such as maximum likelihood and Bayesian phylogenetics. These advances helped to clarify our understanding of the evolutionary relationships and biogeographic history of bats as well as the evolution of echolocation and flight. We have now entered the age of phylogenomics, where phylogenetic datasets represent genome-scale variation. With the recent explosion in available data and the ever-expanding ability to inexpensively produce massive datasets for any organism, we now have the ability to extend phylogenomic approaches to non-model organisms such as bats, which have been historically neglected in studies of molecular evolution. Bats represent an extraordinary group characterized by evolutionary novelty (i.e., echolocation and powered flight) and adaptation (e.g., seven distinct feeding strategies within the family Phyllostomidae) to an extent arguably paralleled by no other group of mammals. As we move into the era of phylogenomics, it is time for bats to move to the forefront of the study of evolutionary novelty and adaptation, which for mammals has been dominated by rodents due to the mouse and rat models being so ubiquitous in all aspects of biology.