Incorporating tree-thinking and evolutionary time scale into developmental biology
Shigehiro Kuraku1,*, Nathalie Feiner2, Sean D. Keeley1 andYuichiro Hara1
Version of Record online: 5 JAN 2016
DOI: 10.1111/dgd.12258
© 2016 Japanese Society of Developmental Biologists
Development, Growth & Differentiation
Special Issue: TIME IN DEVELOPMENT
Volume 58, Issue 1, pages 131–142, January 2016
Abstract
Keywords: cryptic pan-vertebrate genes; hidden paralogy; molecular evolution; orthology; tree-thinking
Phylogenetic approaches are indispensable in any comparative molecular study involving multiple species. These approaches are in increasing demand as the amount and availability of DNA sequence information continues to increase exponentially, even for organisms that were previously not extensively studied. Without the sound application of phylogenetic concepts and knowledge, one can be misled when attempting to infer ancestral character states as well as the timing and order of evolutionary events, both of which are frequently exerted in evolutionary developmental biology. The ignorance of phylogenetic approaches can also impact non-evolutionary studies and cause misidentification of the target gene or protein to be examined in functional characterization. This review aims to promote tree-thinking in evolutionary conjecture and stress the importance of a sense of time scale in cross-species comparisons, in order to enhance the understanding of phylogenetics in all biological fields including developmental biology. To this end, molecular phylogenies of several developmental regulatory genes, including those denoted as “cryptic pan-vertebrate genes”, are introduced as examples.
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