P207
Evolution of the molecular clockworks in animals: Non-congruence of gene
trees for individual clock genes with clock species tree analyses.
V INC ENT C ASSONE1
1
Biology, University of Kentucky, Lexington, KY, UNITED STATES
One of the signature features of the well-established molecular circadian clockworks is the fact that they are
remarkably conserved among animals, defined by highly conserved “positive elements” in clock and
Bmal1, “negative elements” period (1,2 or 3), timeless, and/or cryptochrome (1,2,…n), other recursive
transcriptional loops (rorA, ReverbA, and/or vrille), as well as other players such as kinases and
photoreceptor inputs . Now that these components have been isolated and characterized in many organisms,
the evolutionary contexts for this conservatism has been repeatedly analyzed phylogenetically in terms of
“gene trees” of individual loci . While a gene tree gives a satisfactory first order approximation for many
families of organisms and processes, the relationships between individual gene trees and their composite (a
species tree, eg .) does not always hold . Gene trees and species trees can be incongruent due to a variety of
factors, including differential rates of evolution, gene loss and duplication, and gene flow through
hybridization, horizontal transfer and recombination among taxa . As a first approximation of the phylogeny
of the composite molecular clockworks, multi-locus species trees were constructed using Bayesian and deep
coalescence analytical methods using published clock gene sequences from 13 species of arthropod, 1
species of cephalochordate,and multiple vertebrates, ranging from fish (4 species), amphibians (2 species),
birds (6 species) and mammals (7 species, including humans) . These species were selected from those that
have complete genomes sequenced so as to minimize false negative data . Even so, the species coverage is
grossly uneven, with, for example, very few non-insect arthropods, no non-arthropod protostomes, and
uneven coverage among vertebrate taxa . Even so, some patterns emerge from these analyses . First, as comembers of PAS domain transcription factors, the period loci diverge from the positive elements early in animal
evolution, predating protostome-deuterostome divergence (PTD) . Secondly, per gene duplication occurs after
protochordate-vertebrate divergence . Thirdly, the loss of per1 from the avian genome is a derived feature,
unique to amniote non-mammals studied thus far . Fourth, vertebrate cry1s diverge earlier than PTD, and
insect cry, which are photoreceptive, form a monophyletic clade with some but not all anamniote crys,
and do not align with an avian crys, which have been suggested, but not proven, as photosensitive . While
these studies are ongoing and much more data are available than can be presented in abstract, the picture
that emerges is that while selection for circadian clock function occurs at the level of the organism, reflected
in the species trees, the genes that comprise the clockworks evolve at different rates due at least to gene
loss, duplication and differential gene evolution rates . This study further identifies key organisms that
should be studied to resolve evolutionary divergence of molecular components of the clock .