Although some have been assigned to extant vent polychaete groups, morphological identifications are not generally consistent with estimates of molecular divergence (Little & Vrijenhoek, 2003; Vrijenhoek, 2013) and there is potential confusion with morphologically similar polychaete tubes (Kiel & Dando, 2009).
The apparent widespread multiplication of formin-encoding genes in diverse lineages raises the question whether any of the extant formins can be assigned to well-defined groups of orthologues beyond those identified in previous phylogenetic studies [ 5, 6, 8].
Arboretum allows genes to change their module assignment during evolution, but at any ancestral or extant species, every gene (if present in that species) must be assigned to exactly one module for a particular response.
For the calibration of the molecular clock, stringent constraints were applied based on fossils that can be unambiguously assigned to extant clades and whose unique skeletal characters can be unequivocally recognized in fossil coralla.
For the estimation of divergence times, the molecular-clock was calibrated using the oldest Mesozoic fossils that can be unequivocally assigned to extant genera/families, Caryophyllia for Caryophylliidae, Flabellum for Flabellidae, and Palaeopsammia for Dendrophylliidae (see Methods).
A number of fossils can therefore be readily assigned to extant lineages such as the Gulper shark genus Centrophorus [ 25] or the Viper dogfish Trigonognathus [ 26], without the need to erect distinct genera for extinct forms whose phylogenetic affinities are unclear.
In a conservative approach, the oldest age of the stratigraphic layer in which a fossil was found was used to represent the earliest occurrence of that lineage, and potential calibrations were limited to fossils that are reliably assigned to extant clades.
Of the 10340 domains listed in Pfam-A database, 58 and 85 domains were assigned to be extant in proteins with FYVE and PX domains respectively.
Of the 91,881 reads, 83,736 were assigned to 13,162 extant loci, and 8145 were mapped to 3745 contig regions that did not have prior annotated gene models (Table 1).
