Calibration Choice, Rate Smoothing, and the Pattern of Tetrapod Diversification According to the Long Nuclear Gene RAG-1

Abstract

A phylogeny of tetrapods is inferred from nearly complete sequences of the nuclear RAG-1 gene sampled across 88 taxa encompassing all major clades, analyzed via parsimony and Bayesian methods. The phylogeny provides support for Lissamphibia, Theria, Lepidosauria, a turtle-archosaur clade, as well as most traditionally accepted groupings. This tree allows simultaneous molecular clock dating for all tetrapod groups using a set of well-corroborated calibrations. Relaxed clock (PLRS) methods, using the amniote = 315 Mya (million years ago) calibration or a set of consistent calibrations, recovers reasonable divergence dates for most groups. However, the analysis systematically underestimates divergence dates within archosaurs. The bird-crocodile split, robustly documented in the fossil record as being around approximately 245 Mya, is estimated at only approximately 190 Mya, and dates for other divergences within archosaurs are similarly underestimated. Archosaurs, and particulary turtles have slow apparent rates possibly confounding rate modeling, and inclusion of calibrations within archosaurs (despite their high deviances) not only improves divergence estimates within archosaurs, but also across other groups. Notably, the monotreme-therian split ( approximately 210 Mya) matches the fossil record; the squamate radiation ( approximately 190 Mya) is younger than suggested by some recent molecular studies and inconsistent with identification of approximately 220 and approximately 165 Myo (million-year-old) fossils as acrodont iguanians and approximately 95 Myo fossils colubroid snakes; the bird-lizard (reptile) split is considerably older than fossil estimates (< or = 285 Mya); and Sphenodon is a remarkable phylogenetic relic, being the sole survivor of a lineage more than a quarter of a billion years old. Comparison with other molecular clock studies of tetrapod divergences suggests that the common practice of enforcing most calibrations as minima, with a single liberal maximal constraint, will systematically overestimate divergence dates. Similarly, saturation of mitochondrial DNA sequences, and the resultant greater compression of basal branches means that using only external deep calibrations will also lead to inflated age estimates within the focal ingroup.

Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes

“…Our rooted tree indicates that snake hepadnaviruses are probably paraphyletic and that bird hepadnaviruses (endogenous þ exogenous) are closer to mammalian than to snake hepadnaviruses, which is incongruent with the host phylogeny (in which birds are closer to snakes than to mammals [64]). This suggests that these viruses probably jumped between vertebrate hosts as well.…”

Towards a uniform nomenclature for ground squirrels: the status of the Holarctic chipmunks

“…Cytb has frequently been used in mammals to assess phylogenetic relationships above the family level (e.g., Agnarsson et al 2011) and has been shown to be surprisingly effective at these deeper nodes (Tobe et al 2010). As noted earlier, although saturation may introduce systemic bias in age estimates (Hugall et al 2007, Dornburg et al 2014, such bias should influence both the chipmunk and Holarctic ground squirrel clades equally as long as no calibrating fossils are incorporated a priori. At present, the best available dataset (Cytb) provides a compelling and unambiguous argument that the three chipmunk lineages exhibit genus-level genetic differentiation.…”

“…Systemic bias in molecular age estimates has been demonstrated in numerous studies (Ho and Jermiin 2004, Jansa et al 2006, Norris et al 2015. Deep branches may be underestimated relative to more recent branches (Ho and Larson 2006), especially in situations where fast-evolving genes have become saturated (Hugall et al 2007, Dornburg et al 2014). If such systemic bias is present, it may affect both chipmunks and Holarctic ground squirrels equally, but the bias would be corrected only for the Holarctic ground squirrels, thanks to the presence of a calibrating fossil.…”

Do missing data influence the accuracy of divergence-time estimation with BEAST?

“…One outgroup taxon was included (the rhynchocephalian, Sphenodon punctatus), and this species is widely recognized as the living sister group to extant Squamata (e.g. Hugall et al, 2007;Alfaro et al, 2009;Mulcahy et al, 2012). Previous studies have estimated the crown-group of living Squamata to be roughly 180-240 Myr old (review in Mulcahy et al, 2012).…”