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Rate shifts and positive selection in dinosaur forelimb evolution



A new paper that hasn't been mentioned yet on the list -- the
publication is not concerned exclusively with dinosaurs, but one of
the questions the authors try to answer using their new method is
where in the bird lineage of dinosaurs there is evidence for
departures from the background rate of relative forelimb length
evolution:


Baker J, Meade A, Pagel M, Venditti C 2015 Positive phenotypic
selection inferred from phylogenies. Biol J Linn Soc
doi:10.1111/bij.12649
http://onlinelibrary.wiley.com/doi/10.1111/bij.12649/abstract

Rates of phenotypic evolution vary widely in nature and these rates
may often reflect the intensity of natural selection. Here we outline
an approach for detecting exceptional shifts in the rate of phenotypic
evolution across phylogenies. We introduce a simple new
branch-specific metric ∆V/∆B that divides observed phenotypic change
along a branch into two components: (1) that attributable to the
background rate (∆B), and (2) that attributable to departures from the
background rate (∆V). Where the amount of expected change derived from
variation in the rate of morphological evolution doubles that
explained by to the background rate (∆V/∆B > 2), we identify this as
positive phenotypic selection. We apply our approach to six datasets,
finding multiple instances of positive selection in each. Our results
support the growing appreciation that the traditional gradual view of
phenotypic evolution is rarely upheld, with a more episodic view
taking its place. This moves focus away from viewing phenotypic
evolution as a simple homogeneous process and facilitates
reconciliation with macroevolutionary interpretations from a genetic
perspective, paving the way to novel insights into the link between
genotype and phenotype. The ability to detect positive selection when
genetic data are unavailable or unobtainable represents an attractive
prospect for extant species, but when applied to fossil data it can
reveal patterns of natural selection in deep time that would otherwise
be impossible.


-- 
David Černý