Belinda Chang

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Arrival and Departure

Saturday July 22 - Wednesday July 26

Lecture Materials

Protein Evolution & Ancestral Reconstruction

Adaptive Protein Evolution

Demo and Tutorials


Ancestral Sequence Reconstruction References:

Gaucher et al. 2008 Nature Palaeotemperature trend for Precambrian life inferred from resurrected proteins

Kratzer et al. 2014 PNAS Evolutionary history and metabolic insights of ancient mammalian uricases

Bickelmann et al. 2015 Evolution The molecular origin and evolution of dim-light vision in mammals

Kuang et al. 2006 PNAS Ancestral reconstruction of the ligand-binding pocket of Family C G protein-coupled receptors

Ugalde et al. 2004 Science Evolution of coral pigments recreated

Edited Book on Ancestral Sequence Reconstruction

Pollack and Chang 2007 Book chapter Dealing with uncertainty in ancestral sequence reconstruction: sampling from the posterior distribution

Bar-Rogovsky et al. 2015 Assessing the prediction fidelity of ancestral reconstruction by a library approach

Clade Model Methods Papers

Bielawski and Yang 2004 JME Maximum likelihood methods for detecting functional divergence at individual codon sites with application to gene family evolution

Weadick and Chang 2012 MBE An improved likelihood ratio test for detecting site-specific functional divergence among clades of protein-coding genes

Experimental Models for Detecting Adaptive Evolution

Elde et al. 2009 Nature Protein kinase R reveals an evolutionary model for defeating viral mimicry

Hauser et al. 2017 MBE Accelerated evolution and functional divergence of the dim light visual pigment accompanies cichlid colonization of Central America

Van Nynatten et al. 2015 Biol Lett Out of the blue: Adaptive visual pigment evolution accompanies Amaon invasion

Castiglione et al. 2017 PNAS Evolution of nonspectral rhodopsin function at high altitudes

Moury and Simon 2011 PNAS dN/dS-based methods detect positive selection linked to trade-offs between different fitness traits in the coast protein of Potato virus Y

Loughran et al 2012 MBE Neutrophil-mediated host response to infection

Aagaard et al 2013 PloS Gen Sperm-egg recognition proteins

Baker et al 2016 Transcription factors mediating stem cell pluripotency in development

Dungan et al 2016 Spectral tuning of killer whale rhodopsin: Evidence for positive selection and functional adaptation in a cetacean visual pigment

Schott et al 2016 Evolutionary transformation of rod photoreceptors in the all-cone retina of a diurnal garter snake

Sequence Capture Methods for Detecting Adaptive Evolution

Schott et al 2017 Targeted capture of complete coding regions across divergent species