Convergence for everyone?Detecting disparate signals of

genomic adaptive convergence in several different datasets:

Initial results, lessons & perspectives

16th September 2014

Joe Parker, Queen Mary University London

Adaptive molecular convergence

• Definition• Methods to detect• Datasets and results• Sampling issues• Interpretational issues• Future

Defining molecular convergence

• Surprisingly hard• It isn’t:

– Divergence (adaptive or neutral)– Conservation or purifying selection– Retention of ancestral states with secondary

changes in outgroups– ‘Neutral’ homoplasy

• It ought to be:– ‘Adaptive’ homoplasies– ‘Excess’ homoplasies

Observations

• ‘Adaptive convergence’ predicated on assumption adaptive sites ‘count’ more - conditions for detection?

• Can parallel changes with dN/dS ~ 1 be ‘convergent’

• ‘Excess’ - a problematic definition without a good null model– Odds-ratio based?– Empirical CDF?– Eyeball…

Methods

• Species phylogeny and inputs• Selection detection• Site-based methods• Tree-based methods

Site-based methods

• Look at tips– Sample balance?

Site-based methods

• Look at tips

• Reconstruct ancestral changes

Site-based methods

• Look at tips• Reconstruct ancestral changes

• Pairwise P(conv) ~ P(div) changes

Site-based methods

• Look at tips• Reconstruct ancestral changes• Pairwise P(conv) ~ P(div) changes

• BEB posterior probabilities

Tree-based methods

• de novo tree search– Inference error– Signal : noise– Multiple phylogenies

Tree-based methods

• ∆SSLS (likelhood comparison)– Which hypotheses?– Multiple simultaneous comparisons?– Models insensitive– How extreme

Tree-based methods

• Unrestricted / ennumerated phylogeny fitting

Trees and sites methods

• dN/dS and ∆SSLS correlation

Trees and sites methods

• Random control tree correction

Genomic approaches

• Pool information across sites– Are loci comparable– Error rates?

• Orthology, paralogy

Sampling

• Sampling balance– Within locus– Between loci

• Gene selection / ascertainment bias• Networks• Tree selection• a priori phylogenies

Convergence in echolocating mammals

• 22 mammals, 2,326 loci• Convergence signals across

genome

Convergence in echolocating bats

• The• The

Convergence in mole-rats

• The• The

Interpretational issues

• Relative measure• Strength of evidence• Null model? Sampling? Which

phylogenies

Interpretation

• Notional convergence detected genomically, or not at all

• Selection, incongruence• Which trees?

Which Trees?

• Choice of hypothesis, subtly different from usual practice

• If we accept tree space distance important…

• … Hypotheses are parameters• Ennumerate over trees?

Future directions

• Null model• Alternative (convergent) model• Tree space distance

Conclusion

• Strong evidence molecular convergence, or something like our best definition of it, is a pervasive force

• Very early work; contrast with e.g. early dN/dS tests

Acknowlegements

• Colleagues• Institutions• Funding

Further information

• Reading– Li, Liu, Castoe, Parker

• Resources– SVN, site, j.d.parker@qmul.ac.uk