UH Manoa Phylogenetics and Math Day

Information:  Thursday, March 21, 2019.  1:00 pm - 5:00 pm. Keller Hall 301. University of Hawaii at Manoa.  

Organizers:  Elizabeth Gross (UH Manoa, Dept of Math), Sean Harrington (UH Manoa, Dept of Biology), Robert Thomson (UH Manoa, Dept of Biology)

About:   An interdisciplinary symposium to bring together mathematicians that think about phylogenies with phylogeneticists that think about math for an informal afternoon of talks and discussion. All are welcome to attend.


1:00 - 1:30 Coffee and Welcome
1:30 - 1:55 Robert Thomson, UH Manoa
Title: Detecting causes of conflict in phylogenomic datasets
Abstract: As the application of genomic data in phylogenetics has become routine, a number of cases have arisen where different data sets that were assembled to address the same question strongly support conflicting conclusions. Ultimately, this conflict must arise from analytical decisions, either relating to which regions of the genome are targeted or how the variation contained in those genomic regions is modeled. This sensitivity to analytical decisions has prevented firm resolution of some of the most recalcitrant nodes in the tree of life. To better understand the causes and nature of this sensitivity, we analyzed several phylogenomic data sets using methods that are designed to measure conflict and that provide a way forward in detecting its causes. We find that a small number of genes can drive conflicting results, and that the role of systematic error in driving gene tree variation may be larger than has generally been recognized.
2:00 - 2:25 Joseph Rusinko, Hobart and William Smith Colleges
Title: A guide for selecting taxa for inclusion in a species tree analysis
Abstract: We introduce a introduce a coalescent-based methodology for determining if you have sufficient data a collection of taxa in a species tree analysis.  To address this problem we introduce a coalescent-based quartet weighting system which can also be used to enhance certain pipelines for species tree reconstruction.  Finally we analyze the impact of missing taxa on species tree reconstruction in general.
2:30 - 2:45 Break
2:45 - 3:10 Rosana Zenil-Ferguson, UH Manoa
Title: Interacting associations between ploidy, breeding system, and lineage diversification 
Abstract: If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be understood as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rate differences is tricky, though, because of the many traits available to consider and the statistical challenge of testing for associations from phylogenetic data. Two traits that have been repeatedly suggested as drivers of differential diversification are whether a lineage is diploid or polyploid, and whether it is self-incompatible or self-compatible. In this talk I investigate the role of each of these traits, and their interaction, on speciation and extinction rates in Solanaceae.
3:15 - 3:40 Grady Weyenberg, UH Hilo
Title: Dimension reduction for collections of phylogenetic trees
Abstract: The phylogenetic trees used to describe and estimate the evolutionary relationships between organisms are complex high-dimensional objects containing a wealth of information. Advances in high-throughput sequencing have made it possible to estimate trees using sequences from many different loci across the genome, but analysis techniques for summarizing and comparing collections of trees is lacking. Principal Component Analysis (PCA) is a highly popular method of reducing the dimension of complex datasets, in many cases revealing structures in the data which are not obvious in the high dimensional setting. Unfortunately, the structure of trees contains much information which is not well captured by the classical PCA methodology. We present some new PCA-inspired techniques adapted for non-standard metric spaces better adapted to the structure of trees. These techniques define low-dimensional subsets of the metric space and attempt to find best-fitting surfaces onto which a dataset of trees can be projected. We present some results of applying this idea to the Billera-Holmes-Vogtmann metric space as well as a metric space defined by the Tropical (max-plus) geometry.
3:45 - 4:00 Break
4:00 - 4:25 Sean Harrington, UH Manoa
Title: Performance of phylogenetic MCMC in empirical systems
Abstract: Bayesian Markov chain Monte Carlo (MCMC) methods are commonly used for phylogenetic inference. Despite the prevalence of MCMC methods in phylogenetics, our understanding of how well these standard implementations perform in empirical systems remains relatively limited. To address this, we performed a survey of MCMC performance across more than 30,000 empirical phylogenetic analyses. We show that most analyses mix and converge well, as indicated by all applicable convergence diagnostics. In cases where MCMC does not perform well, the commonly recommended solutions of altering heating parameters for Metropolis-coupled chains or using model-averaging does not universally improve convergence. We find that improving performance requires identifying and correcting the specific cause of the failure, such as sampling the chain for a larger number of generations or specifying more appropriate models.
4:30 - 4:55 Katherine St. John, City University of New York and American Museum of Natural History
Title: The Shape of Phylogenetic Tree Space
Abstract: Trees are a canonical structure for representing evolutionary histories.  Many popular criteria used to infer optimal trees are computationally hard, and the number of possible tree shapes grows super-exponentially in the number of taxa. The underlying structure of the spaces of trees yields rich insights that can improve the search for optimal trees, both in accuracy and running time, and the analysis and visualization of results. We review the past work on analyzing and comparing trees by their shape as well as recent work that incorporates trees with weighted branch lengths. This talk will highlight some of the elegant questions that arise from improving search and visualizing the results in this highly structured space.  All are welcome.