THE Applied Phylogenetics Lab at USC


Macroevolution and the genotype-phenotype map

A major theme of our research is studying the long-term evolution of phenotypes. Dr. Pennell is the lead developer of one of the most popular software applications for phylogenetic biology, we have derived novel statistical approaches for assessing the explanatory power of evolutionary hypotheses, and have synthesized the literature to help researchers make better inferences from interspecific data. In addition to this theoretical work, we have also conducted large-scale empirical analyses. For example, we have combined these statistical approaches with mathematical modelling to understand the evolutionary processes that drive changes in genomic rearrangement and the evolution of sex chromosomes, developmental constraints on morphological evolution, and the evolution of physiological characteristics in animals and plants.

Our current work in this area is focused on developing methods to use phylogenetic data to investigate the genetic underpinning of phenotypes and to analyze comparative transcriptomic and proteomic data.

Key Papers:

Dimayacyac+ BioRχiv

Porto+ Systematic Biology

Uyeda+ Systematic Biology

Pennell+ Molecular Ecology

Pennell+ Bioinformatics

Evolutionary immunology

It has long been appreciated that within-individual antibody diversity is generated by evolutionary processes including recombination, mutation, and selection. In our group, we take this idea literally and are developing new phylogenetic methods to reconstruct the processes and events that shaped the antibody repertoire. We are also working towards reconstructing the evolutionary history of the germline genes that encode the antigen-recognition sequences of antibodies ( immunoglobulins) across the vertebrate tree of life.

In our research, we want to understand the evolutionary processes that have generated and maintained tremendous diversity at the immunoglobulin loci and how variation at these loci trickles down to variation in the evolved antibody response.

Key Papers:

Pennell + Trends in Immunology

Key Papers:

MacPherson+ Systematic Biology

Louca + Pennell Current Biology

Louca + Pennell Nature

Henao Diaz+ PNAS

Schluter + Pennell Nature

Lineage diversification

A major goal of our research is to understand the processes that generate diversity in the number of lineages. This is a primary challenge in the field of macroevolution; we are only beginning to be able to explain why some branches of the Tree of Life are so much more diverse than others. We have used meta-analyses of molecular phylogenies to uncover some apparent regularities to how patterns of biodiversity arise; for example, the formation of new species often appears fastest where there are fewer other species around. But we have also identified some fundamental limits to how much we can learn about these patterns from molecular data alone. In an article published in Nature, we discovered that there was fundamentally insufficient information in molecular phylogenies (no matter how large) to distinguish between some alternative hypotheses for why some groups are more diverse than others; without additional (non-molecular) data, researchers cannot for example, disentangle changes in historical rates of species formation from that of extinction. We have since demonstrated that this finding likely resolves a 30-year old mystery in evolutionary biology — why extinction estimates from molecular phylogenies are often unrealistically low — and also applies to inferences from molecular epidemiology.
Currently, we are developing novel statistical methods for integrating classic (non-phylogenetic) epidemiological models with phylogenetic tools to make more robust inferences about disease dynamics.