Phylogenetic Methods
Phylogenetic analysis, the estimation of evolutionary trees,
has become the cornerstone of evolutionary biology. In addition
to their more traditional applications in evolutionary biology,
molecular phylogenies (i.e., phylogenies that have been estimated
from molecular data such as DNA sequences) are being applied
to an ever-widening array of disciplines. These include biomedicine
(e.g., tracing infection pathways for HIV and other pathogens),
bioinformatics (e.g., genome evolution), and forensics (phylogenies
estimated from HIV sequences have recently been allowed as evidence
in murder trial). Because of this, the development and testing
of phylogenetic methods assumes a position of critical importance
and extremely broad relevance. Furthermore, the influx of molecular
sequence data and the adoption of an explicitly statistical approach
to data analysis have led to the requirement to refine methods
of phylogenetic inference. We have focussed on model selection, from both
frequentist and Bayesian perspectives. You can see more detail by following
this link.
Comparative Phylogeography: Predicting Cryptic Diversity
This project surveys genetic diversity in multiple elements of mesic
forests of the Pacific Northwest in the context of explicit biogeographic
and landscape hypotheses that make testable genetic predictions. The general
objective of this research is to build a sufficient database of genetically
and ecologically characterized endemics that we can predict the presence of
crytpic diversity in taxa for which we only have distributional data. This requires
one to differentiate the influence of past geological and climatic events from current landscape level processes
on the geographic structure of genetic variation in several codistributed
highland forest species. You can read more details on comparative pylogeography by following this link.
Divergence-with-gene-flow in Chipmunks
Determining the frequency and genetic impact of hybridization during animal
speciation remains a central and unresolved issue in evolutionary biology. If
reproductive isolation is incomplete when nascent species come into contact, even
moderate gene flow may result in population fusion. Thus, recurrent hybridization
among animal species has traditionally been viewed as rare. Alternatively, genetic
factors underlying speciation may continue to accumulate between divergent
populations despite on-going gene flow, eventually leading to the evolution of
complete reproductive isolation. Consistent with this second model (divergence
with gene flow), several recent studies have shown that closely related taxa may
retain differentiation despite high levels of cryptic hybridization and introgression.
The radiation of western American chipmunks (Tamias,
subgenus Neotamias) represents an excellent study system for diversification with
gene flow. Thus, we are estimating the phylogeny of the genus using a diverse array
of data sets, including mtDNA, and genomics. You can read more here.
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