Research

I. Molecular systematics, phylogeography, and historical biogeography

A large component of my research uses genomic data to infer the evolutionary history of vertebrates, particularly reptiles and amphibians. I am particularly interested in exploring novel ways that next-generation DNA sequencing data can be used to infer phylogenetic relationships, species limits and biogeographic history. More recently, I have become interested in critically examining the propensity for reticulated evolution in different clades. Most of my current research focuses on evolutionary patterns and processes in phrynosomatid lizards and venomous snakes (vipers). Examples of common research questions include the following: 

(1) What are the spatial and temporal patterns of lineage diversification and how does biotic evolution correlate with climatic and geologic perturbations throughout Earth's history?

(2) What is the propensity for undescribed, cryptic lineages and species within single widespread taxa?

(3) How do broad-scale biogeographic patterns relate to paleoclimate change, orogenesis, changes in sea level and continental drift over deep timescales?

(4) How can molecular tools/results be used for conservation purposes?

(5) Is gene flow common between species, and if so, how does the incorporation of introgression affect demographic inference?

Current projects at different stages of development 

1. Phylogeography, species delimitation, and demographic history in phrynosomatid lizards. 

2. Phylogenomics of Old World vipers.

3. Systematics of Mexican Sceloporus.

4. Descriptions of new species.

II. Comparing phylogenetic and population genetic methods

Simulated data sets are vital to assess the relative performance of different phylogenetic and population genetic methods. However, simulated data are often overly simplistic and make assumptions that do not hold with real genomic data. Although I have tested the performance of methods using simulations (see Blair et al. 2012, Mol. Ecol. Res.), I have recently become interested in the rigorous comparison of methods using real data. As an example, many theoretical and simulation studies have shown that species trees inferred using concatenation (i.e. the supermatrix method) are incorrect in the presence of incomplete lineage sorting (ILS). However, several recent empirical (genomic) studies (e.g. Blair et al. 2018, Mol. Ecol. Res.; Blair et al. 2022, Biol. J. Linn. Soc.) have shown highly congruent or identical topologies inferred with both techniques, even in cases of rapid speciation. This suggests that concatenation is still an important analytical approach for phylogenomic data, the results of which can also help researchers assign individuals to putative species for subsequent coalescent-based analyses.

Current projects at different stages of development 

1. Using genomic data to determine if/how different methods of gene tree inference influence species networks that take gene trees as input.

III. DNA barcoding

Next-generation DNA sequencing (NGS) has found a place in nearly all aspects of biology. Recently, these methods have been applied to DNA barcoding studies. I am interested in using metabarcoding data to delimit putative species using single-locus, coalescent-based species delimitation methods. Single locus markers such as mtDNA and cpDNA continue to be criticized, in part, because each genome is essentially one large linked locus. However, the information that can be provided by these genomes is vast, and can help researchers formulate new hypotheses. Decades of resources are available for use, and often the best approach is to supplement new genomic data with information from organellar DNA. I have used large mtDNA data sets of horned lizards to compare commonly-used single locus species delimitation methods. Results suggested a large degree of discordance, depending on the methods compared (Blair & Bryson 2017, Mol. Ecol. Res.).