Research interests

In our research we seek to deepen our understanding of speciation and adaptation by gathering critical genetic data from a variety of species in field and laboratory settings, by developing and applying novel statistical analyses to genetic data, and through the development of theoretical models.

One goal of our research is to understand the genetic architecture of boundaries between species. Geographic contact between previously isolated lineages can lead to their coalescence through introgression, or to the maintenance of derived characteristics in divergent lineages. Part of our work involves identifying the genetic conditions that favor either outcome.

A second and related goal of our research is to contribute to our growing understanding of the genetics of adaptation. We are developing statistical genetics methods for use in this area. We're also interested in the use of natural hybrid zones and other admixed populations for mapping loci underlying adaptive phenotypes and components of isolation between taxa.

Video of a July 2012 presentation that Alex gave at the Molecular Ecology Symposium in Ottawa. The title of the talk is "A 2012 Perspective On Research In Speciation & Hybridization".

Below is a description of some of the research projects that Alex Buerkle participates in or leads. Additional projects are described on the webpages of individual members of the lab.

Genetic architecture of species boundaries

Barriers to gene flow allow discrete groups of organisms, such as species, to persist. In many cases reproductive barriers between taxa are incomplete and hybridization occurs in zones of geographic contact. A central focus of our research is to understand how different genetic architectures influence the fate of hybridizing taxa, and includes studies of the origin of diploid species through hybridization.

Examples of research projects include:

1. Zach Gompert (former Ph.D. student) and I work on statistical models for mapping components of reproductive isolation and adaptive introgression (Gompert and Buerkle 2009, Gompert and Buerkle 2011, Gompert et al. 2012a, Gompert and Buerkle 2012). This builds on methods development for the analysis of Populus hybrid zones (Lexer et al. 2007) and earlier research (Buerkle and Rieseberg 2001, Rieseberg and Buerkle 2002). We have developed software that implements our approach (bgc, Gompert and Buerkle 2012; and introgress, Gompert and Buerkle 2010) and continue to maintain stand-alone software for quantifying the genetic composition of hybrids (hindex, Buerkle 2005). In collaborative projects we have examined the genetics of isolation in a variety of taxa (e.g., sculpins, Nolte et al. 2009; mouse, Teeter et al. 2010; sunflowers, Scascitelli et al. 2010; Populus, Lexer et al. 2010 and Lindtke et al. 2012). We have recently applied these methods to the analysis of reproductive isolation between butterfly species (Gompert et al. 2012b).

2. 

   I have modeled the ecological and genetic conditions that affect the origin of species through hybridization, and specifically hybrid species that have arisen without an increase in ploidy (Buerkle et al. 2000). We also modeled the risk of extinction through hybridization (Buerkle et al. 2003).

   In a related study, we used genetic maps from three hybrid species of sunflowers and junction theory to infer the rate of genome stabilization that followed diploid hybrid speciation (Buerkle and Rieseberg 2008).

Genetics of adaptation

Variation at molecular markers makes it possible to study how specific genomic regions contribute to the expression of quantitative traits and allows an analysis of the genetic basis of adaptation and speciation.

Examples of research projects include:

1. Hybrid zones contain naturally recombinant individuals that may be used for genetic mapping (Rieseberg and Buerkle 2002, Buerkle and Lexer 2008). We continue to develop methods for mapping quantitative traits and identifying regions of the genome under selection in natural hybrid zones and other admixed populations. In a collaboration with Christian Lexer and other colleagues who work with Populus, and with Zach Gompert, we have made some more progress in developing tools to identify genome regions associated with fitness variation in hybrids (Lexer et al. 2007, Gompert and Buerkle 2009, Gompert and Buerkle 2011b, Gompert et al. 2012a), including software that implements our approach (bgc, Gompert and Buerkle 2012; and introgress, Gompert and Buerkle 2010).

2. Monia Haselhorst (Ph.D. student) is studying hybridization in North American spruce with the initial goal of improving our knowledge of species distributions and the ecological affinities for spruce in western North America (Haselhorst and Buerkle 2013).

3. Tom Parchman (postdoctoral researcher) is studying lodgepole pine population structure (Parchman et al. 2011) and is using genome-wide association mapping to dissect the genetics of serotiny (Parchman et al. 2012). Additionally, he has used high-throughput sequencing to characterize a large fraction of the transcribed genes in lodgepole pines (Parchman et al. 2010).

4. We have a variety of projects underway to utilize new technologies for the rapid acquisition of population genomic data through genotyping by sequencing. We also continue to develop new analytical tools for inference with these large data sets. For example, Zach Gompert led a first Bayesian analysis of molecular variance in population genomic data that he collected from Lycaeides butterflies (Gompert et al. 2010). We have extended this model to estimate locus-specific differentiation, which gives rise to genome scans and identification of exceptional, outlier loci that deviate from the evolutionary history of most of the genome (Gompert and Buerkle 2011a, Gompert et al. 2012b).

(Follow link for full Google scholar profile)

Selected publications

C. A. Buerkle and Z. Gompert. 2013. Population genomics based on low coverage sequencing: how low should we go? Molecular Ecology 22: 3028–3035. (article)

Parchman, T. L., Z. Gompert, M. J. Braun, R. T. Brumfield, D. B. McDonald, J. A. C. Uy, E. D. Jarvis, B. A. Schlinger, and C. A. Buerkle. 2013. The genomic consequences of adaptive divergence and reproductive isolation between species of manakins. Molecular Ecology 22: 3304–3317. (article)

Haselhorst, M.S.H., and C. A. Buerkle. 2013. Population genetic structure of Picea engelmannii, P. glauca and their previously unrecognized hybrids in the central Rocky Mountains. Tree Genetics and Genomes 9: 669--681. (article)

Nice, C. C., Z. Gompert, J. A. Fordyce, M. L. Forister, L. K. Lucas, and C. A. Buerkle. 2013. Hybrid speciation and independent evolution in lineages of alpine butterflies. Evolution 67: 1055–1068. (article)

Nosil, P., Z. Gompert, T. E. Farkas, A. Comeault, J. L. Feder, C. A. Buerkle, and T. L. Parchman. 2013. Genomic consequences of multiple speciation processes in a stick insect. Proceedings of the Royal Society, B. 279: 5058 5065. (article)

Gompert, Z. and C. A. Buerkle. 2012. bgc: Software for Bayesian estimation of genomic clines. Molecular Ecology Resources 12: 1168–1176. (article)

Lindtke, D., C. A. Buerkle, T. Barbará, B. Heinze, S. Castiglione, D. Bartha, C. Lexer. 2012. Recombinant hybrids retain heterozygosity at many loci: new insights into the genomics of reproductive isolation in Populus. Molecular Ecology 21: 5042–5058. (article).

Parchman, T. L., Z. Gompert, J. Mudge, F. D. Schilkey, C. W. Benkman, and C. A. Buerkle. 2012. Genome-wide association genetics of an adaptive trait in lodgepole pine. Molecular Ecology 21: 2991–3005. (article).

Gompert, Z., L. K. Lucas, C. C. Nice, J. A. Fordyce, M. L. Forister, and C. A. Buerkle. 2012b. Genomic regions with a history of divergent selection affect fitness of hybrids between two butterfly species. Evolution 66: 2167–2181. (article)

Gompert, Z., T. L. Parchman, and C. A. Buerkle. 2012a. Genomics of isolation in hybrids. Philosophical Transactions of the Royal Society, B: 367: 439–450. (article)

Gompert, Z. and C. A. Buerkle. 2011b. Bayesian estimation of genomic clines. Molecular Ecology 20: 2111–2127. (article)

Parchman, T. L., C. W. Benkman, B. Jenkins, and C. A. Buerkle. 2011. Low levels of population genetic structure in lodgepole pine across a geographic mosaic of coevolution. American Journal of Botany 98: 669–679. (article)

Buerkle, C. A., Z. Gompert, and T. L. Parchman. 2011. The n=1 constraint in population genomics. Molecular Ecology 20: 1575–1581. (article)

Gompert, Z. and C. A. Buerkle. 2011a. A hierarchical Bayesian model for next-generation population genomics. Genetics 187: 903–917. (article)

Lexer, C., J. Joseph, M. van Loo, T. Barbará, B. Heinze, D. Bartha, S. Castiglione, M. F. Fay and C. A. Buerkle. 2010. Genomic admixture analysis in European Populus spp. reveals unexpected patterns of reproductive isolation and mating. Genetics 186: 699–712. (article)

Gompert, Z., M. L. Forister, J. A. Fordyce, C. C. Nice, R. J. Williamson and C. A. Buerkle. 2010. Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies. Molecular Ecology 19: 2455–2473. (article)

Parchman, T.L., K. S. Geist, J. A. Grahnen, C. W. Benkman and C. A. Buerkle. 2010. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 11:180. (article)

Scascitelli, M., K. D. Whitney, R. A. Randell, M. King, C. A. Buerkle and L. H. Rieseberg. 2010. Genome scan of hybridizing sunflowers from Texas (Helianthus annuus and H. debilis) reveals asymmetric patterns of introgression and small islands. Molecular Ecology 19: 521–541. (article)

Teeter, K. C., L. M. Thibodeau, Z. Gompert, C. A. Buerkle, M. W. Nachman, and P. K. Tucker. 2010. The variable genomic architecture of isolation between hybridizing species of house mice. Evolution 64: 472–485. (article)

Gompert, Z. and C. A. Buerkle. 2010. introgress: a software package for mapping components of isolation in hybrids. Molecular Ecology Resources 10: 378–384. (article)

Nolte, A. W., Z. Gompert, and C. A. Buerkle. 2009. Variable patterns of introgression in two sculpin hybrid zones suggest that genomic isolation differs among populations. Molecular Ecology 18: 2615–2627. (article)

Buerkle, C. A.. 2009. Ecological context shapes hybridization dynamics. Molecular Ecology 18: 2077–2079. (article)

Gompert, Z. and C. A. Buerkle. 2009. A powerful regression-based method for admixture mapping of isolation across the genome of hybrids. Molecular Ecology 18: 1207–1224. (article)

Buerkle, C. A. and C. Lexer. 2008. Admixture as the basis for genetic mapping. TREE 23: 686–694. (article)

Buerkle, C. A. and L. H. Rieseberg. 2008. The rate of genome stabilization in homoploid hybrid species. Evolution 62: 266–275. (article)

Lexer, C., C. A. Buerkle, J. A. Joseph, B. Heinze, and M. F. Fay. 2007. Admixture in European Populus hybrid zones makes feasible the mapping of loci that contribute to reproductive isolation and trait differences. Heredity 98: 74–84. (article)

Buerkle, C. A. 2005. Maximum-likelihood estimation of a hybrid index based on molecular markers. Molecular Ecology Notes 5: 684–687. (article)

Buerkle, C. A., D. E. Wolf, and L. H. Rieseberg. 2003. The origin and extinction of species through hybridization. in Population Viability in Plants: Conservation, Management, and Modeling of Rare Plants, pp. 117–141. Springer Verlag.

Rieseberg, L. H., and C. A. Buerkle. 2002. Genetic mapping in hybrid zones. American Naturalist 159: S36–S50. (article)

Peichel, C. L., K. Nereng, K. A. Ohgi, B. L. E. Cole, P. F. Colosimo, C. A. Buerkle, D. Schluter, and D. M. Kingsley. 2001. The genetic architecture of divergence between threespine stickleback species. Nature 414: 901–905. (article)

Buerkle, C. A., and L. H. Rieseberg. 2001. Low intraspecific variation for genomic isolation between hybridizing sunflower species. Evolution 55: 684–691. (article)

Buerkle, C. A., R. J. Morris, M. A. Asmussen, and L. H. Rieseberg. 2000. The likelihood of homoploid hybrid speciation. Heredity 84: 441–451. (article)