Research in the Pfeifer Lab focuses on three areas of computational and evolutionary genomics:
(i) Anthropological – mutation and recombination rate variation in primates
Interactions between mutation, recombination, natural selection, and population history shape the genetic differences among individuals, populations, and species. Perhaps for anthropocentric reasons, a focal point of many studies has been the characterization of these processes in humans and their closest extant evolutionary relative, chimpanzees (Auton*, Fledel-Alon*, Pfeifer*, Venn*, et al., Science 2012; Leffler*, Gao*, Pfeifer*, Ségurel*, et al., Science 2013; Pfeifer & Jensen, GBE 2016). However, less effort has been put toward comparative genomic analyses by studying non-ape primates. Extending our previous research on the topic, we are working towards gaining a better understanding of fine-scale changes in rates and patterns of mutation and recombination through deeper evolutionary time within the primate clade (Pfeifer, MBE 2017; Pfeifer, Evolution 2017; Tran & Pfeifer, eLS 2018; Pfeifer, Springer Nature (in press); Pfeifer, MBE 2020).
(ii) Ecological – adaptation due to recent environmental change
Understanding the process of adaptation during rapid environmental change remains one of the central focal points of evolutionary biology. The recently formed White Sands system of southern New Mexico and the Sand Hills of Nebraska contain outstanding examples of rapid adaptation for crypsis, with a variety of species – from lizards to mice – having evolved blanched forms on the dunes that contrast with their close relatives in the surrounding dark soil habitats (Harris et al., Heredity 2020). In collaboration with the Rosenblum Lab at Berkeley, we are using model-based statistical inference methods to describe the demographic and adaptive history characterising the colonisation of different White Sands lizard species (Laurent*, Pfeifer* et al., Mol Ecol 2016; Ormond et al., Mol Ecol 2016). In collaboration with the Martins Lab at ASU, we are focusing upon the genomic mechanisms underlying coloration in North American Sceloporus lizards (in preparation). In collaboration with the Hoekstra Lab at Harvard, we focus on the evolution of cryptic colouration in Nebraska deer mouse populations, unravelling the interplay between demography and selection within and between populations as well as estimating selection on both phenotype and genotype (using clinal samples (Pfeifer*, Laurent*, Sousa*, Linnen* et al., MBE 2018), as well as large-scale field experiments (Barrett*, Laurent*, Mallarino* et al., Science 2019)).
(iii) Clinical – virus evolution
Human cytomegalovirus (HCMV) is a large b-herpesvirus critically important to human health due to its ubiquitous occurrence – with adult infection rates ranging from 30–90% in industrialized countries to almost 100% in emerging countries. Although ‘primary’ infections are generally asymptomatic in healthy hosts, HCMV infections can lead to severe effects in immuno-suppressed or immuno-naïve hosts, including fetuses and newborns. HCMV infections affect ~0.5% of all live births in the United States – making it the most common source of infection-related congenital (i.e., before birth) infections. HCMV utilizes effective immune evasion techniques and, as a result, it is currently neither possible to prevent transmission from mother to fetus (due to an absence of an effective vaccine), nor to reduce severity of disease in the infant. As a consequence, a better understanding of the underlying biological and evolutionary processes at play during infection is indispensable to the future development of novel disease prevention and treatment strategies. In collaboration with the Jensen, Kowalik, and Trumble Labs, we work to characterize the evolutionary processes driving infection (e.g., Renzette et al., J. Virol. 2017; Pokalyuk et al., Mol. Ecol. 2017; Sackman et al., Pathogens 2018). This characterization will better illuminate the causes and consequences underlying this major threat to global health.
The Pfeifer Lab is in the School of Life Sciences at Arizona State University, and we are part of a large and collaborative group in evolutionary genomics at ASU – see ASUpopgen.org. We are also members of the Center for Evolution & Medicine, and the Center for Mechanisms of Evolution.