I am interested in a broad range of ecological and evolutionary topics, with a focus on using molecular methods to reconstruct demographic history, although several upcoming projects will also focus on identifying the signs of selection in natural populations. Much of my work deals with insects, but I don't like to limit myself, and enjoy working with a variety of organisms and systems.

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Pollinator genetics/genomics and conservation

Comparative landscape genomics of adaptation across montane systems

I have just received an NSF award, in collaboration with Michael Dillon, an insect flight physiologist at the University of Wyoming, and Jamie Strange, expert bumble bee biologist at the USDA Pollinating Insect Research Unit and Utah State, to investigate the influence of abiotic variation associated with latitude and altitude on intraspecific genomic, morphological, and physiological variation of bumble bees across the Sierra Cascade Mountain ranges of CA, OR, and WA. This is a particularly exciting project that promises to tell us a great deal about the origins of biodiversity, the role of intraspecific variation in climate adaptation from genotype-to-phenotype, and how climate change may impact population connectivity of native pollinators in the coming years.

Conservation genomics

At the University of Alabama, my lab has been investigating the utility of next generation sequencing approaches to understand various aspects of evolution, ecology, and conservation, and have been applying these methods to various organisms from bees to fish. I have recently been interested in using RAD-tag sequencing to increase genomic coverage for estimating genetic diversity levels in species of conservation concern, and comparing such estimates with those derived from more traditional genetic markers. We have previously used molecular markers to evaluate various genetic parameters in the six primary target species (B. occidentalis, B. bifarius, B. vosnesenskii, B. pensylvanicus, B. impatiens, and B. bimaculatus). Results suggest weak genetic differentiation of populations over large geographic scales that indicates extensive gene flow in these species. An interesting observation is that genetic diversity in populations of the declining species is lower than most of the stable species, and the lab is currently working to tease apart the significance of this finding. Results suggest that comparisons of genomic data and other population genetic markers may be less than straightforward in many cases, and that genomic, technical, and analytical biases may impact both approaches.

I am also interested in novel methods for mining data from natural history collection specimens. One recent project has involved a comparative genetic analysis of stable (B. impatiens) and declining (B. pensylvanicus) species collected in Illinois in the late 1960's and in 2008, with results demonstrating an increase in population structure for contemporary B. pensylvanicus populations. Current work involves extracting historical DNA from bumble bee gut pathogens in order to explicitly test a leading hypothesis that recent pathogen invasions have caused decline in several species. I welcome any students who have an interest in exploring the use of natural history collections for population genetics.

Population genomics of phylogeography, phenotype,
and adaptation

We have been working on various aspects of bumble bee evolution using population genomic data, including RAD-seq, transcriptomes, and moving into whole genome sequencing. This research involves studying phylogeography, speciation/species delimitation, and local adaptation to environmental heterogeneity using both morphology and genetics. One focus at the moment is Color-Pattern Evolution and Phylogeographomics. One interesting critter is the two-formed bumble bee Bombus bifarius (see figure to the right). We have shown that landscape heterogeneity substantially impacts gene flow in this species (Lozier et al. 2013), and that color pattern loosely correlates with this structure (Lozier et al. 2011; 2013) using microsatellites. We are now conducting full transcriptome and RADtag sequencing across a color pattern transect to better understand both complex phylogeographic patterns, and the genomic mechanisms underlying this phenotypic variation. My student Jason Jackson is currently hard at work assembling and analyzing the RADtag sequences, and this work should be presented at Evolution 2014. Much of this work is very much in progress and any interested students should be sure to contact me.


Bumble bee decline project

I have been working with Sydney Cameron's lab at the University of Illinois on a large nationwide project aimed at bumble bee (Bombus) conservation across the USA. This project involves collaboration with Dr. James Strange (USDA), Dr. Terry Griswold (USDA), Dr. Leellen Solter (U of IL, INHS), Nils Cordes (U of IL), and Jonathan Koch (Utah State).

Native bumble bees perform critical roles as pollinators in terrestrial ecosystems and are important for a number of agricultural commodities, especially where managed as pollinators for greenhouse crops. With the decline of managed honey bee populations associated with colony collapse disorder, pollination services from native pollinators like bumble bees are becoming increasingly important. Unfortunately, there is increasing observational evidence suggesting that once widespread species have undergone precipitous population declines in recent years. There are few quantitative data, however, on current status or potential causes of decline of any US bumble bee species. The USDA funded bumble bee decline project involves a multidisciplinary team of bee systematists, geneticists, and pathologists with the goal of quantifying apparent ongoing decline of targeted US bumble bee species and investigate two potential causes of putative decline: low levels of genetic variation in fragmented populations and susceptibility to disease. 

Our research utilized intensive surveys of wild populations and specimens from natural history collections to investigate the current and historical distribution and abundance of several species. We documented several species undergoing serious population declines (B. occidentalis, B. affinis, B. terricola and B. pensylvanicus), while others have remained stable, or even expanded (B. bifarius, B. vosnesenskii, B. impatiens and B. bimaculatus). Notably, these species have much higher prevalence of infection with a Microspordian species (Nosema bombi), consistent with a previously suggested hypothesis that introduction of a non-native pathogen could be driving Bombus declines in North America

Nosema invasion hypothesis

I am currently a Co-PI on a USDA funded grant to test the Nosema invasion hypothesis by (a) screening for the presence of N. bombi in museum specimens pre- and post- hypothesized introduction date and (b) assessing phylogeographic history of N. bombi isolates from Europe and North America. For the phylogeographic study, we are utilizing novel genome reduction strategies and next generation DNA sequencing for marker identification and individual genotyping. Post-doc Haw Chuan Lim in Sydney Cameron's lab is taking the lead on much of this work.

Population genetics of biological invasions

Another of my recent projects involved reconstructing the invasion history of the aphid Hyalopterus pruni, in California. H. pruni, or the mealy plum aphid, is a pest of dried plum in the Central Valley and is a potential target for biological control. Understanding key parameters associated with invading populations, including geographic origins, number of introductions, timing of introduction, and levels of genetic diversity, can be important for minimizing impacts and developing targeted management strategies. Biological control, for example, involves the introduction of natural enemy populations from a pest's region of origin, as these populations may possess important coevolutionary or ecological adaptations that may aid their establishment and suppression of invasive pests. I studied population genetic dynamics of H. pruni from throughout its native Mediterranean range and from several invaded regions in North America, and results suggest that multiple invasions have occurred into North America from multiple sources. The next step in this research will be to map the genetic ancestry of invasive North American populations to examine how populations of this species have spread and mixed following invasion.

Evolution of host plant associations in aphids and parasitoids

Host plant associated divergence and cascading host associations

Aphids in the genus Hyalopterus feed on a number of host plants in the genus Prunus (plums, almonds, peaches, and apricots) and are attacked by the parasitic wasp species, Aphidius transcaspicus, throughout their native range. One important question is the degree to which ecological factors, such as host plant use, have led to diversification in these herbivores, and how have these patterns of ecological diversification subsequently affected evolution at the next trophic level (A. transcaspicus)? Results show that Hyalopterus comprises three species (to date!) associated largely with plum, peach, and almond, and the data suggests that all three species co occur on apricot trees, and may even hybridize. I anticipate expanding this project to further investigate the potential for hybridization among these species, and to investigate patterns of variation in a greater portion of the genome with the aim of identifying signs of natural selection associated with host use. Interestingly, A. transcaspicus shows no sign of genetic differentiation associated with host use, with geographic separation playing a much larger role.

This project involved assessing genetic population structure of A. transcaspicus across the Mediterranean to identify possible geographic strains that might correspond to native H. pruni populations and that may be useful for biological control. This work integrates ecological niche models and coalescent genetic models quantifying levels of gene flow to investigate the history of isolation across the Mediterranean.