Research
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, including some exciting new research on freshwater mussels (Unionidae) and their role in the environment.
Pollinator genetics/genomics and conservation
A sample of Bombus pensylvanicus that will be used for chromosome level genome assembly
Sequencing and resequencing new bumble bee genomes
The Beenome100 Project - A large team of bee evolutionary and molecular biologists are activley working towards a comprehensive data set of highly intact North American bee reference genomes (most done using HiFi and HiC data). The Beenome100 team is diverse in taxonomic interests and expertise and the project will end up quite exciting. Our lab is largely interested in bumble bees, and through the effort we have already sequenced a new chromosome level assembly of Bombus hutii, led by collaborator Jon Koch at the Logan Bee Lab. Other forthcoming genomes include some useful species that have color polymorphism and rare or declining species like Bombus pensylvanicus.
Graduate students in the lab are using these new reference genomes to conduct rangewide population genomics of B. pensylvanicus and B. huntii and many other bumble bee species, so these genomes are going to quickly be put to use.
Conservation genomics of bumble bees - 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. We initially used RAD-tag and RNA 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 suggested 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 an ongoing effort in the lab has been to tease apart the significance of this finding and understand drivers of population size variation within and between species. 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. We are now revisiting B. pensylvanicus and B. impatiens and others using whole genome sequences to test many hypotheses about stability and decline evidence in genetic data for once widespread species.
Genetic changes underlying parallel acquisition of mimetic color patterns across bumble bees - In collaboration with Heather Hines at Penn State and Jon Koch at USDA, we are working to understand the genomic basis of color pattern variation in highly polymorphic bumble bee lineages. By looking across fixed phenotype and polymorphic species distributed across highly diverse clades, we hope to uncover transcriptional and/or nucleotide level changes that drive changes in phenotypes within and between species. As part of this project we will be sequencing 100s of new bumble bee genomes across more than ten species, including Bombus flavifrons, Bombus bifarius, Bombus vancouverensis, Bombus centralis, Bombus huntii, and many more!
The Beenome100 Project - A large team of bee evolutionary and molecular biologists are activley working towards a comprehensive data set of highly intact North American bee reference genomes (most done using HiFi and HiC data). The Beenome100 team is diverse in taxonomic interests and expertise and the project will end up quite exciting. Our lab is largely interested in bumble bees, and through the effort we have already sequenced a new chromosome level assembly of Bombus hutii, led by collaborator Jon Koch at the Logan Bee Lab. Other forthcoming genomes include some useful species that have color polymorphism and rare or declining species like Bombus pensylvanicus.
Graduate students in the lab are using these new reference genomes to conduct rangewide population genomics of B. pensylvanicus and B. huntii and many other bumble bee species, so these genomes are going to quickly be put to use.
Conservation genomics of bumble bees - 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. We initially used RAD-tag and RNA 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 suggested 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 an ongoing effort in the lab has been to tease apart the significance of this finding and understand drivers of population size variation within and between species. 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. We are now revisiting B. pensylvanicus and B. impatiens and others using whole genome sequences to test many hypotheses about stability and decline evidence in genetic data for once widespread species.
Genetic changes underlying parallel acquisition of mimetic color patterns across bumble bees - In collaboration with Heather Hines at Penn State and Jon Koch at USDA, we are working to understand the genomic basis of color pattern variation in highly polymorphic bumble bee lineages. By looking across fixed phenotype and polymorphic species distributed across highly diverse clades, we hope to uncover transcriptional and/or nucleotide level changes that drive changes in phenotypes within and between species. As part of this project we will be sequencing 100s of new bumble bee genomes across more than ten species, including Bombus flavifrons, Bombus bifarius, Bombus vancouverensis, Bombus centralis, Bombus huntii, and many more!
Comparative genomics, epigenetics, and metabolomics of adaptation in montane systems
The Mountain Bees Project - We are currently working hard on several NSF awards, in collaboration with Michael Dillon, an insect flight physiologist at the University of Wyoming, Jamie Strange, expert bumble bee biologist at Ohio State, Jon Koch, a bumble bee expert at the USDA Logan Bee lab, Janna Fierst, a computational biologist at UA, and Franco Basile, a chemist at UW, 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. This research was funded by NSF DEB 1457645 and a recently awarded NSF URoL 1921985.
The Mountain Bees Landscape Genomics Project - As part of our mountain bee project we sequenced reference genomes for several bumble bee species. These efforts are using a combination of long-read Oxford Nanopore technology and high coverage paired-end Illumina sequencing. The Bombus vosnsesnskii, B. vancouverensis, and Bombus bifarius genome projects are complete and we have published initial draft assemblies as part of Sam Heraghty's dissertation work. We are currently working on finishing up a whole genome resequencing-based comparative analysis of western montane species, including landscape genomics of Bombus vosnesenskii and B. vancouverensis (our two favorite species!) and some others that will be an important background for our new NSF epigenetics grant. Sam Heraghty recently published a large population genomics study using whole genome sequencing in B. vancouverensis ( Whole Genome Sequencing Reveals the Structure of Environment-Associated Divergence in a Broadly Distributed Montane Bumble Bee, Bombus vancouverensis, Insect Systematics and Diversity, Volume 6, Issue 5, September 2022, 5, https://doi.org/10.1093/isd/ixac025). Keep an eye out for his equally large scale genomic analysis of B. vosnesenskii.
The Mountain Bees Epigenome Project - We are using several methods to assay range-wide variation in epigenetic modification of bumble bee genomes across species ranges, with a focus on understanding the way epigenetic modification may contribute to climate adaptation. We are combining assays of whole genome methylation profiling from field collected bees with those from physiological experiments to better understand how SNPs, gene expression, and epigenetics may related to thermal tolerance. This research is funded by NSF URoL 1921985.
The Mountain Bees Project - We are currently working hard on several NSF awards, in collaboration with Michael Dillon, an insect flight physiologist at the University of Wyoming, Jamie Strange, expert bumble bee biologist at Ohio State, Jon Koch, a bumble bee expert at the USDA Logan Bee lab, Janna Fierst, a computational biologist at UA, and Franco Basile, a chemist at UW, 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. This research was funded by NSF DEB 1457645 and a recently awarded NSF URoL 1921985.
The Mountain Bees Landscape Genomics Project - As part of our mountain bee project we sequenced reference genomes for several bumble bee species. These efforts are using a combination of long-read Oxford Nanopore technology and high coverage paired-end Illumina sequencing. The Bombus vosnsesnskii, B. vancouverensis, and Bombus bifarius genome projects are complete and we have published initial draft assemblies as part of Sam Heraghty's dissertation work. We are currently working on finishing up a whole genome resequencing-based comparative analysis of western montane species, including landscape genomics of Bombus vosnesenskii and B. vancouverensis (our two favorite species!) and some others that will be an important background for our new NSF epigenetics grant. Sam Heraghty recently published a large population genomics study using whole genome sequencing in B. vancouverensis ( Whole Genome Sequencing Reveals the Structure of Environment-Associated Divergence in a Broadly Distributed Montane Bumble Bee, Bombus vancouverensis, Insect Systematics and Diversity, Volume 6, Issue 5, September 2022, 5, https://doi.org/10.1093/isd/ixac025). Keep an eye out for his equally large scale genomic analysis of B. vosnesenskii.
The Mountain Bees Epigenome Project - We are using several methods to assay range-wide variation in epigenetic modification of bumble bee genomes across species ranges, with a focus on understanding the way epigenetic modification may contribute to climate adaptation. We are combining assays of whole genome methylation profiling from field collected bees with those from physiological experiments to better understand how SNPs, gene expression, and epigenetics may related to thermal tolerance. This research is funded by NSF URoL 1921985.
Bumble bee decline project
I got my love of the bumbles 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
I got my love of the bumbles 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
We recently completed a USDA funded project 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.
We recently completed a USDA funded project 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.
Mussel Biodiversity Genomics
In collaboration with Carla Atkinson at UA and some folks over at Ole Miss we have a big Dimensions of Biodiversity grant to integrate ecology, genomics, phylogenomics, and microbiomes to understand how diversity is structured in southeastern freshwater mussels.
No need to duplicate effort here: you can read all about it at mussels.ua.edu!
No need to duplicate effort here: you can read all about it at mussels.ua.edu!
Older Research Projects--- maybe to return someday???
Population genetics of biological invasions
Another of my past 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. I maintain a general interest in invasions, and would like to continue to pursue research in this area.
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.
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.