Research

My research centers on the evolution of ecologically important traits. I aim to address this by integrating genomic data with methods including physiology, phylogeography, and ecological niche modeling. I use this integral approach to better understand how genomic variation drives trait differences, and how these lead to larger patterns in species distributions and interactions. This includes the evolution of traits such as temperature and desiccation tolerance, and parasite success. As DNA sequencing technology has advanced, I have utilized these new methods to more fully explore the genomic basis of adaptation, particularly in non model organisms.

 

The genomic basis of host-parasite interactions

I am currently a postdoc working with Christoph Vorburger to study the evolution of increased infectivity of the parasitoid Lysiphlebus fabarum. These tiny wasps reproduce via eggs deposited in aphids, and successful parasitism is fatal to the aphid. Thus, this is an excellent arena to study antagonistic co-evolution and the genomic basis of parasitoid virulence. However, added to this interaction is the protective microbiome found in most aphid species; this suite of bacterial endosymbionts can give strong protection against enemies such as fungi and parasitoid. Variation has been observed in both parasitoid success and endosymbiont protection, and previous work by our group has demonstrated that co-evolutionary forces are acting between bacteria and parasitoids. To investigate the basis of infective variability of parasitoids, we are using wild sourced populations of L. fabarum and the dominant endosymbiont in the field, the bacterium Hamiltonella defensa.

To explore the variability and genetic basis of L. fabarum infectivity, we have experimentally reared wasp populations in the presence of different strains of H. defensa. In just ten generations, wasps reared on bacterially defended aphids show increased rates of parasitism in their home aphid ‘environment’, but not in the other two aphid lines. We are now using transcriptomic comparisons among lineages to identify differentially expressed genes associated with this variable and strain-specific infective ability.  In conjunction with this, I am assembling and annotating the genome of L. fabarum. This will provide a useful resource for future work in this system, and will be used to explore the potential integration of symbiotic viruses associated with virulence in related parasitoids.

 

The evolution of freeze tolerance in alpine stick insects

Adaptation to novel environments is an important process driving species diversification and defining range limits, and temperature is one of the most significant environmental features. As a postdoctoral researcher at Landcare Research, I was part of a collaborative project to investigate the evolution of cold tolerance in New Zealand stick insects. This endemic radiation has been diversifying for approximately 30 million years and contains more than 21 species and 8 genera (more here). Despite their tropical origins (their closest relatives come from lovely New Caledonia), several species are found in the cooler southern and high altitude portions of New Zealand.

Using field surveys and winter caging, we found that more than one species overwinters, in an active state, demonstrating their functional abilities in the cold. Through a series of physiological comparisons, we identified at least two new freeze tolerant species and found that different montane species may utilize different strategies to survive the cold (freeze tolerance and freeze avoidance). Using transcriptomic sequencing, we compared gene expression following cold shock in all major genera of New Zealand stick insects. From this, we identified a set of cuticular genes are both differentially expressed and evolving under positive selection in many genera.

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Dennis, Alice B., Luke T. Dunning, Brent J. Sinclair, and Thomas R. Buckley. 2015. Parallel molecular routes to cold adaptation in eight genera of New Zealand stick insects. Scientific Reports, 5: 13965, doi:10.1038/srep13965

Luke T. Dunning, Alice B. Dennis, Brent J. Sinclair, Richard D. Newcomb, and Thomas R. Buckley. 2014. Divergent transcriptional responses to low temperature among populations of alpine and lowland species of New Zealand stick insects (Micrarchus). Molecular Ecology 23(11): 2712–2726

Dunning, Luke T., Alice B. Dennis, Geoffrey Thomson, Brent J. Sinclair, Richard D. Newcomb, Thomas R. Buckley. 2013. Positive Selection in a Core Energy Conversion Pathway among Australasian Stick Insects. BMC Evolutionary Biology 13:215

Dennis, Alice B., Luke T. Dunning, Christopher J. Dennis, Brent J. Sinclair and Thomas R. Buckley. 2014. Overwintering in New Zealand stick insects. New Zealand Entomologist 37(1):35-44

Dunning, Luke T., Alice B. Dennis, Duckchul Park, Brent J. Sinclair, Richard D. Newcomb, and Thomas R. Buckley. 2013. Identification of cold-responsive genes in a New Zealand alpine stick insect using RNA-Seq. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 8(1): 24–31.

 

 

Freeze tolerance and range limits in Melampus

Species richness varies across the globe, and the cause of these striking patterns is not entirely understood. One factor may be the limited abilities of tropical species to adapt to cooler temperatures and expand their ranges away from the equator. To investigate this, my dissertation research focused on the evolution of freeze tolerance in the salt marsh snail, Melampus.

Melampus is an abundant member of the high intertidal community across the globe and reaches its highest species densities at low latitudes. Despite its tropical inclination, several species inhabit higher, cooler, latitudes. This includes M. bidentatus, a freeze tolerant species found as far north as Nova Scotia. Within this nominal species, we identified three cryptic species with differing latitudinal range extents. A series of physiological comparisons among populations and species suggested that the acquisition of freeze tolerance enabled these species to move to the temperate zone in historical time, but that range limits in cooler habitats were not set by physiological limits. Using field surveys, ecological niche modeling and estimations of population connectivity, we inferred that current temperate range limits may instead be determined by subtle differences in microhabitat preference among species.

Thanks to a generous Transition Grant from EAWAG, I am continuing my work with Melampus bidentatus. In collaboration with Prof. Dr. habil Joerg Fettke, I am using protein and transcriptomic sequencing to further investigate the genomic basis of freeze tolerance and its origin in Melampus.

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Dennis, Alice B., S. H. Loomis and M. E. Hellberg. 2014. Latitudinal variation in freeze tolerance in an intertidal marine snail (Melampus). Physiological and Biochemical Zoology. 87(4): 517-526

Hellberg, Michael E., Alice B. Dennis, Patricia Arbour-Reily, Jan E. Aagaard, and Willie J. Swanson. 2012. The Tegula Tango: a coevolutionary dance of interacting, positively selected sperm and egg proteins. Evolution 66(6):1681-1694.

Dennis, Alice B. and Michael E. Hellberg. 2010. Ecological partitioning among parapatric cryptic species. Molecular Ecology 19:3206-3225.

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