Publications by EEOB faculty December 1 - December 31

January 8, 2015

Stress tolerance in a polyextremophile: the southernmost insect

R.E. Lee Jr., D.L. Denlinger. 2015. Canadian Journal of Zoology, 93:1–8


Since biotic interactions within the simple terrestrial communities on the Antarctic Peninsula are limited compared with tropical and temperate regions, survival is largely dictated by the numerous abiotic challenges. Our research focuses on adaptations to environmental stresses experienced by the Antarctic midge (Belgica antarctica Jacobs, 1900), the southernmost free-living insect. Midge larvae can survive freezing and anoxia year-round. Not only can frozen larvae undergo rapid cold-hardening (RCH) at temperatures as low as –12 °C, but RCH develops more rapidly in frozen compared with supercooled larvae. Whether larvae overwinter in a frozen state or cryoprotectively dehydrated may depend on hydration levels within their hibernacula. Larvae constitutively up-regulate genes encoding heat shock proteins, as well as the antioxidant enzymes superoxide dismutase and catalase. Larvae accumulate osmoprotectants in response to freezing, desiccation, and exposure to seawater; exposure to one of these osmotic stressors confers cross-tolerance to the others. Molecular responses to dehydration stress include extensive genome-wide changes that include differential expression of aquaporins among tissues, upregulation of pathways associated with autophagy, inhibition of apoptosis, and downregulation of metabolism and ATP production.

Fine-scale phylogeography reveals cryptic biodiversity in Pederson's cleaner shrimp, Ancylomenes pedersoni (Crustacea: Caridea: Palaemonidae), along the Florida Reef Tract

Benjamin M. Titus and Marymegan Daly. 2014. DOI: 10.1111/maec.12237


Populations of continuously distributed marine organisms that disperse via pelagic larvae are often assumed to exist in a state of genetic panmixia because of their potential ability for long-distance dispersal. However, obligate symbionts may have more restricted gene flow due to recruitment limitations, making host specificity an important potential driver of biodiversity. To explore the tension between broad dispersal ability and limited recruitment potential, we used sequences of mtDNA cytochrome c oxidase subunit I (COI) to assess the fine-scale phylogeography of the cleaner shrimp, Ancylomenes pedersoni, an obligate symbiont of sea anemones, along 300 km of the Florida Reef Tract (FRT). The results indicate high genetic diversity within A. pedersoni populations along the FRT. Pair-wise ϕST values indicate significant genetic structuring between northern (Fort Lauderdale and Upper Keys) and southwestern (Lower Keys) populations, with significant isolation by distance. Two divergent COI haplotype lineages were detected through statistical parsimony analysis: one evenly distributed across the entire FRT (Clade 1) and one found primarily in two sample localities in the Lower Keys (Clade 2). Phylogenetic analyses using 16S-rDNA indicates that this genetic diversity is of paraphyletic origin, and possibly the result of multiple colonization events. These results reveal a complex demographic and evolutionary history for A. pedersoni populations and provide the first evidence of highly divergent intra-specific lineages independently colonizing the FRT. Because the FRT is a highly impacted coral reef system, understanding phylogeographic patterns along it has value beyond documentation of the factors that generate genetic diversity in tropical reef systems: these data are critical for creating scientifically based management strategies.

Gene Prediction and Annotation in Penstemon (Plantaginaceae): A Workflow for Marker Development from Extremely Low-Coverage Genome Sequencing

Paul D. Blischak, Aaron J. Wenzel, and Andrea D. Wolfe. 2014. Applications in Plant Sciences 2(12):1400044.


Penstemon (Plantaginaceae) is a large and diverse genus endemic to North America. However, determining the phylogenetic relationships among its 280 species has been difficult due to its recent evolutionary radiation. The development of a large, multilocus data set can help to resolve this challenge.
Using both previously sequenced genomic libraries and our own low-coverage whole-genome shotgun sequencing libraries, we used the MAKER2 Annotation Pipeline to identify gene regions for the development of sequencing loci from six extremely low-coverage Penstemon genomes (∼0.005×−0.007×). We also compared this approach to BLAST searches, and conducted analyses to characterize sequence divergence across the species sequenced.
Annotations and gene predictions were successfully added to more than 10,000 contigs for potential use in downstream primer design. Primers were then designed for chloroplast, mitochondrial, and nuclear loci from these annotated sequences. MAKER2 identified longer gene regions in all six Penstemon genomes when compared with BLASTN and BLASTX searches. The average level of sequence divergence among the six species was 7.14%.
Combining bioinformatics tools into a workflow that produces annotations can be useful for creating potential phylogenetic markers from thousands of sequences even when genome coverage is extremely low and reference data are only available from distant relatives. Furthermore, the output from MAKER2 contains information about important gene features, such as exon boundaries, and can be easily integrated with visualization tools to facilitate the process of marker development.

Species-specific transpiration responses to intermediate disturbance in a northern hardwood forest

Ashley M. Matheny, Gil Bohrer, Christoph S. Vogel, Timothy H. Morin, Lingli He, Renato Prata de Moraes Frasson, Golnazalsadat Mirfenderesgi, Karina V. R. Schäfer, Christopher M. Gough, Valeriy Y. Ivanov and Peter S. Curtis. 2014. Journal of Geophysical Research: Biogeosciences. DOI: 10.1002/2014JG002804


Intermediate disturbances shape forest structure and composition, which may in turn alter carbon, nitrogen, and water cycling. We used a large-scale experiment in a forest in northern lower Michigan where we prescribed an intermediate disturbance by stem girdling all canopy-dominant early successional trees to simulate an accelerated age-related senescence associated with natural succession. Using 3 years of eddy covariance and sap flux measurements in the disturbed area and an adjacent control plot, we analyzed disturbance-induced changes to plot level and species-specific transpiration and stomatal conductance. We found transpiration to be ~15% lower in disturbed plots than in unmanipulated control plots. However, species-specific responses to changes in microclimate varied. While red oak and white pine showed increases in stomatal conductance during postdisturbance (62.5 and 132.2%, respectively), red maple reduced stomatal conductance by 36.8%. We used the hysteresis between sap flux and vapor pressure deficit to quantify diurnal hydraulic stress incurred by each species in both plots. Red oak, a ring porous anisohydric species, demonstrated the largest mean relative hysteresis, while red maple, bigtooth aspen, and paper birch, all diffuse porous species, had the lowest relative hysteresis. We employed the Penman-Monteith model for LE to demonstrate that these species-specific responses to disturbance are not well captured using current modeling strategies and that accounting for changes to leaf area index and plot microclimate are insufficient to fully describe the effects of disturbance on transpiration.

Documenting bee decline or squandering scarce resources

V. J. Tepedino, Susan Durham, Sydney A. Cameron and Karen Goodell. 2014. Conservation Biology. DOI: 10.1111/cobi.12439


No abstract available