Publications by EEOB faculty January 1 - January 31

January 22, 2018
eeob 2016

Exudation rates and δ13C signatures of tree root soluble organic carbon in a riparian forest

Gougherty, S.W., Bauer, J.E. & Pohlman, J.W. Biogeochemistry. 2017.
Tree root exudation (TRE) of water soluble organic carbon (WSOC) is an important but under-assessed component of net primary production, and is thought to strongly influence rhizosphere biogeochemistry. Riparian systems in particular are often viewed as biogeochemical hot spots fueled partially by root exudate WSOC. However, TRE rates have not been previously reported for these systems. The δ13C signatures of exudates may provide important insights into plant physiology and inform isotope-based methods to identify sources of soil CO2 fluxes, but this information is also generally lacking. In the present study, root exudate WSOC was collected in situ to assess both net exudation rates and exudate δ13C values in a temperate riparian forest. Net TRE rates were found to be most strongly related to a combination of tree species, root characteristics and net ecosystem exchange (Adj. R2 = 0.73; p < 0.001). In contrast, exudate δ13C values were correlated to time-lagged vapor pressure deficit (Adj. R2 = 0.21; p < 0.05) and air temperature (Adj. R2 = 0.43; p < 0.05), suggesting a rapid transfer of photosynthate from the canopy to the rhizosphere. Extrapolation of mean net TRE rates (13 µmol C g root−1 day−1) from a root mass basis to the entire sampling area suggests that TRE may account for as much as 3% of net annual C uptake and represents an important input of organic matter to riparian soils. Our findings of predictable TRE rates and exudate δ13C values in the present study suggest that future studies examining δ13C values of different plant components, soil organic matter and respired soil CO2 would benefit by accounting for the impact of root exudates.

Genomic signals of selection predict climate-driven population declines in a migratory bird

Rachael A. Bay, Ryan J. Harrigan, Vinh Le Underwood, H. Lisle Gibbs, Thomas B. Smith, Kristen Ruegg. 2018. Science  05 Jan 2018: Vol. 359, Issue 6371, pp. 83-86. DOI: 10.1126/science.aan4380
The ongoing loss of biodiversity caused by rapid climatic shifts requires accurate models for predicting species’ responses. Despite evidence that evolutionary adaptation could mitigate climate change impacts, evolution is rarely integrated into predictive models. Integrating population genomics and environmental data, we identified genomic variation associated with climate across the breeding range of the migratory songbird, yellow warbler (Setophaga petechia). Populations requiring the greatest shifts in allele frequencies to keep pace with future climate change have experienced the largest population declines, suggesting that failure to adapt may have already negatively affected populations. Broadly, our study suggests that the integration of genomic adaptation can increase the accuracy of future species distribution models and ultimately guide more effective mitigation efforts.


Forest structure in space and time: Biotic and abiotic determinants of canopy complexity and their effects on net primary productivity

Alex T.Fotis, Timothy H. Morin, Robert T.Fahey, Brady S. Hardiman, Gil Bohrer, Peter S.Curtis. 2018. Agricultural and Forest Meteorology. Volumes 250–251, 15 March 2018, Pages 181-191.
The structural dynamics of forest canopies involve complex interactions among the abiotic environment, stand structure, species composition and disturbance regimes. How the re-arrangement of tree canopies in space and time affects forest aboveground net primary productivity (ANPP) remains poorly understood, however. In this study, we analyzed a long-term dataset from a temperate deciduous forest in Northern Michigan, USA, to investigate two primary objectives: 1) what abiotic and biotic factors influence canopy complexity and its inter-annual variability, and 2) the direct and indirect effects that abiotic, biotic and canopy complexity variables have on ANPP. We hypothesized that inter-annual variability in canopy complexity would be lower in high complexity canopies and that temporal variability in complexity metrics would be inversely related to ANPP. We found that canopy complexity was highest in more taxonomically diverse stands with high variability in tree diameters and in stands dominated by Populus tremuloides and Populus grandidentata. Canopy complexity was lowest in stands dominated by Quercus rubra and Pinus strobus, which also had lower ANPP. Stands with a high stem density had lower inter-annual variation in canopy complexity, exhibited more height growth and an increase in canopy open space, which in turn enhanced ANPP. Our results provide novel empirical evidence linking temporal stability in canopy complexity to ANPP, and suggest that variability in canopy complexity over time, in addition to the overall mean canopy complexity, may be important when considering drivers of forest carbon uptake.

Extent of pollen-mediated gene flow and seed longevity in switchgrass (Panicum virgatum L.): Implications for biosafety procedures

Hsiaochi Chang, Allison A. Snow, Evans, Mutegi, Emily M. Lewis, Emily A.Heaton, Maria N. Miriti. 2018.

New switchgrass (Panicum virgatum L.) bioenergy cultivars are being bred through genetic engineering; however, baseline information is urgently needed to establish guidelines for small-scale field trials prior to commercialization. In this study, we documented the pattern of pollen-mediated gene flow and the extent of seed longevity in field experiments. To mimic crop-to-wild, pollen-mediated gene flow, we planted wild recipient switchgrass ramets at various distances away from cultivar donor ramets at two sites in Ohio. Percent hybridization at each distance was estimated from seed set on recipient ramets, which were self-incompatible clones. The pattern of gene flow was best described by negative exponential models, and the minimum isolation distance for a 0.01% gene flow threshold was predicted to be 69 m and 109 m away from the pollen source at the two sites. To investigate seed longevity, we buried seeds of six cultivars and ten wild biotypes in Ohio and Iowa in 2011. A subset of the seeds were exhumed, germinated, and tested for dormancy over three years. Cultivars lost seed viability and dormancy significantly sooner than wild biotypes at both locations in the first year, and most biotypes lost dormancy by the second year. Cultivar seeds buried in the cooler, drier Iowa site had an overall greater longevity than those buried in Ohio. Our findings suggest that substantial amounts of pollen-mediated gene flow could occur in the immediate vicinity of switchgrass pollen sources, and current switchgrass cultivars are unlikely to persist in the seed bank for more than three years.

Evaluating the adaptive evolutionary convergence of carnivorous plant taxa through functional genomics

Gregory L Wheeler​, Bryan C Carstens. 2018. PeerJ Preprints 6:e3525v1


Carnivorous plants are striking examples of evolutionary convergence, displaying complex and often highly similar adaptations despite lack of shared ancestry. Using available carnivorous plant genomes along with non-carnivorous reference taxa, this study examines the convergence of functional overrepresentation of genes previously implicated in plant carnivory. Gene Ontology (GO) coding was used to quantitatively score functional representation in these taxa, in terms of proportion of carnivory-associated functions relative to all functional sequence. Statistical analysis revealed that, in carnivorous plants as a group, only two of the 24 functions tested showed a signal of substantial overrepresentation. However, when the four carnivorous taxa were analyzed individually, 11 functions were found to be significant in at least one taxon. Though carnivorous plants collectively may show overrepresentation in functions from the predicted set, the specific functions that are overrepresented vary substantially from taxon to taxon. While it is possible that some functions serve a similar practical purpose such that one taxon does not need to utilize both to achieve the same result, it appears that there are multiple approaches for the evolution of carnivorous function in plant genomes. Our approach could be applied to tests of functional convergence in other systems provided on the availability of genomes and annotation data for a group.

Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections

M Ruffley, M L Smith, A Espíndola, B C Carstens, J Sullivan, D C Tank. 2018. Mol Ecol. doi:10.1111/mec.14491


Model selection approaches in phylogeography have allowed researchers to evaluate the support for competing demographic histories, which provides a mode of inference and a measure of uncertainty in understanding climatic and spatial influences on intraspecific diversity. Here, to rank all models in the comparison set, and determine what proportion of the total support the top-ranked model garners, we conduct model selection using two analytical approaches –allele frequency-based, implemented in fastsimcoal2, and gene tree-based, implemented in PHRAPL. We then expand this model-selection framework by including an assessment of absolute fit of the models to the data. For this, we utilize DNA isolated from existing natural history collections that span the distribution of red alder (Alnus rubra) in the Pacific Northwest of North America to generate genomic data for the evaluation of 13 demographic scenarios. The quality of DNA recovered from herbarium specimen leaf tissue was assessed for its utility and effectiveness in demographic model selection, specifically in the two approaches mentioned. We present strong support for the use of herbarium tissue in the generation of genomic DNA, albeit with the inclusion of additional quality control checks prior to library preparation and analyses with multiple approaches that incorporate various data. Analyses with allele frequency spectra and gene trees predominantly support A. rubra having experienced an ancient vicariance event with intermittent and frequent gene flow between the disjunct populations. Additionally, the data consistently fit the most frequently selected model, corroborating the model selection techniques. Finally, these results suggest that the A. rubra disjunct populations do not represent separate species.

Geographical range size and latitude predict population genetic structure in a global survey

Tara A. Pelletier, Bryan C. Carstens. 2018. Royal Society Publishing Biology Letters. January 2018 Volume 14, issue 1. DOI: 10.1098/rsbl.2017.0566


While genetic diversity within species is influenced by both geographical distance and environmental gradients, it is unclear what other factors are likely to promote population genetic structure. Using a machine learning framework and georeferenced DNA sequences from more than 8000 species, we demonstrate that geographical attributes of the species range, including total size, latitude and elevation, are the most important predictors of which species are likely to contain structured genetic variation. While latitude is well known as an important predictor of biodiversity, our work suggests that it also plays a key role in shaping diversity within species.

Revision of the world species of the genus Habroteleia Kieffer (Hymenoptera, Platygastridae, Scelioninae)

Hua-yan Chen, Elijah J. Talamas, Lubomír Masner, Norman F. Johnson. 2018. ZooKeys 730: 87-122 (17 Jan 2018)


The genus Habroteleia Kieffer is revised. Seven species are recognized, three are redescribed: H. flavipes Kieffer, H. persimilis (Kozlov & Kononova), H. ruficoxa (Kieffer); and four species are described as new: H. mutabilis Chen & Talamas, sp. n., H. salebra Chen & Talamas, sp. n., H. soa Chen & Talamas, sp. n., and H. spinosa Chen & Johnson, sp. n. Four species are treated as junior synonyms of Habroteleia flavipes Kieffer: Chrestoteleia bakeri Kieffer, syn. n., Habroteleia bharatensis Saraswat, syn. n., Habroteleia browni Crawford, syn. n., and Habroteleia kotturensis (Sharma), syn. n. Habroteleia dagavia (Kozlov & Lê), syn. n. is treated as junior synonym of Habroteleia persimilis (Kozlov & Kononova). Baryconus vindhiensis (Sharma), comb. n. is transferred out of Habroteleia Kieffer. Habroteleia impressa (Kieffer) and H. scapularis (Kieffer) remain valid species but their identity and status are unclear.