Publications by EEOB faculty September 1 - September 30

September 12, 2016
eeob 2016

Phylogenetic relationships at the base of Ericaceae: Implications for vegetative and mycorrhizal evolution

Freudenstein, John V.; Broe, Michael B.; Feldenkris, Emily R. 2016. Taxon. 65(4):794-804. DOI:


The relationships among pyroloids, monotropoids, arbutoids and the remainder of Ericaceae continue to be unresolved even though significant progress has been made in understanding the phylogenetic structure of the family. This means that, in addition to uncertainty in classification, evolutionary patterns in vegetative structure and mycorrhizal diversity in the family have also been uncertain. This study analyzes nuclear, plastid and mitochondrial sequence data in order to provide a basis for classification and character analysis. Parsimony and maximum likelihood analyses of partitioned and combined data are largely in agreement; organellar data differ from nuclear data with respect to the position of pyroloids. Based on nuclear, plastid and combined data analyses, monotropoids are sister to arbutoids, and these are together sister to pyroloids, and thence to a core Ericaceae and finally to Enkianthus. This suggests that a reduction in woodiness and increased mycotrophy has occurred in parallel in pyroloids and monotropoids and that the arbutoid and ericoid mycorrhizal types were each derived from the arbuscular type in Ericaceae.

Anticipated impacts of climate change on 21st century Maumee River discharge and nutrient loads

Andreas M. Culbertson, Jay F. Martin, Noel Aloysius, Stuart A. Ludsin. 2016. DOI:


Climate change holds great potential to affect the Lake Erie ecosystem by altering the timing and magnitude of precipitation driven river discharge and nutrient runoff in its highly agricultural watershed. Using the SWAT hydrologic model and an ensemble of global climate models, we predicted Maumee River (Ohio) discharge during the 21st century under two Intergovernmental Panel on Climate Change (IPCC) greenhouse gas emissions scenarios: RCP4.5 (mid-range, moderate reductions) and RCP8.5 (high, “business as usual”). Annual discharge was projected to increase under both scenarios, both in the near-century (RCP4.5 = 6.5%; RCP8.5 = 2.0%) and late-century (RCP4.5 = 9.2%; RCP8.5 = 15.9%), owing to increased precipitation and reduced plant stomatal conductance. Holding fertilizer application rates at baseline levels, we found that reduced winter surface runoff and increased plant phosphorus (P) uptake led to a respective decrease in annual total P (TP) runoff in the near-century (RCP4.5 = − 4.3%; RCP8.5 = − 6.6%) and by the late-century (RCP4.5 = − 14.6%; RCP8.5 = − 7.8%). Likewise, soluble reactive P (SRP) runoff was predicted to decrease under both scenarios in the near-century (RCP4.5 = − 0.5%; RCP8.5 = − 3.5%) and by the late-century (RCP4.5 = − 11.8%; RCP8.5 = − 8.6%). By contrast, when fertilizer application was modeled to increase at the same rate as plant P uptake, TP loading increased 4.0% (0.9%) in the near-century and 9.9% (24.6%) by the late-century and SRP loading increased 10.5% (6.1%) in the near-century and 26.7% (42.0%) by the late-century under RCP4.5 (RCP8.5). Our findings suggest that changes in agricultural practices (e.g., fertilization rates) will be key determinants of Maumee River discharge during the 21st century.

Distribution of coalescent histories under the coalescent model with gene flow

Yuan Tian, Laura S. Kubatko. 2016. Molecular Phylogenetics and Evolution. DOI:


We propose a coalescent model for three species that allows gene flow between both pairs of sister populations. The model is designed for multilocus genomic sequence alignments, with one sequence sampled from each of the three species, and is formulated using a Markov chain representation that allows use of matrix exponentiation to compute analytical expressions for the probability density of coalescent histories. The coalescent history distribution as well as the gene tree topology distribution under this coalescent model with gene flow are then calculated via numerical integration. We analyze the model to compare the distributions of gene tree topologies and coalescent histories for species trees with differing effective population sizes and gene flow rates. Our results suggest conditions under which the species tree and associated parameters are not identifiable from the gene tree topology distribution when gene flow is present, but indicate that the coalescent history distribution may identify the species tree and associated parameters. Thus, the coalescent history distribution can be used to infer parameters such as the ancestral effective population sizes and the rates of gene flow in a maximum likelihood (ML) framework. We conduct computer simulations to evaluate the performance of our method in estimating these parameters, and we apply our method to an Afrotropical mosquito data set (Fontaine et al., 2015).

Impact of warming on CO2 emissions from streams countered by aquatic photosynthesis

Benoît O. L. Demars, Gísli M. Gíslason, Jón S. Ólafsson, J. Russell Manson, Nikolai Friberg, James M. Hood, Joshua J. D. Thompson & Thomas E. Freitag. 2016. Nature Geoscience. doi:10.1038/ngeo2807


Streams and rivers are an important source of CO2 emissions1. One important control of these emissions is the metabolic balance between photosynthesis, which converts CO2 to organic carbon, and respiration, which converts organic carbon into CO2 (refs 2,3). Carbon emissions from rivers could increase with warming, independently of organic carbon inputs, because the apparent activation energy is predicted to be higher for respiration than photosynthesis4, 5. However, physiological CO2-concentrating mechanisms may prevent the increase in photorespiration, limiting photosynthesis with warming6. Here we report the thermal response of aquatic photosynthesis from streams located in geothermal areas of North America, Iceland and Kamchatka with water temperatures ranging between 4 and 70 °C. Based on a thermodynamic theory of enzyme kinetics, we show that the apparent activation energy of aquatic ecosystem photosynthesis is approximately 0.57 electron volts (eV) for temperatures ranging from 4 to 45 °C, which is similar to that of respiration4, 5, 7, 8, 9. This result and a global synthesis of 222 streams suggest that warming will not create increased stream and river CO2 emissions from a warming-induced imbalance between photosynthesis and respiration. However, temperature could affect annual CO2 emissions from streams if ecosystem respiration is independent of gross primary production, and may be amplified by increasing organic carbon supply.

Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms

Ryan A. Folk, Jennifer R. Mandel and John V. Freudenstein. 2016. Syst Biol. doi: 10.1093/sysbio/syw083


While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages – clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp) and mitochondrial (~470,000 bp) data. We analyze these data using multiple concatenation and coalescence strategies.
The nuclear phylogeny is consistent with previous work and with morphology, confidently suggesting a monophyletic Heuchera. By contrast, analyses of both organellar genomes recover a grossly polyphyletic Heuchera, consisting of three primary clades with relationships extensively rearranged within these as well. A minority of nuclear loci also exhibit phylogenetic discord; yet these topologies remarkably never resemble the pattern of organellar loci and largely present low levels of discord inter alia. Two independent estimates of the coalescent branch length of the ancestor of Heuchera using nuclear data suggest rare or non-existent incomplete lineage sorting with related clades, inconsistent with the observed gross polyphyly of organellar genomes (confirmed by simulation of gene trees under the coalescent). These observations, in combination with previous work, strongly suggest hybridization as the cause of this phylogenetic discord.