TY - JOUR T1 - Challenges and opportunities for maintaining ponderosa pine forests in the southwestern U.S. JF - Tree Planters’ Notes Y1 - 2019 A1 - T.E Kolb A1 - A. Dixit A1 - O. Burney AB -

Deforestation caused by wildfire and bark beetle attacks in southwestern ponderosa pine (Pinus ponderosa Douglas ex P. Lawson & C. Lawson.) forests have increased over the past century due to climate warming. Continued warming is expected to increase deforestation. Ponderosa pine regeneration after deforestation often is inadequate in the region. Opportunities exist for active management to mitigate deforestation. First, planting can promote reforestation, but survival of planted seedlings is generally poor and highly variable among sites. The region needs more research about improving early seedling performance. Secondly, improving aridity adaptation of planted seedlings by seed source selection may improve outplanting performance. New common garden studies of seedling aridity adaptation of Arizona and New Mexico provenances suggest genetic variation in aridity adaptation among populations. Early results show genetic variation in survival under extreme drought conditions. Greenhouse experiments are investigating genetic variation in mechanisms of aridity tolerance. Promotion of forest recovery using these emerging approaches will be critical for sustaining forests in the increasingly arid southwestern U.S.

VL - 62:104-112 UR - https://rngr.net/publications/tpn/62-1-2/challenges-and-opportunities-for-maintaining-ponderosa-pine-forests-in-the-southwestern-united-states/?searchterm=kolb ER - TY - THES T1 - Getting to the Root of Change: How Plants Respont to Novel Climates, Soils, and Soil Biota T2 - Forestry Y1 - 2019 A1 - Michael J. Remke ED - Matthew Bowker ED - Nancy Johnson ED - Catherine Gehring ED - Thomas Kolb KW - arbuscular mycorrhizal KW - climate change KW - ecto-mycorrhizal KW - Plants KW - soil biota KW - soils AB -

Global climate change is having profound and widespread effects on plant growth and survival. For the southwestern United States, warmer temperatures, more variable precipitation and more extreme droughts are expected. As plant populations experience these changes they may adapt and persist in place or may experience increasing environmental stress, eventually leading to mortality. An interesting component of environmental change is that different edaphic conditions may mitigate or exacerbate changes in the environment. As an example, coarse soils with low water holding capacity may exacerbate a change in water availability. Additionally, soil biota may play a critical role in facilitating plant survival during environmental change. Mycorrhizal fungi and plant growth promoting rhizobacteria both have been shown to have an impact on plant water uptake and physiological regulation. Interestingly, plants migrating to new locations maybe experiencing different novel environments by migrating across edaphic boundaries. Novel edaphic environments may have vastly different physical and chemical properties to which plant populations are adapted to. Furthermore, plant migration often occurs independently of the migration of associated soil microbes, including mycorrhizal fungi. Both arbuscular mycorrhizal (AM) fungi and ecto-mycorrhizal (EM) fungi play important roles in plant nutrient and water uptake. While plant responses to changes in climate, or even soils are fairly well understood, few studies have examined the impact of simultaneous change in climate, soil, and soil biota on plant performance To better understand adaptation to novel environments, the grass Bouteloua gracilis was grown at six field sites: two natal source sites, a +2°C site, a +3°C site, a -2°C site and -3°C site where the warmer sites simulate in situ warming and precipitation changes whereas the cooler sites simulate plant migration. In these papers we define home as soil communities from the plants site of origin, and away as soil communities from the transplant site. Plants at all of the transplant sites were then grown in the following combinations of soil and soil biota: 1) home soil, home soil biota, 2) away soil, home soil biota, 3) home soil, away soil biota and 4) away soil, away soil biota. Home refers to soil or soil biota from the same site as the plant, whereas away represents soil or soil biota from the transplant site. We found plants generally grew more in cooler/wetter environments than in warm/dry environments. In warm/dry environments, we also found that home soil biota generally facilitated plant growth and plants were larger than those grown with away soil biota. Away soils originating from one site in particular, had a dramatic negative effect on plant growth. In general, our results demonstrate that warmer temperatures have a negative effect on plant growth that can be mitigated partly by plant associated soil biota. In order to better understand plant physiological responses to changes in environment, we conducted a similar, parallel study with the tree Pinus ponderosa where we grew P. ponderosa at three field sites: one natal source site, a +2°C site and a -2°C site. We used the same treatment combinations described above. We monitored plant growth and leaf physiology metrics during the monsoon season. Trees grown at the +2°C site grew as large as those grown at the home site when they had their home soil biota, but not when they had their away soil biota. Trees with their home soil biota maintained nearly 2× the maximum net photosynthetic rate and stomatal conductance rate than those grown with their away soil biota. These results imply that home soil biota play a critical role in either water uptake or physiological regulation and away soil biota do not have the same effect. Lastly, we conducted a third experiment to more closely examine how the plant symbiosis with home soil biota influence plant growth differs from that with away soil biota. In this experiment, we grew the grass Bouteloua gracilis from a relatively wet and relatively dry site with either home or away soil biota. We then subjected plants to a watering regime that simulated or moderate drying or extreme drying and monitored plant growth. At the termination of the experiment we recorded fungal structures colonizing plant roots. We observed that home plant-soil biota combinations grew larger and had a greater portion of roots colonized by AM fungi structures for nutrient exchange and uptake (hyphae and arbuscules). In contrast, away plant-soil biota combinations resulted in a greater portion of roots colonized by less beneficial AM fungi structures that are used for fungal carbon storage (vesicles). These results may indicate that home plant-fungal pairings generally have greater mutualistic function, partially due to fungal allocation. Plants responding to changes in their environment will be exposed to a wide array of scenarios and thus exhibit a wide range of responses. In general, our studies indicate that soil biota mitigate some of the negative effects of warmer drier environments on plant growth. We also demonstrate that plants migrating to novel cooler and wetter environments are much less dependent on these soil biota, however, edaphic boundaries are likely to be a barrier to plant growth with certain soil environments a greater barrier than others.

JF - Forestry PB - Northern Arizona University CY - Flagstaff, Arizona, USA VL - Doctor of Philosophy in Forest Science UR - https://www.sega.nau.edu/sites/default/files/Getting_to_the_Root_of_Change.pdf ER - TY - CONF T1 - Design and Implementation of an Energy-Neutral Solar Energy System for Wireless Sensor-Actuator Nodes T2 - IEEE Global IoT Summit (GIoTS-2017) Y1 - 2017 A1 - Knapp,J A1 - PG Flikkema JF - IEEE Global IoT Summit (GIoTS-2017) T3 - IEEE Global IoT Summit (GIoTS-2017) CY - Geneva, Switzerland VL - 2017 N1 - [Original String]:Knapp, J. and Flikkema, P.G. “Design and Implementation of an Energy-Neutral Solar Energy System for Wireless Sensor-Actuator Nodes”, 2017 IEEE Global IoT Summit (GIoTS-2017), 6-9 June 2017, Geneva, Switzerland. ER - TY - JOUR T1 - Genetics-based interactions of foundation species affect community diversity, stability and network structure. JF - Proceedings of the Royal Society B Biological ... Y1 - 2017 A1 - AR Keith A1 - JK Bailey A1 - Lau,MK A1 - TG Whitham AB - react-text: 446 A central issue in the field of community genetics is the expectation that trait variation among genotypes play a defining role in structuring associated species and in forming community phenotypes. Quantifying the existence of such community phenotypes in two common garden environments also has important consequences for our understanding of gene-by-environment interactions at the community... /react-text react-text: 447 /react-text [Show full abstract] VL - 284 UR - http://europepmc.org/abstract/MED/28490623 IS - 1854 ER - TY - JOUR T1 - Local biotic adaptation of trees and shrubs to plant neighbors. JF - Okios Y1 - 2017 A1 - Grady, K.C. A1 - Wood, T. E. A1 - Kolb, T. E. A1 - Hersch-Green, E. A1 - Shuster, S.M. A1 - Gehring, C. A. A1 - Hart, S.C. A1 - Allan, G.J. A1 - T. G. Whitham AB -

Natural selection as a result of plant–plant interactions can lead to local biotic adaptation. This may occur where species frequently interact and compete intensely for resources limiting growth, survival, and reproduction. Selection is demonstrated by comparing a genotype interacting with con‐ or hetero‐specific sympatric neighbor genotypes with a shared site‐level history (derived from the same source location), to the same genotype interacting with foreign neighbor genotypes (from different sources). Better genotype performance in sympatric than allopatric neighborhoods provides evidence of local biotic adaptation. This pattern might be explained by selection to avoid competition by shifting resource niches (differentiation) or by interactions benefitting one or more members (facilitation). We tested for local biotic adaptation among two riparian trees, Populus fremontii and Salix gooddingii, and the shrub Salix exigua by transplanting replicated genotypes from multiple source locations to a 17 000 tree common garden with sympatric and allopatric treatments along the Colorado River in California. Three major patterns were observed: 1) across species, 62 of 88 genotypes grew faster with sympatric neighbors than allopatric neighbors; 2) these growth rates, on an individual tree basis, were 44, 15 and 33% higher in sympatric than allopatric treatments for P. fremontii, S. exigua and S. gooddingii, respectively, and; 3) survivorship was higher in sympatric treatments for P. fremontii and S. exigua. These results support the view that fitness of foundation species supporting diverse communities and dominating ecosystem processes is determined by adaptive interactions among multiple plant species with the outcome that performance depends on the genetic identity of plant neighbors. The occurrence of evolution in a plant‐community context for trees and shrubs builds on ecological evolutionary research that has demonstrated co‐evolution among herbaceous taxa, and evolution of native species during exotic plants invasion, and taken together, refutes the concept that plant communities are always random associations.

VL - 126 UR - https://onlinelibrary.wiley.com/doi/full/10.1111/oik.03240 IS - 4 ER - TY - CONF T1 - Southwestern white pine performance across an elevational gradient. T2 - National Silviculture Workshop Y1 - 2017 A1 - DaBell,J A1 - K Waring A1 - TE Kolb A1 - AV Whipple JF - National Silviculture Workshop T3 - National Silviculture Workshop CY - Flagstaff, Arizona, USA ER - TY - CONF T1 - Southwestern white pine performance across an elevational gradient. T2 - North American Forest Ecology Workshop Y1 - 2017 A1 - DaBell,J A1 - K Waring A1 - TE Kolb A1 - AV Whipple AB -

DaBell, J., Waring, K., Kolb, T. and Whipple, A. 2017. Southwesternwhite pine performance across an elevational gradient. North American Forest Ecology Workshop, June 18-22, 2017, Edmonton, Canada. Also presented at the National Silviculture Workshop, July 18-20, 2017, Flagstaff, AZ.

JF - North American Forest Ecology Workshop T3 - North American Forest Ecology Workshop CY - Edmonton Canada VL - 2017 N1 - [Original String]:DaBell, J., Waring, K., Kolb, T. and Whipple, A. 2017. Southwestern white pine performance across an elevational gradient. North American Forest Ecology Workshop, June 18-22, 2017, Edmonton, Canada. Also presented at the National Silviculture Workshop, July 18-20, 2017, Flagstaff, AZ. ER - TY - CONF T1 - Support of distributed ecological experiments via closed-loop environmental control T2 - 2017 IEEE Conference on Technologies for Sustainability (SusTech), Y1 - 2017 A1 - J.D. Knapp A1 - M. Middleton A1 - P.L. Heinrich A1 - A.V. Whipple A1 - P.G. Flikkema KW - closed-loop KW - distributed experiments KW - Ecology KW - environmental control KW - SEGA KW - technology AB -

Improved understanding of the effects of climate and weather patterns on plant survival and growth is critical for improving management of wildland, rangeland, and crop ecosystems. The Southwest Experimental Garden Array (SEGA) is a distributed research instrument comprising of an array of 10 common gardens across an elevational gradient in Northern Arizona. SEGA's cyber infrastructure facilitates monitoring and control of soil moisture at experimental plots using drip irrigation and wireless sensor/actuator nodes. This paper describes development of software-based workflows for the sensing and control of soil moisture conditions across experimental plots and gardens with different temperature and rainfall regimes, and the necessary hardware and software infrastructure to support this capability.

JF - 2017 IEEE Conference on Technologies for Sustainability (SusTech), PB - IEEE SusTech CY - Phoenix, AZ UR - https://ieeexplore.ieee.org/document/8333478/ ER - TY - JOUR T1 - Bud phenology and growth are subject to divergent selection across a latitudinal gradient in Populus angustifolia and impact adaptation across the distributional range and associated arthropods. JF - Ecology and evolution Y1 - 2016 A1 - Evans,Luke M A1 - Kaluthota,Sobadini A1 - Pearce,David W A1 - Allan,Gerard J A1 - Floate,Kevin A1 - Rood,Stewart B A1 - Whitham,Thomas G AB -

Temperate forest tree species that span large geographical areas and climatic gradients often have high levels of genetic variation. Such species are ideal for testing how neutral demographic factors and climate-driven selection structure genetic variation within species, and how this genetic variation can affect ecological communities. Here, we quantified genetic variation in vegetative phenology and growth traits in narrowleaf cottonwood, Populus angustifolia, using three common gardens planted with genotypes originating from source populations spanning the species' range along the Rocky Mountains of North America (ca. 1700 km). We present three main findings. First, we found strong evidence of divergent selection (Q ST > F ST) on fall phenology (bud set) with adaptive consequences for frost avoidance. We also found evidence for selection on bud flush duration, tree height, and basal diameter, resulting in population differentiation. Second, we found strong associations with climate variables that were strongly correlated with latitude of origin. More strongly differentiated traits also showed stronger climate correlations, which emphasizes the role that climate has played in divergent selection throughout the range. We found population × garden interaction effects; for some traits, this accounted for more of the variance than either factor alone. Tree height was influenced by the difference in climate of the source and garden locations and declined with increasing transfer distance. Third, growth traits were correlated with dependent arthropod community diversity metrics. Synthesis. Overall, we conclude that climate has influenced genetic variation and structure in phenology and growth traits and leads to local adaptation in P. angustifolia, which can then impact dependent arthropod species. Importantly, relocation of genotypes far northward or southward often resulted in poor growth, likely due to a phenological mismatch with photoperiod, the proximate cue for fall growth cessation. Genotypes moved too far southward suffer from early growth cessation, whereas those moved too far northward are prone to fall frost and winter dieback. In the face of current and forecasted climate change, habitat restoration, forestry, and tree breeding efforts should utilize these findings to better match latitudinal and climatic source environments with management locations for optimal future outcomes.

VL - 6 UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=27386097&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 13 ER - TY - JOUR T1 - Cheatgrass invasion alters the abundance and composition of dark septate fungal communities in sagebrush steppe. JF - Botany Y1 - 2016 A1 - CA Gehring A1 - Hayer,M A1 - L Flores-Renteria A1 - Krohn,AL A1 - Schwartz,E A1 - P Dijkstra AB - Invasive, non-native plant species can alter soil microbial communitiesin ways that contribute to their persistence. While most studies emphasize mycorrhizal fungi, invasive plants also may influence communities of dark septate fungi (DSF), which are common root endophytes that can function like mycorrhizas. We tested the hypothesis that a widespread invasive plant in the western United States, cheatgrass (Bromus tectorum L.), influenced the abundance and community composition of DSF by examining the roots and rhizosphere soils of cheatgrass and two native plant species in cheatgrass-invaded and noninvaded areas of sagebrush steppe. We focused on cheatgrass because it is negatively affected by mycorrhizal fungi and colonized by DSF. We found that DSF root colonization and operational taxonomic unit (OTU) richness were significantly higher in sagebrush (Artemisia tridentata Nutt.) and rice grass (Achnatherum hymenoides (Roem. & Schult.) Barkworth) from invaded areas than noninvaded areas. Cheatgrass roots had similar levels of DSF colonization and OTU richness as native plants. The community composition of DSF varied with invasion in the roots and soils of native species and among the roots of the three plant species in the invaded areas. The substantial changes in DSF we observed following cheatgrass invasion argue for comparative studies of DSF function in native and non-native plant species. VL - 9 IS - 6 N1 - [Original String]:Gehring, C. A., Hayer, M. Flores-Renteria, L. Krohn, A. L., Schwartz, E. and Dijkstra, P. (In press). Cheatgrass invasion alters the abundance and composition of dark septate fungal communities in sagebrush steppe. Botany. ER - TY - JOUR T1 - Genetic variation in Pinus strobiformis growth and drought tolerance from southwestern US populations. JF - Tree physiology Y1 - 2016 A1 - Goodrich,Betsy A A1 - Waring,Kristen M A1 - Kolb,Thomas E KW - Adaptation, Physiological KW - Droughts KW - Genetic Variation KW - Pinus KW - Southwestern United States KW - Trees AB -

The persistence of some tree species is threatened by combinations of novel abiotic and biotic stressors. To examine the hypothesis that Pinus strobiformis Engelm., a tree threatened by an invasive forest pathogen and a changing climate, exhibits intraspecific genetic variation in adaptive traits, we conducted a common garden study of seedlings at one location with two watering regimes using 24 populations. Four key findings emerged: (i) growth and physiological traits were low to moderately differentiated among populations but differentiation was high for some traits in water-stressed populations; (ii) seedlings from warmer climates grew larger, had higher stomatal density and were more water-use efficient (as measured by the carbon isotope ratio) than populations from colder climates; (iii) seedlings from the northern edge of the species' distribution had lower water-use efficiency, higher stomatal conductance, slower growth and longer survival in a lethal drought experiment compared with seedlings from more southern populations; and (iv) based on non-metric multidimensional scaling analyses, populations clustered into southern and northern groups, which did not correspond to current seed transfer zones. Our discovery of a clinal geographic pattern of genetic variation in adaptive traits of P. strobiformis seedlings will be useful in developing strategies to maintain the species during ongoing climate change and in the face of an invasive pathogen.

VL - 36 SN - 0829-318X UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=27344065&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 10 ER - TY - JOUR T1 - Genotypic variation in foundation species generates network structure that may drive community dynamics and evolution. JF - Ecology Y1 - 2016 A1 - Lau,Matthew K A1 - Keith,Arthur R A1 - Borrett,Stuart R A1 - Shuster,Stephen M A1 - Whitham,Thomas G KW - Animals KW - Biological Evolution KW - Computer Simulation KW - Food Chain KW - Genetic Variation KW - Genotype KW - Insecta KW - Models, Biological KW - Populus AB -

Although genetics in a single species is known to impact whole communities, little is known about how genetic variation influences species interaction networks in complex ecosystems. Here, we examine the interactions in a community of arthropod species on replicated genotypes (clones) of a foundation tree species, Populus angustifolia James (narrowleaf cottonwood), in a long-term, common garden experiment using a bipartite "genotype-species" network perspective. We combine this empirical work with a simulation experiment designed to further investigate how variation among individual tree genotypes can impact network structure. Three findings emerged: (1) the empirical "genotype-species network" exhibited significant network structure with modularity being greater than the highly conservative null model; (2) as would be expected given a modular network structure, the empirical network displayed significant positive arthropod co-occurrence patterns; and (3) furthermore, the simulations of "genotype-species" networks displayed variation in network structure, with modularity in particular clearly increasing, as genotypic variation increased. These results support the conclusion that genetic variation in a single species contributes to the structure of ecological interaction networks, which could influence eco-ogical dynamics (e.g., assembly and stability) and evolution in a community context.

VL - 97 SN - 0012-9658 UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=27197399&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 3 ER - TY - JOUR T1 - Local-Scale Drought Adaptation of Ponderosa Pine Seedlings at Habitat Ecotones JF - Forest Science Y1 - 2016 A1 - TE Kolb A1 - Grady,KC A1 - Mcettrick,MP A1 - Herrero,A AB - Abstract Understanding the magnitude and pattern of intraspecific variation in tree adaptation to drought is needed to evaluate forest capacity to respond to climate change and for management planning. This understanding is important for species growing at ecotonal sites near the trailing edge of their geographic range where impacts of climate warming are predicted to be most severe. We used a greenhouse common garden to investigate phenotypic variations in growth, drought-adaptive structural traits (e.g., wood specific gravity, shoot-root ratio, and specific leaf area), and survival during experimental drought in seedlings of ponderosa pine (Pinus ponderosa Doug. Ex. Laws) sampled from 17 sites in northern Arizona over gradients of elevation, precipitation, and soil parent material. Phenotypic variation was significant in most seedling traits, and the most variation occurred among maternal families within site populations. Growth rate was negatively correlated with wood specific gravity. The large amount of phenotypic variation within populations suggests the potential for future evolution of stress tolerance in trailing-edge populations. The strongest geographic pattern in phenotypic variation was a negative relationship between seedling biomass allocation to roots and precipitation of the population site. Families with the longest survival in a lethal drought experiment tended to come from low-elevation, drier sites. VL - 62 UR - http://www.ingentaconnect.com/content/saf/fs/pre-prints/content-forsci16049 ER - TY - JOUR T1 - Long-term thinning alters ponderosa pine reproduction in northern Arizona. JF - Forest Ecology and Management Y1 - 2016 A1 - Flathers,KN A1 - TE Kolb A1 - Bradford,JB A1 - Waring,KM A1 - Moser,WK VL - 374 N1 - [Original String]:Flathers, K. N., Kolb, T. E., Bradford, J. B. Waring, K. M. and Moser, W. K. (2016). Long-term thinning alters ponderosa pine reproduction in northern Arizona. Forest Ecology and Management 374:154-165. ER - TY - JOUR T1 - Phylogenetic organization of bacterial activity. JF - The ISME journal Y1 - 2016 A1 - Ember M Morrissey A1 - Mau,Rebecca L A1 - Egbert Schwartz A1 - Caporaso,J Gregory A1 - P Dijkstra A1 - van Gestel,Natasja A1 - BJ Koch A1 - Liu,Cindy M A1 - Hayer,Michaela A1 - McHugh,Theresa A A1 - Jane C Marks A1 - Lance B Price A1 - Hungate,Bruce A KW - Bacteria KW - Biological Evolution KW - Carbon Isotopes KW - Ecology KW - Ecosystem KW - Oxygen Isotopes KW - Phenotype KW - Phylogeny AB -

Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with (13)C and (18)O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions.

VL - 10 SN - 1751-7362 UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=26943624&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 9 ER - TY - CONF T1 - Southwestern white pine seedling tolerances to a changing climate: early results from common gardens across an elevational gradient. T2 - Society of American Foresters National Convention Y1 - 2016 A1 - DaBell,J A1 - K Waring A1 - TE Kolb A1 - AV Whipple A1 - Madison,WI JF - Society of American Foresters National Convention T3 - Society of American Foresters National Convention CY - Madison, Wisconsin, USA VL - 2016 N1 - [Original String]:DaBell, J., Waring, K., Kolb, T., and Whipple, A. 2016. Southwestern white pine seedling tolerances to a changing climate: early results from common gardens across an elevational gradient. Society of American Foresters National Convention, November 2-5, 2016, Madison, WI. ER - TY - CONF T1 - Sustaining southwestern white pine by combining experimental work and genomic tools. Y1 - 2016 A1 - Castilla,AR A1 - R Sniezko A1 - K Waring A1 - Cushman,S A1 - Eckert,A.J A1 - Flores,L A1 - Still,C A1 - Wehenkel,C A1 - Whipple,A A1 - Wing,M A1 - TE Kolb A1 - Goodrich,B.A. ER - TY - CONF T1 - Taxon-Specific Responses To Whole System Carbon Cycling In The Root Microbiome. T2 - Phytobiomes from microbes to plant ecosystems Y1 - 2016 A1 - P Dijkstra A1 - RL Mau A1 - McHugh,TA A1 - BJ Koch A1 - Marks,JC A1 - van Groenigen,K-J A1 - Liu,X-J A1 - Schwartz,E A1 - Morrissey,EM A1 - Hungate,BA AB -

Dijkstra, P., Mau, R.L., McHugh, T.A., Koch, B.J., Marks, J.C., vanGroenigen, K-J., Liu, X-J. A., Schwartz, E., Morrissey, E.M. and Hungate, B.A. (2016). From Taxon-Specific Responses To Whole System Carbon Cycling In The Root Microbiome. Phytobiomes: from microbes to plant ecosystems. Nov 2016, .

JF - Phytobiomes from microbes to plant ecosystems T3 - Phytobiomes from microbes to plant ecosystems CY - Santa Fe, New Mexicao, USA N1 - [Original String]:Dijkstra, P., Mau, R.L., McHugh, T.A., Koch, B.J., Marks, J.C., van Groenigen, K-J., Liu, X-J. A., Schwartz, E., Morrissey, E.M. and Hungate, B.A. (2016). From Taxon-Specific Responses To Whole System Carbon Cycling In The Root Microbiome. Phytobiomes: from microbes to plant ecosystems. Nov 2016, Santa Fe NM. ER - TY - JOUR T1 - Assessing the value of potential “native winners” for restoration of cheatgrass-invaded habitat. JF - Western North American Naturalist Y1 - 2015 A1 - Barak,RS A1 - Fant,JB A1 - Kramer,AT A1 - Skogen,KA AB - Barak, R. S., Fant, J. B., Kramer, A. T. and Skogen, K. A. (2015).Assessing the value of potential “native winners” for restoration of cheatgrass-invaded habitat. Western North American Naturalist 75: 58-69. VL - 75 N1 - [Original String]:Barak, R. S., Fant, J. B., Kramer, A. T. and Skogen, K. A. (2015). Assessing the value of potential “native winners” for restoration of cheatgrass-invaded habitat. Western North American Naturalist 75: 58-69. ER - TY - JOUR T1 - High carbon use efficiency in soil microbial communities is related to growth, not storage compound synthesis. JF - Soil Biology and Biochemistry Y1 - 2015 A1 - P Dijkstra A1 - Salpas,E A1 - Fairbanks,D A1 - Miller,EB A1 - Hagerty,SB A1 - KJ van Groenigen A1 - Hungate,BA A1 - Marks,JC A1 - GW Koch A1 - Schwartz,E VL - 89 N1 - [Original String]:Dijkstra, P., Salpas, E., Fairbanks, D., Miller EB, Hagerty, S.B., van Groenigen, K.J., Hungate, B.A., Marks, J.C., Koch, G.W., and Schwartz, E. (2015). High carbon use efficiency in soil microbial communities is related to growth, not storage compound synthesis. Soil Biology and Biochemistry 89, 35-43. ER - TY - Generic T1 - Influence of varying nitrogen availability on soil microbial growth efficiency. T2 - Ecological Society of America Annual Meeting Y1 - 2015 A1 - Hagerty,SB A1 - KJ van Groenigen A1 - Schwartz,E A1 - Hungate,BA A1 - GW Koch A1 - P Dijkstra JF - Ecological Society of America Annual Meeting T3 - Ecological Society of America Annual Meeting PB - ESA CY - Baltimore, MD, USA N1 - [Original String]:Hagerty, S.B., van Groenigen, K.J., Schwartz, E., Hungate, B.A., Koch, G.W. and Dijkstra, P. (2015). Influence of varying nitrogen availability on soil microbial growth efficiency. ESA Aug 9-14, Baltimore. ER - TY - JOUR T1 - Linking soil bacterial biodiversity and soil carbon stability. JF - The ISME journal Y1 - 2015 A1 - Mau,Rebecca L A1 - Liu,Cindy M A1 - Aziz,Maliha A1 - Egbert Schwartz A1 - P Dijkstra A1 - Jane C Marks A1 - Lance B Price A1 - Keim,Paul A1 - Hungate,Bruce A KW - Bacteria KW - biodiversity KW - Biomass KW - Carbon KW - Ecosystem KW - Glucose KW - Isotopes KW - Oxygen KW - RNA, Ribosomal, 16S KW - Soil KW - Soil Microbiology AB -

Native soil carbon (C) can be lost in response to fresh C inputs, a phenomenon observed for decades yet still not understood. Using dual-stable isotope probing, we show that changes in the diversity and composition of two functional bacterial groups occur with this 'priming' effect. A single-substrate pulse suppressed native soil C loss and reduced bacterial diversity, whereas repeated substrate pulses stimulated native soil C loss and increased diversity. Increased diversity after repeated C amendments contrasts with resource competition theory, and may be explained by increased predation as evidenced by a decrease in bacterial 16S rRNA gene copies. Our results suggest that biodiversity and composition of the soil microbial community change in concert with its functioning, with consequences for native soil C stability.

VL - 9 SN - 1751-7362 UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=25350158&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 6 ER - TY - CONF T1 - Towards Intelligent Closed-Loop Workflows for Ecological Research Dynamic Data-driven Environmental Systems T2 - Dynamic Data-driven Environmental Systems Science Conference (DyDESS) Y1 - 2014 A1 - Knapp,J A1 - Elo,M A1 - Schaffer,J A1 - PG Flikkema JF - Dynamic Data-driven Environmental Systems Science Conference (DyDESS) T3 - Dynamic Data-driven Environmental Systems Science Conference (DyDESS) PB - DyDESS CY - Cambridge, MA, USA VL - 2014 N1 - [Original String]:Knapp, J.D., M. Elo, J. Shaeffer, and P.G. Flikkema. 2014. Towards Intelligent Closed-Loop Workflows for Ecological Research. Dynamic Data-driven Environmental Systems Science Conference (DyDESS), November 5-7, 2014, Cambridge, MA. ER - TY - JOUR T1 - Conservative leaf economic traits correlate with fast growth of genotypes of a foundation riparian species near the thermal maximum extent of its geographic range . JF - Functional Ecology Y1 - 2013 A1 - Grady,KC A1 - Laughlin,DC A1 - Ferrier,SM A1 - TE Kolb A1 - Hart,SC A1 - GJ Allan A1 - TG Whitham VL - 27 N1 - [Original String]:Grady KC, Laughlin DC, Ferrier SM, Kolb TE, Hart SC, Allan GJ, Whitham TG. 2013. Conservative leaf economic traits correlate with fast growth of genotypes of a foundation riparian species near the thermal maximum extent of its geographic range . Functional Ecology 27:427-438. ER - TY - JOUR T1 - Patterns of phytochemical variation in Mimulus guttatus (yellow monkeyflower). JF - Journal of chemical ecology Y1 - 2013 A1 - Holeski,Liza M A1 - Keefover-Ring,Ken A1 - Bowers,M Deane A1 - Harnenz,Zoe T A1 - Lindroth,Richard L KW - Animals KW - Biological Evolution KW - Butterflies KW - Genetic Variation KW - Glucosides KW - Glycosides KW - Herbivory KW - Larva KW - Mimulus KW - Phenols KW - Phenotype KW - Pheromones KW - Plant Leaves AB -

The search for general patterns in the production and allocation of plant defense traits will be facilitated by characterizing multivariate suites of defense, as well as by studying additional plant taxa, particularly those with available genomic resources. Here, we investigated patterns of genetic variation in phytochemical defenses (phenylpropanoid glycosides, PPGs) in Mimulus guttatus (yellow monkeyflower). We grew plants derived from several natural populations, consisting of multiple full-sibling families within each population, in a common greenhouse environment. We found substantial variation in the constitutive multivariate PPG phenotype and in constitutive levels of individual phytochemicals within plants (among leaves of different ages), within populations (among full-sibling families), and among populations. Populations consisting of annual plants generally, but not always, had lower concentrations of phytochemicals than did populations of perennial plants. Populations differed in their plastic response to artificial herbivory, both in the overall multivariate PPG phenotype and in the individual phytochemicals. The relationship between phytochemistry and another defense trait, trichomes, differed among populations. Finally, we demonstrated that one of the PPGs, verbascoside, acts as a feeding stimulant rather than a feeding deterrent for a specialist herbivore of M. guttatus, the buckeye caterpillar (Junonia coenia Nymphalidae). Given its available genetic resources, numerous, easily accessible natural populations, and patterns of genetic variation highlighted in this research, M. guttatus provides an ideal model system in which to test ecological and evolutionary theories of plant-herbivore interactions.

VL - 39 SN - 0098-0331 UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=23468225&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 4 ER - TY - JOUR T1 - The Proportion of Three Foundation Plant Species and Their Genotypes Influence an Arthropod Community: Restoration Implications for the Endangered Southwes... JF - Restoration Ecology Y1 - 2013 A1 - RK Bangert A1 - Ferrier,SM A1 - Evans,L A1 - Kennedy,K A1 - Grady,KC AB - As part of a restoration project, multiple genotypes of two tree species, Fremont cottonwood (Populus fremontii) and Goodding's willow (Salix gooddingii), and one shrub species, Coyote willow (S. exigua), were experimentally planted in different proportions at the Palo Verde Ecological Reserve near Blythe, California, U.S.A. These common woody plant species are important to the endangered southwestern willow flycatcher, providing perch, nesting, and foraging habitat. We conducted this study to evaluate plant species proportion and plant genotype effects on the arthropod community, the prey base for the endangered southwestern willow flycatcher. Three patterns emerged. First, plant species proportions were important; the arthropod community had the greatest richness and diversity (H芒聙虏) when Goodding's willow proportion was high and Fremont cottonwood proportion was lower; that is, fewer Fremont cottonwoods are required to positively affect overall arthropod diversity. Second, we found significant genotypic effects, for all three plant species, on arthropod species accumulation. Third, while both planting proportion and genotype effects were significant, we found that the effect of planting proportion on arthropod richness was about twice as large as the effect of plant genotype. This shows that both plant species proportions and genotype should be utilized in restoration projects to maximize habitat heterogeneity and arthropod richness. Similar studies can determine which planting proportion and specific genotypes may result in a more favorable arthropod prey base for the southwestern willow flycatcher and other species of concern. Greater attention to planting design and genotype can result in significant gains in diversity at little or no additional project cost. VL - 21 UR - http://onlinelibrary.wiley.com/doi/10.1111/j.1526-100X.2012.00910.x/abstract IS - 4 ER - TY - JOUR T1 - Biogeochemical and ecological feedbacks in grassland responses to warming JF - Nature Climate Change Y1 - 2012 A1 - Wu,Z A1 - Dijkstra, A1 - GW Koch A1 - B Hungate VL - 2 ER - TY - JOUR T1 - Community specificity: life and afterlife effects of genes. JF - Trends in plant science Y1 - 2012 A1 - Whitham,Thomas G A1 - Gehring,Catherine A A1 - Lamit,Louis J A1 - Wojtowicz,Todd A1 - Evans,Luke M A1 - Keith,Arthur R A1 - Smith,David Solance KW - Animals KW - Arthropods KW - Biological Evolution KW - Ecosystem KW - Genotype KW - Herbivory KW - Host-Parasite Interactions KW - Models, Biological KW - Plants KW - Species Specificity AB -

Community-level genetic specificity results when individual genotypes or populations of the same species support different communities. Our review of the literature shows that genetic specificity exhibits both life and afterlife effects; it is a widespread phenomenon occurring in diverse taxonomic groups, aquatic to terrestrial ecosystems, and species-poor to species-rich systems. Such specificity affects species interactions, evolution, ecosystem processes and leads to community feedbacks on the performance of the individuals expressing the traits. Thus, genetic specificity by communities appears to be fundamentally important, suggesting that specificity is a major driver of the biodiversity and stability of the world's ecosystems.

VL - 17 SN - 1360-1385 UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=22322002&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 5 ER - TY - BOOK T1 - From genes to ecosystems: emerging concepts bridging ecological and evolutionary dynamics. Y1 - 2012 A1 - JK Bailey A1 - Schweitzer,JA A1 - Fitzpatrick,BM A1 - Genung,MA A1 - Pregitzer,CC A1 - M Zinkgraf A1 - TG Whitham A1 - Keith,A A1 - Reilly-Wapstra,JM A1 - Potts,BM A1 - Rehill,BJ A1 - LeRoy,CJ A1 - Fischer,DG A1 - Iason,GR A1 - Dicke,M A1 - Hartley,SE ED - Iason,GR ED - Dicke,M ED - Hartley,SE PB - Cambridge University Press CY - New York N1 - [Original String]:Bailey JK, Schweitzer JA, Úbeda F, Fitzpatrick BM, Genung MA, Pregitzer CC, Zinkgraf M, Whitham TG, Keith A, O’Reilly-Wapstra JM, Potts BM, Rehill BJ, LeRoy CJ, Fischer DG. 2012. From genes to ecosystems: emerging concepts bridging ecological and evolutionary dynamics. In Iason GR, Dicke M, Hartley SE, editors The ecology of plant secondary metabolites: from genes to global processes New York (NY): Cambridge University Press; p 269-286. ER - TY - JOUR T1 - Genes to ecosystems: exploring the frontiers of ecology with one of the smallest biological units. JF - The New phytologist Y1 - 2011 A1 - Wymore,Adam S A1 - Keeley,Annika T H A1 - Yturralde,Kasey M A1 - Schroer,Melanie L A1 - Propper,Catherine R A1 - Whitham,Thomas G KW - Animals KW - Cell Respiration KW - climate change KW - Ecosystem KW - Environmental Pollution KW - Female KW - Fishes KW - Gene Expression KW - Haplotypes KW - Humans KW - Introduced Species KW - Male KW - Plants KW - Population Dynamics KW - Sciuridae AB -

Genes and their expression levels in individual species can structure whole communities and affect ecosystem processes. Although much has been written about community and ecosystem phenotypes with a few model systems, such as poplar and goldenrod, here we explore the potential application of a community genetics approach with systems involving invasive species, climate change and pollution. We argue that community genetics can reveal patterns and processes that otherwise might remain undetected. To further facilitate the community genetics or genes-to-ecosystem concept, we propose four community genetics postulates that allow for the conclusion of a causal relationship between the gene and its effect on the ecosystem. Although most current studies do not satisfy these criteria completely, several come close and, in so doing, begin to provide a genetic-based understanding of communities and ecosystems, as well as a sound basis for conservation and management practices.

VL - 191 SN - 0028-646X UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=21631507&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 1 ER - TY - JOUR T1 - Genetic variation in productivity of foundation riparian species at the edge of their distribution: implications for restoration and assisted migration in a warming climate . JF - Global Change Biology Y1 - 2011 A1 - Grady,KC A1 - Ferrier,SM A1 - TE Kolb A1 - Hart,SC A1 - Allan,GA A1 - TG Whitham VL - 17 N1 - [Original String]:Grady KC, Ferrier SM, Kolb TE, Hart SC, Allan GA, Whitham TG. 2011. Genetic variation in productivity of foundation riparian species at the edge of their distribution: implications for restoration and assisted migration in a warming climate . Global Change Biology 17:3724-3735. ER - TY - JOUR T1 - Hybridization among foundation tree species influences the structure of associated understory plant communities JF - Botany-botanique Y1 - 2011 A1 - Lamit,LJ A1 - Wojtowicz,T A1 - Kovacs,Z A1 - Wooley,SC A1 - M Zinkgraf AB - Understanding how genetic identity influences community structure is a major focus in evolutionary ecology, yet few studies examine interactions among organisms in the same trophic level within this context. In a common garden containing trees from a hybrid system (S. Wats. × James), we tested the hypothesis that the structure of establishing understory plant communities is influenced by genetic differences among trees and explored foliar condensed tannins (CTs) and photosynthetically active radiation (PAR) as mechanisms. Several findings support our hypothesis: () Understory biomass and cover increase along the genetic gradient from to . () Along the same hybridization gradient, species richness decreases and species composition shifts. () foliar CT concentrations and PAR decrease from to . () Understory species richness increases with foliar CTs; however, biomass, cover, and composition show no relationship with CTs, and no understory variables correlate with PAR. () Structural equation modeling suggests that foliar CTs are a primary mechanism linking overstory tree genetics with understory richness. Using an experimental system dominated by naturally colonizing exotic species, this study demonstrates that a genetic gradient created by tree hybridization can influence understory plants.Pour l'écologie évolutive, la compréhension de l'influence de l'identité génétique sur la structure des communautés constitue un enjeu majeur; pourtant, il existe peu d'études ayant examiné les interactions entre les organismes occupant la même échelle trophique dans ce contexte. Dans un jardin commun comportant des arbres provenant d'un système hybride (S. Wats.× James), les auteurs ont vérifié l'hypothèse à l'effet que la structure de la mise en place des communautés végétales de sous bois se fait sous l'influence des différences génétiques entre les arbres, en utilisant comme mécanismes les tannins foliaires condensés (CTs) et les radiations photosynthétiquement actives (PAR). Plusieurs constatations supportent cette hypothèse. () La biomasse de sous bois et la couverture augmentent le long d'un gradient génétique, à partir du jusqu'au . () Le long du même gradient d'hybridation, la richesse en espèces diminue et la composition en espèces se déplace. () La teneur en CT foliaires et les PAR des diminuent du vers le . () La richesse en espèces du sous-bois augmente avec les CTs foliaires, cependant, la couverture et la composition de la neige ne montrent pas de relation avec les CTs, et aucune variable du sous-bois ne montre de corrélation avec les PAR. () La modélisation de l'équation structurale suggère que les CTs constituent un mécanisme primaire liant la génétique des arbres de la canopée avec la richesse en sous-étage. 08 l'aide d'un système expérimental dominé par la colonisation naturelle avec des espèces exotiques, cette étude démontre qu'un gradient génétique créé par l'hybridation des arbres peut influencer les plantes de sous-bois. VL - 89 UR - http://www.ingentaconnect.com/content/nrc/bot/2011/00000089/00000003/art00003 IS - 3 ER - TY - JOUR T1 - Responses of ecosystem carbon cycling to climate change treatments along an elevation gradient JF - Ecosystems Y1 - 2011 A1 - Wu,Z A1 - GW Koch A1 - P Dijkstra A1 - MA Bowker A1 - B Hungate VL - 14 IS - 7 ER - TY - JOUR T1 - A conditional trophic cascade: birds benefit faster growing trees with strong links between predators and plants. JF - Ecology Y1 - 2010 A1 - Bridgeland,William T A1 - Beier,Paul A1 - Kolb,Thomas A1 - Whitham,Thomas G KW - Animals KW - Birds KW - Food Chain KW - Insecta KW - Predatory Behavior KW - Time Factors KW - Trees AB -

Terrestrial systems are thought to be organized predominantly from the bottom-up, but there is a growing literature documenting top-down trophic cascades under certain ecological conditions. We conducted an experiment to examine how arthropod community structure on a foundation riparian tree mediates the ability of insectivorous birds to influence tree growth. We built whole-tree bird exclosures around 35 mature cottonwood (Populus spp.) trees at two sites in northern Utah, USA, to measure the effect of bird predation on arthropod herbivore and predator species richness, abundance, and biomass, and on tree performance. We maintained bird exclosures over two growing seasons and conducted nondestructive arthropod surveys that recorded 63652 arthropods of 689 morphospecies representing 19 orders. Five major patterns emerged: (1) We found a significant trophic cascade (18% reduction in trunk growth when birds were excluded) only at one site in one year. (2) The significant trophic cascade was associated with higher precipitation, tree growth, and arthropod abundance, richness, and biomass than other site-year combinations. (3) The trophic cascade was weak or not evident when tree growth and insect populations were low apparently due to drought. (4) Concurrent with the stronger trophic cascade, bird predation significantly reduced total arthropod abundance, richness, and biomass. Arthropod biomass was 67% greater on trees without bird predation. This pattern was driven largely by two herbivore groups (folivores and non-aphid sap-feeders) suggesting that birds targeted these groups. (5) Three species of folivores (Orthoptera: Melanoplus spp.) were strong links between birds and trees and were only present in the site and the year in which the stronger trophic cascade occurred. Our results suggest that this trophic system is predominately bottom-up driven, but under certain conditions the influence of top predators can stimulate whole tree growth. When the most limiting factor for tree growth switched from water availability to herbivory, the avian predators gained the potential to reduce herbivory. This potential could be realized when strong links between the birds and plant, i.e., species that were both abundant herbivores and preferred prey, were present.

VL - 91 SN - 0012-9658 UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=20380198&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 1 ER - TY - JOUR T1 - A genetic basis to community repeatability and stability. JF - Ecology Y1 - 2010 A1 - Keith,Arthur R A1 - JK Bailey A1 - Whitham,Thomas G KW - Animals KW - Arthropods KW - Biological Evolution KW - Ecosystem KW - Genotype KW - Populus AB -

Recent studies have shown that genetically based traits of plants can structure associated arthropod and microbial communities, but whether the effects are consistent and repeatable across years is unknown. If communities are both heritable (i.e., related individuals tend to support similar communities) and repeatable (i.e., the same patterns observed over multiple years), then plant genetics may also affect community properties previously thought to be emergent, such as "stability." Using replicated clones of narrowleaf cottonwood (Populus angustifolia) and examining an arthropod community of 103 species, we found that (1) individual tree genotypes supported significantly different arthropod communities, which exhibited broad-sense heritability; (2) these findings were highly repeatable over three consecutive years (repeatability = 0.91) indicating that community responses to individual tree genotypes are consistent from year to year; (3) differences among tree genotypes in community stability (i.e., changes in community composition over multiple years) exhibited broad-sense heritability (H(C)2 = 0.32). In combination, these findings suggest that an emergent property such as stability can be genetically based and thus subject to natural selection.

VL - 91 SN - 0012-9658 UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=21141200&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 11 ER - TY - JOUR T1 - From genes to ecosystems: a synthesis of the effects of plant genetic factors across levels of organization. JF - Philosophical transactions of the Royal Society of London. Series B, Biological sciences Y1 - 2009 A1 - JK Bailey A1 - Jennifer A Schweitzer A1 - Ubeda,Francisco A1 - Koricheva,Julia A1 - LeRoy,Carri J A1 - Madritch,Michael D A1 - Rehill,Brian J A1 - RK Bangert A1 - Fischer,Dylan G A1 - Allan,Gerard J A1 - Whitham,Thomas G KW - Animals KW - Arthropods KW - Ecosystem KW - Genetic Variation KW - Genetics, Population KW - Models, Genetic KW - Plant Development KW - Plants AB -

Using two genetic approaches and seven different plant systems, we present findings from a meta-analysis examining the strength of the effects of plant genetic introgression and genotypic diversity across individual, community and ecosystem levels with the goal of synthesizing the patterns to date. We found that (i) the strength of plant genetic effects can be quite high; however, the overall strength of genetic effects on most response variables declined as the levels of organization increased. (ii) Plant genetic effects varied such that introgression had a greater impact on individual phenotypes than extended effects on arthropods or microbes/fungi. By contrast, the greatest effects of genotypic diversity were on arthropods. (iii) Plant genetic effects were greater on above-ground versus below-ground processes, but there was no difference between terrestrial and aquatic environments. (iv) The strength of the effects of intraspecific genotypic diversity tended to be weaker than interspecific genetic introgression. (v) Although genetic effects generally decline across levels of organization, in some cases they do not, suggesting that specific organisms and/or processes may respond more than others to underlying genetic variation. Because patterns in the overall impacts of introgression and genotypic diversity were generally consistent across diverse study systems and consistent with theoretical expectations, these results provide generality for understanding the extended consequences of plant genetic variation across levels of organization, with evolutionary implications.

VL - 364 SN - 0962-8436 UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=19414474&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 1523 ER - TY - JOUR T1 - Genetic and environmental controls of microbial communities on leaf litter in streams . JF - Freshwater Biology Y1 - 2009 A1 - Marks,JC A1 - Haden,GA A1 - Harrop,BA A1 - Reese,EG A1 - Keams,JL A1 - Watwood,ME A1 - TG Whitham VL - 54 N1 - [Original String]:Marks JC, Haden GA, Harrop BA, Reese EG, Keams JL, Watwood ME, Whitham TG. 2009. Genetic and environmental controls of microbial communities on leaf litter in streams . Freshwater Biology 54:2616-2627. ER - TY - JOUR T1 - Genetically based susceptibility to herbivory influences the ectomycorrhizal fungal communities of a foundation tree species. JF - The New phytologist Y1 - 2009 A1 - Sthultz,Christopher M A1 - Whitham,Thomas G A1 - Kennedy,Karla A1 - Deckert,Ron A1 - Gehring,Catherine A KW - Animals KW - DNA, Fungal KW - Ecosystem KW - Host-Pathogen Interactions KW - Models, Biological KW - Moths KW - Mycorrhizae KW - Pinus KW - Symbiosis AB -

Although recent research indicates that herbivores interact with plant-associated microbes in complex ways, few studies have examined these interactions using a community approach. For example, the impact of herbivory on the community structure of ectomycorrhizal fungi (EMF) is not well known. The influence of host plant genetics on EMF community composition is also poorly understood. We used a study system in which susceptibility to herbivory has a genetic basis and a 20-yr insect removal experiment to examine the influence of chronic herbivory and plant genetics on the EMF community structure of Pinus edulis. We compared EMF communities of herbivore resistant trees, herbivore susceptible trees and herbivore susceptible trees from which herbivores were experimentally removed at two dates 10 yr apart. In both years sampled, resistant and susceptible trees differed significantly in EMF community composition. After 10 yr and 20 yr of herbivore removal, the EMF communities of removal trees were similar to those of susceptible trees, but different from resistant trees. The EMF community composition was more strongly influenced by innate genetic differences in plant traits associated with resistance and susceptibility to herbivory than by indirect effects of herbivory on host plant relationships with ectomycorrhizal fungi.

VL - 184 SN - 0028-646X UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=19761493&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 3 ER - TY - JOUR T1 - Separating ontogenetic and environmental determination of resistance to herbivory in cottonwood. JF - Ecology Y1 - 2009 A1 - Holeski,Liza M A1 - Kearsley,Michael J C A1 - Whitham,Thomas G KW - Animals KW - Aphids KW - Biological Evolution KW - Ecosystem KW - Feeding Behavior KW - Populus AB -

We used narrowleaf cottonwood, Populus angustifolia, and the gall-forming aphid, Pemphigus betae, to determine the extent to which ontogenetic variation in resistance to herbivory is due to endogenous, stable genetic influences. In a three-year common garden trial using ramets propagated from the top, middle, and bottom of mature trees, we found that the resistance of trees to aphids was significantly higher in top vs. bottom source ramets, supporting the hypothesis of a stable, genetically programmed component to aphid resistance. The magnitude of ontogenetically based variation in resistance within an individual tree is comparable to the genetic variation in resistance among narrowleaf cottonwood genotypes or populations found in other studies. These ontogenetic-based findings have the potential to alter ecological interactions and evolutionary trajectories of plant-herbivore interactions.

VL - 90 SN - 0012-9658 UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=19967853&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 11 ER - TY - JOUR T1 - A dense linkage map of hybrid cottonwood (Populus fremontii x P. angustifolia) contributes to long-term ecological research and comparison mapping in a model forest tree. JF - Heredity Y1 - 2008 A1 - Woolbright,S A A1 - Difazio,S P A1 - Yin,T A1 - Martinsen,G D A1 - Zhang,X A1 - Allan,G J A1 - Whitham,T G A1 - Keim,P KW - Chimera KW - Chromosome Mapping KW - Ecology KW - Genetic Linkage KW - Genetic Markers KW - Genetics, Population KW - Genome, Plant KW - Linkage Disequilibrium KW - Models, Biological KW - Polymorphism, Restriction Fragment Length KW - Populus KW - Trees AB -

Cottonwoods are foundation riparian species, and hybridization among species is known to produce ecological effects at levels higher than the population, including effects on dependent species, communities and ecosystems. Because these patterns result from increased genetic variation in key cottonwood traits, novel applications of genetic tools (for example, QTL mapping) could be used to place broad-scale ecological research into a genomic perspective. In addition, linkage maps have been produced for numerous species within the genus, and, coupled with the recent publication of the Populus genome sequence, these maps present a unique opportunity for genome comparisons in a model system. Here, we conducted linkage analyses in order to (1) create a platform for QTL and candidate gene studies of ecologically important traits, (2) create a framework for chromosomal-scale perspectives of introgression in a natural population, and (3) enhance genome-wide comparisons using two previously unmapped species. We produced 246 backcross mapping (BC(1)) progeny by crossing a naturally occurring F(1) hybrid (Populus fremontii x P. angustifolia) to a pure P. angustifolia from the same population. Linkage analysis resulted in a dense linkage map of 541 AFLP and 111 SSR markers distributed across 19 linkage groups. These results compared favorably with other Populus linkage studies, and addition of SSR loci from the poplar genome project provided coarse alignment with the genome sequence. Preliminary applications of the data suggest that our map represents a useful framework for applying genomic research to ecological questions in a well-studied system, and has enhanced genome-wide comparisons in a model tree.

VL - 100 SN - 0018-067X UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=17895905&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 1 ER - TY - JOUR T1 - Genetic‐based plant resistance and susceptibility traits to herbivory influence needle and root litter nutrient dynamics JF - Journal of Ecology Y1 - 2007 A1 - Classen,AT A1 - Chapman,SK A1 - TG Whitham A1 - Hart,SC A1 - GW Koch AB - Summary 1 It is generally assumed that the same factors drive the decomposition of both litter and roots and that nutrient release from litter and roots is synchronized. However, few studies have explicitly tested these assumptions, and no studies have examined whether plant genetics (i.e. plant susceptibility to herbivory) could affect these relationships. 2 Here we examine the effects of herbivore susceptibility and resistance on needle and fine root litter decomposition of pi帽on pine, Pinus edulis . The study population consists of individual trees that are either susceptible or resistant to herbivory by the pi帽on needle scale, Matsucoccus acalyptus , or the stem-boring moth, Dioryctria albovittella . Genetic analyses and long-term experimental removals and additions of these insects to individual trees have identified trees that are naturally resistant or susceptible to M. acalyptus and D. albovittella . In addition, these herbivores increase litter chemical quality and alter soil microclimate, both of which mediate decomposition in ecosystems. 3 The effects of herbivore susceptibility and resistance on needle litter mass and phosphorus (P) loss, when significant, are largely mediated by herbivore-induced changes to microclimate. But the effects of herbivore susceptibility and resistance on root litter nitrogen (N) and P retention, and needle litter N retention, are largely governed by herbivore-induced changes to litter chemical quality. Whether a particular tree was resistant or susceptible to herbivores exerted a large influence on net nutrient release, but the direction of herbivore influence varied temporally. 4 The controls on decomposition vary between herbivore-susceptible and herbivore-resistant phenotypes. This suggests that understanding decomposition and nutrient retention in some ecosystems may require considering the effects of herbivores on above- and below-ground processes and how these effects may be governed by plant genetics. 5 Synthesis . Because so few studies have attempted to quantify genetic components of ecosystem processes, the integration of ecosystem ecology with population genetics has the potential to place ecosystem science within a genetic and evolutionary framework. Using field trials of known genetic composition, ecosystem scientists may use quantitative genetics techniques to explore ecosystem traits just as population geneticists have used these techniques to explore traditional traits such as resistance to insects. VL - 95 UR - http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2007.01297.x/full IS - 6 ER - TY - JOUR T1 - Plant genetics predicts intra-annual variation in phytochemistry and arthropod community structure. JF - Molecular ecology Y1 - 2007 A1 - Wimp,G M A1 - Wooley,S A1 - RK Bangert A1 - Young,W P A1 - Martinsen,G D A1 - Keim,P A1 - Rehill,B A1 - R L Lindroth A1 - Whitham,T G KW - Animals KW - Arthropods KW - DNA, Plant KW - Ecosystem KW - Genetics, Population KW - Plant Extracts KW - Polymorphism, Restriction Fragment Length KW - Population Density KW - Population Dynamics KW - Populus KW - Seasons AB -

With the emerging field of community genetics, it is important to quantify the key mechanisms that link genetics and community structure. We studied cottonwoods in common gardens and in natural stands and examined the potential for plant chemistry to be a primary mechanism linking plant genetics and arthropod communities. If plant chemistry drives the relationship between plant genetics and arthropod community structure, then several predictions followed. We would find (i) the strongest correlation between plant genetic composition and chemical composition; (ii) an intermediate correlation between plant chemical composition and arthropod community composition; and (iii) the weakest relationship between plant genetic composition and arthropod community composition. Our results supported our first prediction: plant genetics and chemistry had the strongest correlation in the common garden and the wild. Our results largely supported our second prediction, but varied across space, seasonally, and according to arthropod feeding group. Plant chemistry played a larger role in structuring common garden arthropod communities relative to wild communities, free-living arthropods relative to leaf and stem modifiers, and early-season relative to late-season arthropods. Our results did not support our last prediction, as host plant genetics was at least as tightly linked to arthropod community structure as plant chemistry, if not more so. Our results demonstrate the consistency of the relationship between plant genetics and biodiversity. Additionally, plant chemistry can be an important mechanism by which plant genetics affects arthropod community composition, but other genetic-based factors are likely involved that remain to be measured.

VL - 16 SN - 0962-1083 UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=17927708&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 23 ER - TY - JOUR T1 - Do high-tannin leaves require more roots? JF - Oecologia Y1 - 2006 A1 - Fischer,FG A1 - Hart,SC A1 - Rehill,BJ A1 - Lindroth,RL A1 - Keim,P A1 - and Whitham,TG VL - 149 IS - 4 ER - TY - JOUR T1 - From genes to geography: a genetic similarity rule for arthropod community structure at multiple geographic scales. JF - Molecular ecology Y1 - 2006 A1 - RK Bangert A1 - Allan,G J A1 - Turek,R J A1 - Wimp,G M A1 - Meneses,N A1 - Martinsen,G D A1 - Keim,P A1 - Whitham,T G KW - Animals KW - Arthropods KW - biodiversity KW - Genetic Variation KW - Genetics, Population KW - Models, Genetic KW - Populus KW - Rivers KW - Southwestern United States AB -

We tested the hypothesis that leaf modifying arthropod communities are correlated with cottonwood host plant genetic variation from local to regional scales. Although recent studies found that host plant genetic composition can structure local dependent herbivore communities, the abiotic environment is a stronger factor than the genetic effect at increasingly larger spatial scales. In contrast to these studies we found that dependent arthropod community structure is correlated with both the cross type composition of cottonwoods and individual genotypes within local rivers up to the regional scale of 720,000 km(2) (Four Corner States region in the southwestern USA). Across this geographical extent comprising two naturally hybridizing cottonwood systems, the arthropod community follows a simple genetic similarity rule: genetically similar trees support more similar arthropod communities than trees that are genetically dissimilar. This relationship can be quantified with or without genetic data in Populus.

VL - 15 SN - 0962-1083 UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=17054514&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 13 ER - TY - JOUR T1 - Terrestrial transects for global change research JF - Vegetation Y1 - 1995 A1 - GW Koch A1 - Vitousek,PM A1 - Steffen,WL A1 - Walker,BH AB - The International Geosphere-Biosphere Program has proposed a set of large-scale terrestrial transects to study the effects of changes in climate, land use, and atmospheric composition (“global change”) on biogeochemistry, surface-atmosphere exchange, and vegetation dynamics of terrestrial ecosystems. The transects (≈ 1000 km) will be located along existing environmental and land use intensity gradients that span transitions between biomes in regions likely to be widely affected by forcing from components of global change or where the impacts of global change are likely to feed back to affect atmospheric, climatic, or hydrologic systems. Experimental studies on the transects will examine short-term changes in ecosystem function and biosphere-atmosphere interaction in response to variation in primary controlling variables. A hierarchy of modeling approaches will develop predictions of long-term changes in biome boundaries and vegetation distribution. The proposed initial set of IGBP terrestrial transects are located in four key regions: (1) humid tropical forests undergoing land use change, (2) high latitudes including the transition from boreal forest to tundra, (3) semi-arid tropical regions including transitions from dry forest to shrublands and savannas, and (4) mid latitude semi-arid regions encompassing transitions from shrubland or grassland to forests. We discuss here the rationale and general research design of transect studies proposed for each of these priority regions. VL - 121 UR - http://link.springer.com/article/10.1007/BF00044672 ER -