Open Access. Powered by Scholars. Published by Universities.®

Digital Commons Network

Open Access. Powered by Scholars. Published by Universities.®

Articles 1 - 30 of 118

Full-Text Articles in Entire DC Network

Ragweed And Sagebrush Pollen Can Distinguish Between Vegetation Types At Broad Spatial Scales, Hannah M. Carroll, Alan D. Wanamaker, Lynn G. Clark, Brian J. Wilsey May 2020

Ragweed And Sagebrush Pollen Can Distinguish Between Vegetation Types At Broad Spatial Scales, Hannah M. Carroll, Alan D. Wanamaker, Lynn G. Clark, Brian J. Wilsey

Ecology, Evolution and Organismal Biology Publications

Patterns of vegetation distribution at regional to subcontinental scales can inform understanding of climate. Delineating ecoregion boundaries over geologic time is complicated by the difficulty of distinguishing between prairie types at broad spatial scales using the pollen record. Pollen ratios are sometimes employed to distinguish between vegetation types, although their applicability is often limited to a geographic range. The Neotoma Paleoecology Database offers an unparalleled opportunity to synthesize a large number of pollen datasets. Ambrosia (ragweed) is a genus of mesic‐adapted species sensitive to summer moisture. Artemisia (sagebrush, wormwood, mugwort) is a genus of dry‐mesic‐adapted species resilient ...


Spectrally Derived Values Of Community Leaf Dry Matter Content Link Shifts In Grassland Composition With Change In Biomass Production, H. Wayne Polley, Chenghai Yang, Brian J. Wilsey, Philip A. Fay Jan 2020

Spectrally Derived Values Of Community Leaf Dry Matter Content Link Shifts In Grassland Composition With Change In Biomass Production, H. Wayne Polley, Chenghai Yang, Brian J. Wilsey, Philip A. Fay

Ecology, Evolution and Organismal Biology Publications

Leaf traits link environmental effects on plant species abundances to changes in ecosystem processes but are a challenge to measure regularly and over large areas. We used measurements of canopy reflectance from grassland communities to derive a regression model for one leaf trait, leaf dry matter content (LDMC). Partial least squares regression (PLSR) analysis was used to model community‐weighted (species abundance‐weighted) values of LDMC as a function of canopy reflectance in visible and near‐infrared (NIR) wavebands. The PLSR model then was applied to airborne measurements of canopy reflectance to determine how community LDMC interacts with inter‐annual ...


Nutrient Addition Increases Grassland Sensitivity To Droughts, Siddharth Bharath, Elizabeth T. Borer, Lori A. Biederman, Dana M. Blumenthal, Philip A. Fay, Laureano A. Gherardi, Johannes M. H. Knops, Andrew D. B. Leakey, Laura Yahdjian, Eric W. Seabloom Jan 2020

Nutrient Addition Increases Grassland Sensitivity To Droughts, Siddharth Bharath, Elizabeth T. Borer, Lori A. Biederman, Dana M. Blumenthal, Philip A. Fay, Laureano A. Gherardi, Johannes M. H. Knops, Andrew D. B. Leakey, Laura Yahdjian, Eric W. Seabloom

Ecology, Evolution and Organismal Biology Publications

Grasslands worldwide are expected to experience an increase in extreme events such as drought, along with simultaneous increases in mineral nutrient inputs as a result of human industrial activities. These changes are likely to interact because elevated nutrient inputs may alter plant diversity and increase the sensitivity to droughts. Dividing a system’s sensitivity to drought into resistance to change during the drought and rate of recovery after the drought generates insights into different dimensions of the system’s resilience in the face of drought. Here, we examine the effects of experimental nutrient fertilization and the resulting diversity loss on ...


Dominant Native And Non‐Native Graminoids Differ In Key Leaf Traits Irrespective Of Nutrient Availability, Arthur A. D. Broadbent, Jennifer Firn, James M. Mcgree, Elizabeth T. Borer, Yvonne M. Buckley, W. Stanley Harpole, Kimberly J. Komatsu, Andrew S. Macdougall, Kate H. Orwin, Nicholas J. Ostle, Eric W. Seabloom, Jonathan D. Bakker, Lori Biederman, Maria C. Caldeira, Nico Eisenhauer, Nicole Hagenah, Yann Hautier, Joslin L. Moore, Carla Nogueira, Pablo L. Peri, Anita C. Risch, Christine Roscher, Martin Schütz, Carly J. Stevens Jan 2020

Dominant Native And Non‐Native Graminoids Differ In Key Leaf Traits Irrespective Of Nutrient Availability, Arthur A. D. Broadbent, Jennifer Firn, James M. Mcgree, Elizabeth T. Borer, Yvonne M. Buckley, W. Stanley Harpole, Kimberly J. Komatsu, Andrew S. Macdougall, Kate H. Orwin, Nicholas J. Ostle, Eric W. Seabloom, Jonathan D. Bakker, Lori Biederman, Maria C. Caldeira, Nico Eisenhauer, Nicole Hagenah, Yann Hautier, Joslin L. Moore, Carla Nogueira, Pablo L. Peri, Anita C. Risch, Christine Roscher, Martin Schütz, Carly J. Stevens

Ecology, Evolution and Organismal Biology Publications

Aim: Nutrient enrichment is associated with plant invasions and biodiversity loss. Functional trait advantages may predict the ascendancy of invasive plants following nutrient enrichment but this is rarely tested. Here, we investigate (a) whether dominant native and non-native plants differ in important morphological and physiological leaf traits, (b) how their traits respond to nutrient addition, and (c) whether responses are consistent across functional groups.

Location: Australia, Europe, North America and South Africa.

Time period: 2007–2014.

Major taxa studied: Graminoids and forbs.

Methods: We focused on two types of leaf traits connected to resource acquisition: morphological features relating to light-foraging ...


Soil Health Recovery After Grassland Reestablishment On Cropland: The Effects Of Time And Topographic Position, Mriganka De, Jason A. Riopel, Larry J. Cihacek, Michael Lawrinenko, Rebecca Baldwin-Kordick, Steven J. Hall, Marshall D. Mcdaniel Jan 2020

Soil Health Recovery After Grassland Reestablishment On Cropland: The Effects Of Time And Topographic Position, Mriganka De, Jason A. Riopel, Larry J. Cihacek, Michael Lawrinenko, Rebecca Baldwin-Kordick, Steven J. Hall, Marshall D. Mcdaniel

Ecology, Evolution and Organismal Biology Publications

The Conservation Reserve Program (CRP) is a U.S. federal land conservation program that incentivizes grassland reestablishment on marginal lands. Although this program has many environmental benefits, two critical questions remain: does reestablishing grasslands via CRP also result in soil health recovery, and what parts of restored fields (i.e., topographic positions) recover the fastest? We hypothesized that soil health will recover over time after converting cropland to CRP grassland and that recovery will be greatest at higher topographic positions. To test this, we sampled 241 midwestern U.S. soils along a grassland chronosequence (0–40 yr, including native grasslands ...


Lower Soil Carbon Stocks In Exotic Vs. Native Grasslands Are Driven By Carbonate Losses, Brian Wilsey, Xia Xu, H. Wayne Polley, Kirsten Hofmockel, Steven J. Hall Jan 2020

Lower Soil Carbon Stocks In Exotic Vs. Native Grasslands Are Driven By Carbonate Losses, Brian Wilsey, Xia Xu, H. Wayne Polley, Kirsten Hofmockel, Steven J. Hall

Ecology, Evolution and Organismal Biology Publications

Global change includes invasion by exotic (nonnative) plant species and altered precipitation patterns, and these factors may affect terrestrial carbon (C) storage. We measured soil C changes in experimental mixtures of all exotic or all native grassland plant species under two levels of summer drought stress (0 and +128 mm). After 8 yr, soils were sampled in 10‐cm increments to 100‐cm depth to determine if soil C differed among treatments in deeper soils. Total soil C (organic + inorganic) content was significantly higher under native than exotic plantings, and differences increased with depth. Surprisingly, differences after 8 yr in ...


Genomic Diversifications Of Five Gossypium Allopolyploid Species And Their Impact On Cotton Improvement, Z. Jeffrey Chen, Avinash Sreedasyam, Atsumi Ando, Qingxin Song, Luis M. De Santiago, Amanda M. Hulse-Kemp, Sheron Simpson, Brian E. Scheffler, Corrinne E. Grover, Guanjing Hu, Justin L. Conover, Joseph W. Carlson, Shengqiang Shu, Jonathan F. Wendel, Jeremy Schmutz, Et Al. Jan 2020

Genomic Diversifications Of Five Gossypium Allopolyploid Species And Their Impact On Cotton Improvement, Z. Jeffrey Chen, Avinash Sreedasyam, Atsumi Ando, Qingxin Song, Luis M. De Santiago, Amanda M. Hulse-Kemp, Sheron Simpson, Brian E. Scheffler, Corrinne E. Grover, Guanjing Hu, Justin L. Conover, Joseph W. Carlson, Shengqiang Shu, Jonathan F. Wendel, Jeremy Schmutz, Et Al.

Ecology, Evolution and Organismal Biology Publications

Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in ...


Soil Depth And Grassland Origin Cooperatively Shape Microbial Community Co‐Occurrence And Function, Racheal N. Upton, Aleksandra Checinska Sielaff, Kirsten S. Hofmockel, Xia Xu, H. Wayne Polley, Brian J. Wilsey Jan 2020

Soil Depth And Grassland Origin Cooperatively Shape Microbial Community Co‐Occurrence And Function, Racheal N. Upton, Aleksandra Checinska Sielaff, Kirsten S. Hofmockel, Xia Xu, H. Wayne Polley, Brian J. Wilsey

Ecology, Evolution and Organismal Biology Publications

Many soils are deep, yet soil below 20 cm remains largely unexplored. Exotic plants can have shallower roots than native species, so their impact on microorganisms is anticipated to change with depth. Using environmental DNA and extracellular enzymatic activities, we studied fungal and bacterial community composition, diversity, function, and co-occurrence networks between native and exotic grasslands at soil depths up to 1 m. We hypothesized (1) the composition and network structure of both fungal and bacterial communities will change with increasing depth, and diversity and enzymatic function will decrease; (2) microbial enzymatic function and network connectedness will be lower in ...


Nutrient Availability Controls The Impact Of Mammalian Herbivores On Soil Carbon And Nitrogen Pools In Grasslands, Judith Sitters, Lori A. Biederman, Et Al. Jan 2020

Nutrient Availability Controls The Impact Of Mammalian Herbivores On Soil Carbon And Nitrogen Pools In Grasslands, Judith Sitters, Lori A. Biederman, Et Al.

Ecology, Evolution and Organismal Biology Publications

Grasslands are subject to considerable alteration due to human activities globally, including widespread changes in populations and composition of large mammalian herbivores and elevated supply of nutrients. Grassland soils remain important reservoirs of carbon (C) and nitrogen (N). Herbivores may affect both C and N pools and these changes likely interact with increases in soil nutrient availability. Given the scale of grassland soil fluxes, such changes can have striking consequences for atmospheric C concentrations and the climate. Here, we use the Nutrient Network experiment to examine the responses of soil C and N pools to mammalian herbivore exclusion across 22 ...


The Genome Sequence Of Gossypioides Kirkii Illustrates A Descending Dysploidy In Plants, Joshua A. Udall, Evan Long, Thiruvarangan Ramaraj, Justin L. Conover, Daojun Yuan, Corrinne E. Grover, Lei Gong, Mark A. Arick Ii, Rick E. Masonbrink, Daniel G. Peterson, Jonathan F. Wendel Nov 2019

The Genome Sequence Of Gossypioides Kirkii Illustrates A Descending Dysploidy In Plants, Joshua A. Udall, Evan Long, Thiruvarangan Ramaraj, Justin L. Conover, Daojun Yuan, Corrinne E. Grover, Lei Gong, Mark A. Arick Ii, Rick E. Masonbrink, Daniel G. Peterson, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

One of the extraordinary aspects of plant genome evolution is variation in chromosome number, particularly that among closely related species. This is exemplified by the cotton genus (Gossypium) and its relatives, where most species and genera have a base chromosome number of 13. The two exceptions are sister genera that have n = 12 (the Hawaiian Kokia and the East African and Madagascan Gossypioides). We generated a high-quality genome sequence of Gossypioides kirkii (n = 12) using PacBio, Bionano, and Hi-C technologies, and compared this assembly to genome sequences of Kokia (n = 12) and Gossypium diploids (n = 13). Previous analysis demonstrated that ...


Beyond The Black Box: Promoting Mathematical Collaborations For Elucidating Interactions In Soil Ecology, Alison E. Bennett, Lori Biederman, Matthew Warren, Et Al. Jul 2019

Beyond The Black Box: Promoting Mathematical Collaborations For Elucidating Interactions In Soil Ecology, Alison E. Bennett, Lori Biederman, Matthew Warren, Et Al.

Ecology, Evolution and Organismal Biology Publications

Understanding soil systems is critical because they form the structural and nutritional foundation for plants and thus every terrestrial habitat and agricultural system. In this paper, we encourage increased use of mathematical models to drive forward understanding of interactions in soil ecological systems. We discuss several distinctive features of soil ecosystems and empirical studies of them. We explore some perceptions that have previously deterred more extensive use of models in soil ecology and some advances that have already been made using models to elucidate soil ecological interactions. We provide examples where mathematical models have been used to test the plausibility ...


Interacting Stressors Matter: Diet Quality And Virus Infection In Honeybee Health, Adam G. Dolezal, Jimena Carrillo-Tripp, Timothy M. Judd, W. Allen Miller, Bryony C. Bonning, Amy L. Toth Feb 2019

Interacting Stressors Matter: Diet Quality And Virus Infection In Honeybee Health, Adam G. Dolezal, Jimena Carrillo-Tripp, Timothy M. Judd, W. Allen Miller, Bryony C. Bonning, Amy L. Toth

Ecology, Evolution and Organismal Biology Publications

Honeybee population declines have been linked to multiple stressors, including reduced diet diversity and increased exposure to understudied viral pathogens. Despite interest in these factors, few experimental studies have explored the interaction between diet diversity and viral infection in honeybees. Here, we used a mixture of laboratory cage and small semi-field nucleus hive experiments to determine how these factors interact. In laboratory experiments, we found that high-quality diets (polyfloral pollen and high-quality single-source pollen) have the potential to reduce mortality in the face of infection with Israeli acute paralysis virus (IAPV). There was a significant interaction between diet and virus ...


Mycorrhizal Colonization And Its Relationship With Plant Performance Differs Between Exotic And Native Grassland Plant Species, Aleksandra Checinska Sielaff, H. Wayne Polley, Andres Fuentes-Ramirez, Kirsten Hofmockel, Brian J. Wilsey Jan 2019

Mycorrhizal Colonization And Its Relationship With Plant Performance Differs Between Exotic And Native Grassland Plant Species, Aleksandra Checinska Sielaff, H. Wayne Polley, Andres Fuentes-Ramirez, Kirsten Hofmockel, Brian J. Wilsey

Ecology, Evolution and Organismal Biology Publications

Many grasslands have been transformed by exotic species with potentially novel ecological interactions. We hypothesized that exotic and native plant species differ, on average, in their percentage mycorrhizal colonization, and that mycorrhizal colonization is positively related to plant performance in the field. We compared colonization by arbuscular mycorrhizae (AM) fungi in perennial native and exotic species that were paired phylogenetically and by functional groups and grown under a common environment in field plots in Central Texas, USA. Roots were collected from plants in monoculture plots, stained, and percent colonization was assessed with a microscope. Aboveground biomass and dominance in mixture ...


Mechanisms Underlying Limited Soil Carbon Gains In Perennial And Cover‐Cropped Bioenergy Systems Revealed By Stable Isotopes, Chenglong Ye, Steven J. Hall Jan 2019

Mechanisms Underlying Limited Soil Carbon Gains In Perennial And Cover‐Cropped Bioenergy Systems Revealed By Stable Isotopes, Chenglong Ye, Steven J. Hall

Ecology, Evolution and Organismal Biology Publications

Removal of biomass for bioenergy production may decrease soil organic carbon. While perennials or cover‐cropped grains often have greater root production than annual grain crops, they variably impact soil carbon and underlying mechanisms remain unclear. We used high‐frequency measurements of soil respiration and natural abundance carbon stable isotopes to differentiate respiration sources, pool sizes, and decomposition rate constants during a 10 month incubation of soils collected to 1 m depth from a 10 year old field experiment in Iowa, United States. Conversion of corn–soybean rotations to reconstructed prairies or addition of a rye cover crop to continuous ...


Unraveling Cis And Trans Regulatory Evolution During Cotton Domestication, Ying Bao, Guanjing Hu, Corrinne E. Grover, Justin Conover, Daojun Yuan, Jonathan F. Wendel Jan 2019

Unraveling Cis And Trans Regulatory Evolution During Cotton Domestication, Ying Bao, Guanjing Hu, Corrinne E. Grover, Justin Conover, Daojun Yuan, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

Cis and trans regulatory divergence underlies phenotypic and evolutionary diversification. Relatively little is understood about the complexity of regulatory evolution accompanying crop domestication, particularly for polyploid plants. Here, we compare the fiber transcriptomes between wild and domesticated cotton (Gossypium hirsutum) and their reciprocal F1 hybrids, revealing genome-wide (~15%) and often compensatory cis and trans regulatory changes under divergence and domestication. The high level of trans evolution (54%–64%) observed is likely enabled by genomic redundancy following polyploidy. Our results reveal that regulatory variation is significantly associated with sequence evolution, inheritance of parental expression patterns, co-expression gene network properties, and genomic ...


The Chromosome-Scale Reference Genome Of Black Pepper Provides Insight Into Piperine Biosynthesis, Lisong Hu, Zhongping Xu, Maojun Wang, Rui Fan, Daojun Yuan, Baoduo Wu, Huasong Wu, Xiaowei Qin, Lin Yan, Lehe Tan, Soonliang Sim, Wen Li, Christopher A. Saski, Henry Daniell, Jonathan F. Wendel, Keith Lindsey, Xianlong Zhang, Chaoyun Hao, Shuangxia Jin Jan 2019

The Chromosome-Scale Reference Genome Of Black Pepper Provides Insight Into Piperine Biosynthesis, Lisong Hu, Zhongping Xu, Maojun Wang, Rui Fan, Daojun Yuan, Baoduo Wu, Huasong Wu, Xiaowei Qin, Lin Yan, Lehe Tan, Soonliang Sim, Wen Li, Christopher A. Saski, Henry Daniell, Jonathan F. Wendel, Keith Lindsey, Xianlong Zhang, Chaoyun Hao, Shuangxia Jin

Ecology, Evolution and Organismal Biology Publications

Black pepper (Piper nigrum), dubbed the ‘King of Spices’ and ‘Black Gold’, is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochromosomes. A phylogenomic analysis of representative plant genomes places magnoliids as sister to the monocots-eudicots clade and indicates that black pepper has diverged from the shared Laurales-Magnoliales lineage approximately 180 million years ago. Comparative genomic analyses reveal specific gene expansions in the ...


More Salt, Please: Global Patterns, Responses And Impacts Of Foliar Sodium In Grasslands, E. T. Borer, E. M. Lind, J. Firn, E. W. Seabloom, T. M. Anderson, E. S. Bakker, L. A. Biederman, K. J. La Pierre, A. S. Macdougall, J. L. Moore, A. C. Risch, M. Schutz, C. J. Stevens Jan 2019

More Salt, Please: Global Patterns, Responses And Impacts Of Foliar Sodium In Grasslands, E. T. Borer, E. M. Lind, J. Firn, E. W. Seabloom, T. M. Anderson, E. S. Bakker, L. A. Biederman, K. J. La Pierre, A. S. Macdougall, J. L. Moore, A. C. Risch, M. Schutz, C. J. Stevens

Ecology, Evolution and Organismal Biology Publications

Sodium is unique among abundant elemental nutrients, because most plant species do not require it for growth or development, whereas animals physiologically require sodium. Foliar sodium influences consumption rates by animals and can structure herbivores across landscapes. We quantified foliar sodium in 201 locally abundant, herbaceous species representing 32 families and, at 26 sites on four continents, experimentally manipulated vertebrate herbivores and elemental nutrients to determine their effect on foliar sodium. Foliar sodium varied taxonomically and geographically, spanning five orders of magnitude. Site‐level foliar sodium increased most strongly with site aridity and soil sodium; nutrient addition weakened the relationship ...


Spectral Heterogeneity Predicts Local-Scale Gamma And Beta Diversity Of Mesic Grasslands, H. Wayne Polley, Chenghai Yang, Brian J. Wilsey, Philip A. Fay Jan 2019

Spectral Heterogeneity Predicts Local-Scale Gamma And Beta Diversity Of Mesic Grasslands, H. Wayne Polley, Chenghai Yang, Brian J. Wilsey, Philip A. Fay

Ecology, Evolution and Organismal Biology Publications

Plant species diversity is an important metric of ecosystem functioning, but field assessments of diversity are constrained in number and spatial extent by labor and other expenses. We tested the utility of using spatial heterogeneity in the remotely-sensed reflectance spectrum of grassland canopies to model both spatial turnover in species composition and abundances (β diversity) and species diversity at aggregate spatial scales (γ diversity). Shannon indices of γ and β diversity were calculated from field measurements of the number and relative abundances of plant species at each of two spatial grains (0.45 m2 and 35.2 m2 ...


Intergenomic Gene Transfer In Diploid And Allopolyploid Gossypium, Nan Zhao, Corrinne E. Grover, Zhiwen Chen, Jonathan F. Wendel, Jinping Hua Jan 2019

Intergenomic Gene Transfer In Diploid And Allopolyploid Gossypium, Nan Zhao, Corrinne E. Grover, Zhiwen Chen, Jonathan F. Wendel, Jinping Hua

Ecology, Evolution and Organismal Biology Publications

Background: Intergenomic gene transfer (IGT) between nuclear and organellar genomes is a common phenomenon during plant evolution. Gossypium is a useful model to evaluate the genomic consequences of IGT for both diploid and polyploid species. Here, we explore IGT among nuclear, mitochondrial, and plastid genomes of four cotton species, including two allopolyploids and their model diploid progenitors (genome donors, G. arboreum: A2 and G. raimondii: D5).

Results: Extensive IGT events exist for both diploid and allotetraploid cotton (Gossypium) species, with the nuclear genome being the predominant recipient of transferred DNA followed by the mitochondrial genome. The nuclear genome has integrated ...


Leaf Nutrients, Not Specific Leaf Area, Are Consistent Indicators Of Elevated Nutrient Inputs, Jennifer Firn, Kimberly J. La Pierre, Lori Biederman, Et Al. Jan 2019

Leaf Nutrients, Not Specific Leaf Area, Are Consistent Indicators Of Elevated Nutrient Inputs, Jennifer Firn, Kimberly J. La Pierre, Lori Biederman, Et Al.

Ecology, Evolution and Organismal Biology Publications

Leaf traits are frequently measured in ecology to provide a ‘common currency’ for predicting how anthropogenic pressures impact ecosystem function. Here, we test whether leaf traits consistently respond to experimental treatments across 27 globally distributed grassland sites across 4 continents. We find that specific leaf area (leaf area per unit mass)—a commonly measured morphological trait inferring shifts between plant growth strategies—did not respond to up to four years of soil nutrient additions. Leaf nitrogen, phosphorus and potassium concentrations increased in response to the addition of each respective soil nutrient. We found few significant changes in leaf traits when ...


Increasing Carbon Footprint Of Grain Crop Production In The Us Western Corn Belt, Chaoqun (Crystal) Lu, Zhen Yu, Hanqin Tian, David A. Hennessy, Hongli Feng, Mahdi Al-Kaisi, Yuyu Zhou, Tom Sauer, Raymond Arritt Nov 2018

Increasing Carbon Footprint Of Grain Crop Production In The Us Western Corn Belt, Chaoqun (Crystal) Lu, Zhen Yu, Hanqin Tian, David A. Hennessy, Hongli Feng, Mahdi Al-Kaisi, Yuyu Zhou, Tom Sauer, Raymond Arritt

Ecology, Evolution and Organismal Biology Publications

Global agriculture is challenged to increase soil carbon sequestration and reduce greenhouse gas emissions while providing products for an increasing population. Growing crop production could be achieved through higher yield per hectare (i.e. intensive farming) or more hectares (extensive farming), which however, have different ecological and environmental consequences. Multiple lines of evidence indicate that expanding cropland for additional production may lead to loss of vegetation and soil carbon, and threaten the survival of wildlife. New concerns about the impacts of extensive farming have been raised for the US Corn Belt, one of the world's most productive regions, as ...


A Malvaceae Mystery: A Mallow Maelstrom Of Genome Multiplications And Maybe Misleading Methods?, Justin L. Conover, Nisa Karimi, Noah Stenz, Cécile Ané, Corrinne E. Grover, C. Skema, Jennifer A. Tate, Kirsten Wolff, Samuel A. Logan, Jonathan F. Wendel, David A. Baum Nov 2018

A Malvaceae Mystery: A Mallow Maelstrom Of Genome Multiplications And Maybe Misleading Methods?, Justin L. Conover, Nisa Karimi, Noah Stenz, Cécile Ané, Corrinne E. Grover, C. Skema, Jennifer A. Tate, Kirsten Wolff, Samuel A. Logan, Jonathan F. Wendel, David A. Baum

Ecology, Evolution and Organismal Biology Publications

Previous research suggests that Gossypium has undergone a 5- to 6-fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested ...


Insights Into The Evolution Of The New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based On Genome Sequencing, Corrinne E. Grover, Mark A. Arick Ii, Adam Thrash, Justin L. Conover, William S. Sanders, Daniel G. Peterson, James E. Frelichowski, Jodi A. Scheffler, Brian E. Scheffler, Jonathan F. Wendel Nov 2018

Insights Into The Evolution Of The New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based On Genome Sequencing, Corrinne E. Grover, Mark A. Arick Ii, Adam Thrash, Justin L. Conover, William S. Sanders, Daniel G. Peterson, James E. Frelichowski, Jodi A. Scheffler, Brian E. Scheffler, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the geographically widely dispersed New World diploid cottons (Gossypium, subg. Houzingenia). Whole genome resequencing data (average of 33X genomic coverage) were generated to reassess the phylogenetic history of the subgenus and provide a temporal framework for its diversification. Phylogenetic analyses indicate that the subgenus likely originated following trans-oceanic dispersal from Africa about 6.6 mya, but that nearly all of the biodiversity evolved following rapid diversification in the mid-Pleistocene (0.5-2.0 mya), with multiple long-distance dispersals required to account for range expansion to Arizona, the Galapagos Islands ...


Microbial Community Structure And Functions Differ Between Native And Novel (Exotic-Dominated) Grassland Ecosystems In An 8-Year Experiment, Aleksandra Checinska Sielaff, Racheal N. Upton, Kirsten S. Hofmockel, Xia Xu, H. Wayne Polley, Brian J. Wilsey Nov 2018

Microbial Community Structure And Functions Differ Between Native And Novel (Exotic-Dominated) Grassland Ecosystems In An 8-Year Experiment, Aleksandra Checinska Sielaff, Racheal N. Upton, Kirsten S. Hofmockel, Xia Xu, H. Wayne Polley, Brian J. Wilsey

Ecology, Evolution and Organismal Biology Publications

A Grasslands dominated by non-native (exotic) spe- cies have replaced purely native-dominated areas in many parts of the world forming ‘novel’ ecosystems. Altered precipitation patterns are predicted to exacerbate this trend. It is still poorly understood how soil microbial communities and their functions differ between high diversity native- and low diversity exotic-dominated sites and how altered precipitation will impact this difference.

Methods We sampled 64 experimental grassland plots in central Texas with plant species mixtures of either all native or all exotic species; half with summer irrigation. We tested how native vs. exotic plant species mixtures and summer irrigation affected ...


Cis–Trans Controls And Regulatory Novelty Accompanying Allopolyploidization, Guanjing Hu, Jonathan F. Wendel Oct 2018

Cis–Trans Controls And Regulatory Novelty Accompanying Allopolyploidization, Guanjing Hu, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

Allopolyploidy is a prevalent process in plants, having important physiological, ecological, and evolutionary consequences. Transcriptomic responses to genomic merger and doubling have been demonstrated in many allopolyploid systems, encompassing a diversity of phenomena including homoeolog expression bias, genome dominance, expression‐level dominance, and revamping of co‐expression networks. Notwithstanding the foregoing, there remains a need to develop a conceptual framework that will stimulate a deeper understanding of these diverse phenomena and their mechanistic interrelationships. Here we introduce considerations relevant to this framework with a focus on cistrans interactions among duplicated genes and alleles in hybrids and allopolyploids. By extending ...


Multiple Facets Of Biodiversity Drive The Diversity–Stability Relationship, Dylan Craven, H. Wayne Polley, Brian Wilsey, Et Al. Oct 2018

Multiple Facets Of Biodiversity Drive The Diversity–Stability Relationship, Dylan Craven, H. Wayne Polley, Brian Wilsey, Et Al.

Ecology, Evolution and Organismal Biology Publications

A substantial body of evidence has demonstrated that biodiversity stabilizes ecosystem functioning over time in grassland ecosystems. However, the relative importance of different facets of biodiversity underlying the diversity–stability relationship remains unclear. Here we use data from 39 grassland biodiversity experiments and structural equation modelling to investigate the roles of species richness, phylogenetic diversity and both the diversity and community-weighted mean of functional traits representing the ‘fast–slow’ leaf economics spectrum in driving the diversity–stability relationship. We found that high species richness and phylogenetic diversity stabilize biomass production via enhanced asynchrony in the performance of co-occurring species. Contrary ...


Spatial Heterogeneity In Species Composition Constrains Plant Community Responses To Herbivory And Fertilisation, Dorothee Hodapp, Lori A. Biederman, Philip A. Fay, Et Al. Sep 2018

Spatial Heterogeneity In Species Composition Constrains Plant Community Responses To Herbivory And Fertilisation, Dorothee Hodapp, Lori A. Biederman, Philip A. Fay, Et Al.

Ecology, Evolution and Organismal Biology Publications

Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major forms of environmental change – fertilisation and herbivore loss – are affected by species pool size and spatial compositional heterogeneity. Fertilisation led to higher rates of ...


Reconciling Multiple Impacts Of Nitrogen Enrichment On Soil Carbon: Plant, Microbial And Geochemical Controls, Chenglong Ye, Dima Chen, Steven J. Hall, Shang Pan, Xuebin Yan, Tongshuo Bai, Hui Guo, Yi Zhang, Yongfei Bai, Shuijin Hu Aug 2018

Reconciling Multiple Impacts Of Nitrogen Enrichment On Soil Carbon: Plant, Microbial And Geochemical Controls, Chenglong Ye, Dima Chen, Steven J. Hall, Shang Pan, Xuebin Yan, Tongshuo Bai, Hui Guo, Yi Zhang, Yongfei Bai, Shuijin Hu

Ecology, Evolution and Organismal Biology Publications

Impacts of reactive nitrogen (N) inputs on ecosystem carbon (C) dynamics are highly variable, and the underlying mechanisms remain unclear. Here, we proposed a new conceptual framework that integrates plant, microbial, and geochemical mechanisms to reconcile diverse and contrasting impacts of N on soil C. This framework was tested using long-term N enrichment and acid addition experiments in a Mongolian steppe grassland. Distinct mechanisms could explain effects of N on particulate and mineral-associated soil C pools, potentially explaining discrepancies among previous N addition studies. While plant production predominated particulate C changes, Ninduced soil acidification strongly affected mineral-associated C through decreased ...


Designations For Individual Genomes And Chromosomes In Gossypium, Kunbo Wang, Jonathan F. Wendel, Jinping Hua Jun 2018

Designations For Individual Genomes And Chromosomes In Gossypium, Kunbo Wang, Jonathan F. Wendel, Jinping Hua

Ecology, Evolution and Organismal Biology Publications

Gossypium, as the one of the biggest genera, the most diversity, and the highest economic value in field crops, is assuming an increasingly important role in studies on plant taxonomy, polyploidization, phylogeny, cytogenetics, and genomics. Here we update and provide a brief summary of the emerging picture of species relationships and diversification, and a set of the designations for individual genomes and chromosomes in Gossypium. This cytogenetic and genomic nomenclature will facilitate comparative studies worldwide, which range from basic taxonomic exploration to breeding and germplasm introgression.


The Global N20 Model Intercomparison Project, Hanqin Tian, Jia Yang, Chaoqun (Crystal) Lu, Rongting Xu, Josep G. Canadell, Robert B. Jackson, Almut Arneth, Jinfeng Chang, Guangsheng Chen, Philippe Ciais, Stefan Gerber, Akihiko Ito, Yuanyuan Huang, Fortunat Joos, Sebastian Lienert, Palmira Messina, Stefan Olin, Shufen Pan, Changhui Peng, Eri Saikawa, Rona L. Thompson, Nicolas Vuichard, Wilfried Winiwarter, Sonke Zaehle, Bowen Zhang, Kerou Zhang, Qiuan Zhu Jun 2018

The Global N20 Model Intercomparison Project, Hanqin Tian, Jia Yang, Chaoqun (Crystal) Lu, Rongting Xu, Josep G. Canadell, Robert B. Jackson, Almut Arneth, Jinfeng Chang, Guangsheng Chen, Philippe Ciais, Stefan Gerber, Akihiko Ito, Yuanyuan Huang, Fortunat Joos, Sebastian Lienert, Palmira Messina, Stefan Olin, Shufen Pan, Changhui Peng, Eri Saikawa, Rona L. Thompson, Nicolas Vuichard, Wilfried Winiwarter, Sonke Zaehle, Bowen Zhang, Kerou Zhang, Qiuan Zhu

Ecology, Evolution and Organismal Biology Publications

Nitrous oxide (N2O) is an important greenhouse gas and also an ozone-depleting substance that has both natural and anthropogenic sources. Large estimation uncertainty remains on the magnitude and spatiotemporal patterns of N2O fluxes and the key drivers of N2O production in the terrestrial biosphere. Some terrestrial biosphere models have been evolved to account for nitrogen processes and to show the capability to simulate N2O emissions from land ecosystems at the global scale, but large discrepancies exist among their estimates primarily because of inconsistent input datasets, simulation protocol, and model structure and parameterization schemes. Based on the consistent model input data ...