Ecology and Evolutionary Biology Commons^™

Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger

Yevgeniy (Eugene) Shakirov

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C₄ grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. …

Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua A. Udall, Lex E. Flagel, Foo Cheung, Andrew W. Woodard, Ran Hovav, Ryan Adam Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel

Dan Nettleton

Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the …

Duplicate Gene Expression In Allopolyploid Gossypium Reveals Two Temporally Distinct Phases Of Expression Evolution, Lex E. Flagel, Joshua A. Udall, Dan Nettleton, Jonathan F. Wendel

Dan Nettleton

Polyploidy has played a prominent role in shaping the genomic architecture of the angiosperms. Through allopolyploidization, several modern Gossypium (cotton) species contain two divergent, although largely redundant genomes. Owing to this redundancy, these genomes can play host to an array of evolutionary processes that act on duplicate genes. We compared homoeolog (genes duplicated by polyploidy) contributions to the transcriptome of a natural allopolyploid and a synthetic interspecific F1 hybrid, both derived from a merger between diploid species from the Gossypium A-genome and D-genome groups. Relative levels of A- and D-genome contributions to the petal transcriptome were determined for 1,383 gene …

Belowground Bud Bank Of Bromus Inermis In Response To Mowing Frequency Over Two Growing Seasons, Denise Olson, Lan Xu, Arvid Boe, N. H. Troelstrup Jr.

Arvid Boe

Smooth bromegrass (Bromus inermis) is a Eurasian C3 perennial grass. It was introduced to North America in 1884 to control soil erosion and for pasture improvement, but has been outcompeting the native grasses of the northern Great Plains, decreasing diversity and altering habitats. Control of smooth bromegrass is a key to improve degraded native dominated grasslands. However, current practices have minimal or only short term effects due to extensive rhizome and tiller production by bromegrass. Even though vegetative reproduction via the belowground bud bank is the primary means for its invasiveness and persistence, the effect of management on its bud …

The Subject Librarian Newsletter, Biology, Fall 2016, Sandy Avila

Sandy Avila

No abstract provided.

The Subject Librarian Newsletter, Biology, Spring 2017, Sandy Avila

Sandy Avila

No abstract provided.

Lethal And Sublethal Effects Of Novel Terrestrial Subsidies From An Invasive Shrub (Lonicera Maackii) On Stream Macroinvertebrates, Ryan W. Mcewan, Kevin W. Custer, Eric B. Borth, Sean D. Mahoney

Ryan McEwan

The biology of headwater streams is intimately linked to that of the surrounding terrestrial environment through organic matter subsidies. Lonicera maackii, an invasive shrub that is becoming abundant in headwater stream riparian areas, deposits substantial quantities of organic matter into the aquatic system. This organic material has allelopathic effects on terrestrial plants and insects, and a growing body of work suggests strong connections between L. maackii invasion and aquatic biota. Lonicera maackii deposits fruit and flowers in quantities and timings that are unique, and we tested the hypothesis that these subsidies would negatively affect survival and growth of laboratory-cultured …

Floristic Response To Urbanization: Filtering Of The Bioregional Flora In Indianapolis, Indiana, Usa, Rebecca W. Dolan, Myla F.J. Aronson, Andrew L. Hipp

Rebecca W. Dolan

PREMISE OF THE STUDY: Globally, urban plant populations are becoming increasingly important, as these plants play a vital role in ameliorating effects of ecosystem disturbance and climate change. Urban environments act as filters to bioregional flora, presenting survival challenges to spontaneous plants. Yet, because of the paucity of inventory data on plants in landscapes both before and after urbanization, few studies have directly investigated this effect of urbanization. METHODS: We used historical, contemporary, and regional plant species inventories for Indianapolis, Indiana USA to evaluate how urbanization filters the bioregional flora based on species diversity, functional traits, and phylogenetic community structure. …

2017_Murphy Et Al._Food Habits Of A Small Fl Bear Population In Endangered Ecosystem.Pdf, Sean M. Murphy, Wade A. Ulrey, Joseph M. Guthrie, David S. Maehr, Warren G. Abrahamson Ii, Sutton C. Maehr, John J. Cox

Warren G. Abrahamson, II

Competition And Propagule Density Affect Sexual And Clonal Propagation Of A Weed, Daniel Z. Atwater, Wonjae Kim, Daniel R. Tekiela, Jacob N. Barney

Wonjae Kim

Invasive Species In An Urban Flora: History And Current Status In Indianapolis, Indiana, Rebecca W. Dolan

Rebecca W. Dolan

Invasive plant species are widely appreciated to cause significant ecologic and economic damage in agricultural fields and in natural areas. The presence and impact of invasives in cities is less well documented. This paper characterizes invasive plants in Indianapolis, Indiana. Based on historical records and contemporary accounts, 69 of the 120 species on the official Indiana state list are reported for the city. Most of these plants are native to Asia or Eurasia, with escape from cultivation as the most common mode of introduction. Most have been in the flora of Indianapolis for some time. Eighty percent of Indianapolis’ invasive …

The Vascular Flora And Community Structure Of Little Calumet Headwaters Nature Preserve, Laporte Country, Indiana, Julia L. Angstmann, Paul E. Rothrock, Thomas W. Post

Julia Angstmann

Little Calumet Headwaters Nature Preserve is a 108-acre tract of woodland and wetland areas that comprise the headwaters of the Little Calumet River in northwestern Indiana. The preserve, consisting of upland hardwood forests, groundwater seeps, and wetland complex, is an area of high diversity due to its topographical variation. A floristic inventory, plot sampling, and seed bank analysis were used to determine the structure and composition of the plant communities. The flora consists of 298 species (27 exotic) representing 188 genera and 84 families. Dominant vegetation of the forest includes Liriodendron tulipifera, Prunus serotina, Packera aurea and Podophyllum peltatum. Each …

Urbanization—The Bad, The Good, And The Very Good, Rebecca Dolan

Rebecca W. Dolan

Great strides have been made in studying effects of urbanization on plant life in recent years. However, much remains to be learned about how the urban environment acts as a filter on flora. There is some evidence that environments in cities are so similar that they all select for the same plants or plants with the same suite of characteristics, resulting in biotic homogenization, but the jury is still out. We do know that some cities harbor a thriving and diverse native flora. Dolan will talk about what cities can do to increase the chances for long-term survival of native …

Hypericum Cumulicola Demography In Unoccupied And Occupied Florida Scrub Patches With Different Time-Since-Fire, Pedro Quintana-Ascencio, Rebecca Dolan, Eric Menges

Rebecca W. Dolan

1 Metapopulation models predict that unoccupied, but suitable, patches will exist for species subject to extinction and colonization dynamics. We compared the demographic responses of Hypericum cumulicola, a rare herbaceous species almost entirely restricted to Florida rosemary scrub, when transplanted to occupied or unoccupied patches. 2 Seedlings were transplanted and seeds buried into Florida rosemary scrub patches differing in time since last fire, and in the presence or absence of H. cumulicola. We used a replicated, factorial design to place the transplants and seeds in the field, and monitored their performance for 18 months. 3 Neither time-since-fire nor prior H. …

Bacon's Swamp- Ghost Of A Central Indiana Natural Area Past, Rebecca W. Dolan

Rebecca W. Dolan

Bacon’s Swamp was identified in the 1920s as a ca. 12 ha glacial kettle lake bog system at the southernmost limits of these habitats in Indiana. Located just 9.6 km from the center of Indianapolis, the site was all but destroyed in the mid-20th century by urban expansion. Prior to habitat conversion at the site, Bacon’s Swamp was a frequent location for Butler University ecology class field trips and student research projects. Herbarium specimens and published inventory records allow for analysis of the historical vegetation of Bacon’s Swamp using modern techniques. Floristic Quality Assessment applied to these historical records reveals …

Community Involvement To Address A Long-Standing Invasive Species Problem: Aspects Of Civic Ecology In Practice, Rebecca W. Dolan, Kelly Harris, Mark Adler

Rebecca W. Dolan

Invasive non-native species (INS) are found in every city around the globe, but their impacts in urban settings as biological agents of visual pollution that block views of natural landscapes and disconnect citizens from nature are not as often addressed as comprehensively as their impacts in natural areas or agricultural settings. The multiple impacts of INS in cities make them ideal candidates for aspects of Civic Ecology Practice, where local environmental stewardship action is taken to enhance green infrastructure and community well-being in urban and other human-dominated systems. We present details of a community driven program focused on removal of …

Changes In Plant Species Composition And Structure In Two Peri-Urban Nature Preserves Over 10 Years, Rebecca W. Dolan, Jessica D. Stepens, Marcia E. Moore

Rebecca W. Dolan

Peri-urban natural areas, at the boundaries of cities and adjacent agricultural/rural land, are subject to ecological threats endemic to both land use types. We used permanent plots to document changes in habitat quality by monitoring herbaceous-layer plant species presence and cover over a decade (1996/97 and 2007) in two peri-urban nature preserves in central Indiana, U.S.A. The preserves are comprised of different forest community types: wet-mesic depressional forest and mesic upland forest. Habitat characteristics, based on Floristic Quality Assessment parameters, showed only a single change for either preserve between survey years: wetness values were lower in the wet-mesic depressional site …

A Regional Comparison Of Water Use Efficiency For Miscanthus, Switchgrass And Maize, Andy Vanloocke, Tracy E. Twine, Marcelo Zeri, Carl J. Bernacchi

Andy VanLoocke

The production of cellulosic feedstocks for renewable fuels will increase over the coming decades. However, it is uncertain which feedstocks will be best suited for bioenergy production. A key factor dictating feedstock selection for a given region is water use efficiency (WUE), the trade-off between evapotranspiration (ET) and carbon uptake or productivity. Using an ecosystem model, two of the top candidate cellulosic feedstocks, Miscanthus × giganteus (miscanthus) and Panicum virgatum(switchgrass) were compared to Zea mays L. (maize), the existing dominant bioenergy feedstock, with 0 and 25% residue removal for the Midwest US. We determined productivity in three ways: harvested yield …

Future Carbon Dioxide Concentration Decreases Canopy Evapotranspiration And Soil Water Depletion By Field-Grown Maize, Mir Zaman Hussain, Andy Vanloocke, Matthew H. Siebers, Ursula M. Ruiz-Vera, R. J. Cody Markelz, Donald R. Ort, Carl J. Bernacchi

Andy VanLoocke

Maize, in rotation with soybean, forms the largest continuous ecosystem in temperate North America, therefore changes to the biosphere-atmosphere exchange of water vapor and energy of these crops are likely to have an impact on the Midwestern US climate and hydrological cycle. As a C4 crop, maize photosynthesis is already CO2-saturated at current CO2 concentrations ([CO2]) and the primary response of maize to elevated [CO2] is decreased stomatal conductance (gs). If maize photosynthesis is not stimulated in elevated [CO2], then reduced gs is not offset by greater canopy leaf area, which could potentially result in a greater ET reduction relative …

Terrestrial Ecosystems In A Changing Environment: A Dominant Role For Water, Carl J. Bernacchi, Andy Vanloocke

Andy VanLoocke

Transpiration—the movement of water from the soil, through plants, and into the atmosphere—is the dominant water flux from the earth's terrestrial surface. The evolution of vascular plants, while increasing terrestrial primary productivity, led to higher transpiration rates and widespread alterations in the global climate system. Similarly, anthropogenic influences on transpiration rates are already influencing terrestrial hydrologic cycles, with an even greater potential for changes lying ahead. Intricate linkages among anthropogenic activities, terrestrial productivity, the hydrologic cycle, and global demand for ecosystem services will lead to increased pressures on ecosystem water demands. Here, we focus on identifying the key drivers of …

The Biophysical Link Between Climate, Water, And Vegetation In Bioenergy Agro-Ecosystems, Justin E. Bagley, Sarah C. Davis, Matei Georgescu, Mir Zaman Hussain, Jesse Miller, Stephen W. Nesbitt, Andy Vanloocke, Carl J. Bernacchi

Andy VanLoocke

Land use change for bioenergy feedstocks is likely to intensify as energy demand rises simultaneously with increased pressure to minimize greenhouse gas emissions. Initial assessments of the impact of adopting bioenergy crops as a significant energy source have largely focused on the potential for bioenergy agroecosystems to provide global-scale climate regulating ecosystem services via biogeochemical processes. Such as those processes associated with carbon uptake, conversion, and storage that have the potential to reduce global greenhouse gas emissions (GHG). However, the expansion of bioenergy crops can also lead to direct biophysical impacts on climate through water regulating services. Perturbations of processes …

Integrated Pest Management (Ipm) For Vertebrates: Do We Need To Broaden This Concept?, John Hadidian

John Hadidian, PhD

The concepts and practices of Integrated Pest Management (IPM) are historically grounded in programs aimed at insects and disease-causing organisms affecting agriculture. When applied to vertebrates, IPM concepts have most often been used in rodent control programs. Still, IPM is a powerful model that arguably can, and should, apply to conflicts with any “pest” or problem-causing organism. It may be time to examine contemporary IPM approaches and their relation to traditional vertebrate pest control more closely. Vertebrate IPM should encompass not only the development of sound and practical steps to shape decision-making and actions, but a dialogue about ethics as …

The Biophysical Link Between Climate, Water, And Vegetation In Bioenergy Agro-Ecosystems, Andy Vanloocke, Justin E. Bagley, Sarah C. Davis, Mir Zaman Hussain, Jesse Miller, Stephen W. Nesbitt, Carl J. Bernacchi

Andy VanLoocke

Next-Generation Field Guides, Elizabeth J. Farnsworth, Miyoko Chu, W. John Kress, Amanda K. Neill, Jason H. Best, John Pickering, Robert D. Stevenson, Gregory W. Courtney, John K. Vandyk, Aaron M. Ellison

John K. VanDyk

To conserve species, we must first identify them. Field researchers, land managers, educators, and citizen scientists need up-to-date and accessible tools to identify organisms, organize data, and share observations. Emerging technologies complement traditional, book-form field guides by providing users with a wealth of multimedia data. We review technical innovations of next-generation field guides, including Web-based and stand-alone applications, interactive multiple-access keys, visual-recognition software adapted to identify organisms, species checklists that can be customized to particular sites, online communities in which people share species observations, and the use of crowdsourced data to refine machine-based identification algorithms. Next-generation field guides are user …

Weed Seed Germplasm Collection 1964-2014 Of The Weed Biology Laboratory, Jack Dekker

Jack Dekker

J. Dekker weed seed germplasm collection; including: Lots 1-3974: 1964-2014; main seed library listed by lot numbers. Lots 649-1457: 1989 all-Iowa Setaria transect study. Lots 1762-1812: 1981; Diane Manthey, North Dakota St. Univ., Setaria collection at Bob Anderson's (USDA, Univ. of Minn) 1960's wild oat study sites. Lots 2389-2595: 1992 north temperate world collection (Japan, Russia, Europe) by J. Dekker. Lots 3270-3685: 1993 Brent Reschly transect study of eastern Iowa conventional and Amish farmers. Lots 3786-3962: 2000 J. Dekker 2000 salt-tolerant Setaria of southern Japan collection. All seed in all these collections belong, and were collected and archived by Jack …

Demographic Viability Of Populations Of Silene Regis In Midwestern Prairies: Relationships With Fire Management, Genetic Variation, Geographic Location, Population Size And Isolation, Eric S. Menges, Rebecca W. Dolan

Rebecca W. Dolan

We studied the demographic viability of populations of a long-lived iteroparous prairie perennial, Silene regia, in relation to management regimes, population sizes, geographical region (Ohio and Indiana vs. Missouri and Arkansas), degree of isolation and amount of genetic variation. Demographic data were collected from 16 populations for up to 7 years. This species has high survivorship, slow growth, frequent flowering and episodic seedling recruitment. Matrix projection methods were used to summarize population performance with and without recruitment. Median finite rates of increase by population varied from 0.57 to 1.82 and from 0.44 to 0.99, respectively. Populations with the highest rates …

A Global Analysis Of The Impacts Of Urbanization On Bird And Plant Diversity Reveals Key Anthropogenic Drivers, Myla F.J. Aronson, Frank A. La Sorte, Charles H. Nilon, Madhusudan Katti, Mark A. Goddard, Christopher A. Lepczyk, Paige S. Warren, Nicholas S.G. Williams, Sarel Cilliers, Bruce Clarkson, Cynnamon Dobbs, Rebecca W. Dolan, Marcus Hedblom, Stefan Klotz, Jip Louwe Kooijmans, Ingolf Kühn, Ian Macgregor-Fors, Mark Mcdonnell, Ulla Mörtberg, Petr Pyšek, Stefan Siebert, Jessica Sushinsky, Peter Werner, Marten Winter

Rebecca W. Dolan

Urbanization contributes to the loss of the world's biodiversity and the homogenization of its biota. However, comparative studies of urban biodiversity leading to robust generalities of the status and drivers of biodiversity in cities at the global scale are lacking. Here, we compiled the largest global dataset to date of two diverse taxa in cities: birds (54 cities) and plants (110 cities). We found that the majority of urban bird and plant species are native in the world's cities. Few plants and birds are cosmopolitan, the most common beingColumba livia and Poa annua. The density of bird and plant species …

Insect Visitation Of Peduncular And Petiolar Extrafloral Nectar Glands On Castor Bean (Ricinus Communis L.) Plants In Southern California, Victor D. Carmona

Victor D. Carmona-Galindo

Castor bean (Ricinus communis L.) is a myrmecophytic plant species with specialized extrafloral nectar (EFN) glands that serve to attract predatory insects, which in return defend plant-tissues against herbivores. The EFN glands on castor bean plants are located along the leaf petioles as well as on the peduncles of its imperfect (unisexual) flowers. This field-project evaluates the richness, diversity, and species assemblage of insects visiting EFN glands located on (female and male) flower peduncles and leaf petioles on castor bean plants growing in a Southern California coastal landscape. We detected that EFN glands on female-flower peduncles were visited by an …

Modelling C3 Photosynthesis From The Choroplast To The Ecosystem, Andy Vanloocke, Carl J. Bernacchi, Justin E. Bagley, Shawn P. Serbin, Ursula M. Ruiz-Vera, David M. Rosenthal

Andy VanLoocke

The Vertebrate Fauna Of The Upper Permian Of Niger. Iv. Nigerpeton Ricqlesi (Temnospondyli: Cochleosauridae), And The Edopoid Colonization Of Gondwana, J. Sebastien Steyer, Ross Damiani, Christian A. Sidor, F. Robin O’Keefe, Hans C.E. Larsson, Abdoulaye Maga, Oumarou Ide

F. Robin O’Keefe

We describe the edopoid temnospondyl Nigerpeton ricqlesi from the Upper Permian Moradi Formation of northern Niger on the basis of two partial skulls and tentatively associated postcranial material. This crocodile-like taxon displays several edopoid characters states such as a long prenarial region with enlarged premaxillae, elongated vomers, large, posteriorly tapering choanae, and a jugal that broadens anteriorly. Nigerpeton possesses a unique carnivorous dentition. It is autapomorphic in its possession of an extremely elongate snout bearing a maxillary bulge that accommodates three hypertrophied caniniform teeth, inner premaxillary tusks, and anterior paired fenestrae, which pierce the skull roof. In addition, both the …