Genetics and Genomics Commons^™

Tree Biomass – A Fragile Carbon Storage In Old-Growth Birch And Aspen Stands In Hemiboreal Latvia, Laura Ķēniņa, Didzis Elferts, Ieva Jaunslaviete, Endijs Bāders, Guntars Šņepsts, Āris Jansons

Aspen Bibliography

Birch (Betula pendula Roth, Betula pubescens Ehrh.) and European aspen (Populus tremula L.) stands dominate the deciduous forests of Northern Europe. Due to increasing forest protections, more deciduous stands will reach the old-growth stage. Thus, data on the carbon storage potential in such areas are essential. We aimed to establish a benchmark for carbon stocks of the main carbon pools in old-growth deciduous hemiboreal stands. Carbon pools were calculated from measurements in forty old-growth (104–148 years-old) deciduous stands in forests on fertile mineral soil. The carbon stock in these stands is distributed across tree biomass (~ 60%), mineral soil (~ …

Aspen Leaves As A "Chemical Landscape" For Fungal Endophyte Diversity - Can Nitrogen And Herbivory Shape The Community Composition In Controlled Conditions?, Johanna Witzell, Vicki Huizu Guo Decker, Marta Agostinelli, Carmen Romeralo Tapia, Michelle Cleary, Benedicte Riber Albrectsen

Aspen Bibliography

The endophytic microbiome may influence the ecological performance of plants, including forest trees. Various abiotic and biotic factors may shape the endophyte communities directly but also indirectly, by modifying the quality of host plants as a substrate. We hypothesized that potentially antifungal or fungistatic condensed tannins (CTs) would determine the quality of aspen (Populus tremula) leaves as a substrate for endophytic fungi. By subjecting the plants to nitrogen fertilization (N) or herbivory (H; leaf beetles) we aimed to change the internal “chemical landscape”, especially the CT levels, in aspen leaves. We expected that this would lead to changes in the …

The First Complete Genome Of The Simian Malaria Parasite Plasmodium Brasilianum, Marko Bajic, Shashidhar Ravishankar, Mili Sheth, Lori A. Rowe, M. Andreina Pacheco, Dhruviben S. Patel, Dhwani Batra, Vladimir Loparev, Christian Olsen, Ananias A. Escalante, Fredrik Vannberg, Venkatachalam Udhayakumar, John W. Barnwell, Eldin Talundzic

Harold W. Manter Laboratory: Library Materials

Naturally occurring human infections by zoonotic Plasmodium species have been documented for P. knowlesi, P. cynomolgi, P. simium, P. simiovale, P. inui, P. inui-like, P. coatneyi, and P. brasilianum. Accurate detection of each species is complicated by their morphological similarities with other Plasmodium species. PCR-based assays offer a solution but require prior knowledge of adequate genomic targets that can distinguish the species. While whole genomes have been published for P. knowlesi, P. cynomolgi, P. simium, and P. inui, no complete genome for P. brasilianum has …

Morphometric And Molecular Characterization Of An Unpigmented Haemosporidian Parasite In The Neotropical Turnip-Tailed Gecko (Thecadactylus Rapicauda), Nubia E. Matta, Leydy P. González, Mario Vargas-Ramírez, Gediminas Valkiūnas, Ananias A. Escalante, M. Andreína Pacheco

Harold W. Manter Laboratory: Library Materials

Morphological traits from blood stages have been the gold standard for determining haemosporidian parasite species. However, the status of some taxa and the value of such traits in parasites from reptiles remain contentious. The scarce sampling of these species worsens the situation, and several taxa lack molecular data. A survey was performed in the Magdalena Department in Colombia, where 16 species of reptiles were captured. A peculiar haemosporidian parasite was found in the Turnip-tailed gecko Thecadactylus rapicauda. This haemosporidian does not show malarial pigment in blood stages under light microscopy; thus, it fits the Garnia genus’s characters belonging to …

Ungulate Herbivores As Drivers Of Aspen Recruitment And Understory Composition Throughout Arid Montane Landscapes, Elizabeth S. Reikowski, Tyler Refsland, J. Hall Cushman

Aspen Bibliography

Herbivory by wild and domestic ungulates can influence tree recruitment and understory forest communities throughout the world. Herbivore-driven declines in tree recruitment have been observed for quaking aspen (Populus tremuloides), a foundation species whose health and management is recognized as a critical priority throughout much of its range. Livestock fencing is commonly used to promote aspen regeneration, but its effectiveness is rarely assessed, especially across large spatial scales. Using a livestock-reduction experiment, we evaluated the effects of ungulate herbivory on aspen in the Great Basin and southern Cascades, an expansive and environmentally heterogeneous region where aspen faces the …

Coping With Environmental Constraints: Geographically Divergent Adaptive Evolution And Germination Plasticity In The Transcontinental Populus Tremuloides, Roos Goessen, Nathalie Isabel, Christian Wehenkel, Nathalie Pavy, Lisa Tischenko, Lyne Touchette, Isabelle Giguère, Marie-Claude Gros-Louis, Jérôme Laroche, Brian Boyle, Raju Soolanayakanahally, Karen E. Mock, Javier Hernández-Velasco, Sergio Leonel Simental-Rodriguez, Jean Bousquet, Ilga M. Porth

Aspen Bibliography

Societal Impact Statement

Syntheses clearly show that global warming is affecting ecosystems and biodiversity around the world. New methods and measures are needed to predict the climate resilience of plant species critical to ecosystem stability, to improve ecological management and to support habitat restoration and human well-being. Widespread keystone species such as aspen are important targets in the study of resilience to future climate conditions because they play a crucial role in maintaining various ecosystem functions and may contain genetic material with untapped adaptive potential. Here, we present a new framework in support of climate-resilient revegetation based on comprehensively understood …

Insights To Protein Pathogenicity From The Lens Of Protein Evolution, Janelle Nunez-Castilla

FIU Electronic Theses and Dissertations

As protein sequences evolve, differences in selective constraints may lead to outcomes ranging from sequence conservation to structural and functional divergence. Evolutionary protein family analysis can illuminate which protein regions are likely to diverge or remain conserved in sequence, structure, and function. Moreover, nonsynonymous mutations in pathogens may result in the emergence of protein regions that affect the behavior of pathogenic proteins within a host and host response. I aimed to gain insight on pathogenic proteins from cancer and viruses using an evolutionary perspective. First, I examined p53, a conformationally flexible, multifunctional protein mutated in ~50% of human cancers. Multifunctional …

Growing Space Management In Boreal Mixedwood Forests: 22 Year Results, Richard Kabzems, George Harper, Che Elkin

Aspen Bibliography

Boreal mixed forests of trembling aspen (Populus tremuloides) and white spruce (Picea glauca) can provide higher outputs of many ecosystem goods and services, combined with resilience for changing environmental conditions. In this study, we examine the growth of white spruce and aspen over a range of stand compositions created by spot and broadcast treatments of broadleaves using manual and chemical means, aspen spacing, and untreated control. Twenty-two growing seasons postharvest, treatment responses created a range of broadleaf densities and spatial arrangements, reflected in significant differences in heights and diameters of the spruce mixedwood component. At this …

Recovery Of Trembling Aspen, Tamarack, And White Spruce Seedlings From Nacl Stress Following Winter Dormancy: Implications For Increased Foliar Potassium, Necrosis, And Sodium Management As Stress Resistance Mechanisms, Nathan T. Lauer

Aspen Bibliography

Revegetation of boreal forest lands disturbed by surface mining for bitumen can be challenging due to fluctuating levels of soil NaCl and harsh winter temperatures. These stressors may hinder the growth and survival of planted tree seedlings. Two experiments were carried out to examine the processes of recovery from NaCl stress and overwintering in trembling aspen, tamarack, and white spruce seedlings. In the recovery experiment, seedlings were treated with 0, 50, or 100 mM NaCl for 60 days and then allowed to recover for 60 days. Most of the examined physiological variables (total dry weight, chlorophyll concentration, photosynthesis, and transpiration) …

Compensatory Phenolic Induction Dynamics In Aspen After Aphid Infestation, Rajarshi Kumar Gaur, Ilka Nacif De Abreu, Benedicte Riber Albrectsen

Aspen Bibliography

Condensed tannins (CTs) are polyphenolics and part of the total phenolic (TP) pool that shape resistance in aspen (Populus tremula). CTs are negatively associated with pathogens, but their resistance properties against herbivores are less understood. CTs shape resistance to pathogens and chewing herbivores and could also shape resistance to aphids. Being chemical pools that are highly variable it can further be questioned whether CT-shaped resistance is better described by constitutive levels, by the induced response potential, or by both. Here, aspen genotypes were propagated and selected to represent a range of inherent abilities to produce and store foliar …

Young Forests And Fire: Using Lidar–Imagery Fusion To Explore Fuels And Burn Severity In A Subalpine Forest Reburn, Kristin H. Braziunas, Diane C. Abendroth, Monica G. Turner

Aspen Bibliography

Anticipating fire behavior as climate change and fire activity accelerate is an increasingly pressing management challenge in fire-prone landscapes. In subalpine forests adapted to infrequent, stand-replacing fire, self-limitation of burn severity in short-interval fire is incompletely understood. Spatially explicit fuels data can support assessments of landscape-scale fire risk and fuel feedbacks on burn severity. For a ~1450-km² largely forested landscape in the US Northern Rocky Mountains, we used airborne lidar and imagery to predict and map canopy and surface fuels. In a fire that burned mature (>125-year-old) and also reburned young (~30-year-old) subalpine forest, we then asked: (1) …

Why Plasmodium Vivax And Plasmodium Falciparum Are So Different? A Tale Of Two Clades And Their Species Diversities, Ananias A. Escalante, Axl S. Cepeda, M. Andreína Pacheco

Harold W. Manter Laboratory: Library Materials

The global malaria burden sometimes obscures that the genus Plasmodium comprises diverse clades with lineages that independently gave origin to the extant human parasites. Indeed, the differences between the human malaria parasites were highlighted in the classical taxonomy by dividing them into two subgenera, the subgenus Plasmodium, which included all the human parasites but Plasmodium falciparum that was placed in its separate subgenus, Laverania. Here, the evolution of Plasmodium in primates will be discussed in terms of their species diversity and some of their distinct phenotypes, putative molecular adaptations, and host–parasite biocenosis. Thus, in addition to a current …

Halodash: The Deep And Shallow History Of Aquatic Life's Passages Between Marine And Freshwater Habitats, Eric T. Schultz, Lisa Park Boush

EEB Articles

This series of papers highlights research into how biological exchanges between salty and freshwater habitats have transformed the biosphere. Life in the ocean and in freshwaters have long been intertwined; multiple major branches of the tree of life originated in the oceans and then adapted to and diversified in freshwaters. Similar exchanges continue to this day, including some species that continually migrate between marine and fresh waters. The series addresses key themes of transitions, transformations, and current threats with a series of questions: When did major colonizations of fresh waters happen? What physiographic changes facilitated transitions? What organismal characteristics facilitate …

Repeated Targets Of Natural Selection During Ecological Transitions Of Fish Across Salinity Boundaries, Jonathan P. Velotta, Stephen D. Mccormick, Andrew Whitehead, Catherine S. Durso, Eric T. Schultz

EEB Articles

Ecological transitions across salinity boundaries have led to some of the most important diversification events in the animal kingdom, especially among fishes. Adaptations accompanying such transitions include changes in morphology, diet, whole-organism performance, and osmoregulatory function, which may be particularly prominent since divergent salinity regimes make opposing demands on systems that maintain ion and water balance. Research in the last decade has focused on the genetic targets underlying such adaptations, most notably by comparing populations of species that are distributed across salinity boundaries. Here, we synthesize research on the targets of natural selection using whole-genome approaches, with a particular emphasis …

Oystershell Scale: An Invasive Threat To Aspen Conservation, Amanda M. Grady, Connor D. Crouch, Nicholas P. Wilhelmi, Richard W. Hofstetter, Kristen M. Waring

Aspen Bibliography

Aspen decline is an acute and chronic problem in Arizona, where high levels of overstory mortality and a lack of recruitment continue to be observed. Oystershell scale (Lepidosaphes ulmi; OSS), an invasive sapsucking insect, has recently become widespread in native aspen stands in the southwestern U.S., further contributing to aspen mortality. Damage is severe in lower elevation stands and within ungulate exclosures created to conserve aspen. Young recruiting aspen that are rare on the landscape incur high levels of OSS-caused mortality when infested (Fig. 1). OSS has only recently become a pest of concern in the Southwest and …

Emulating Succession Of Boreal Mixedwood Forests In Alberta Using Understory Protection Harvesting, Ivan Bjelnanovic, Philip G. Comeau, Sharon Meredith, Brian Roth

Aspen Bibliography

Understory protection harvesting is a form of partial cutting that can be used in aspen (Populus tremuloides Michx.)-dominated stands that have understories of white spruce (Picea glauca (Moench) Voss). This practice involves removing 75% to 85% of the merchantable aspen while minimizing damage to the advance spruce regeneration, in addition to leaving 15% to 25% of the aspen standing to reduce potential windthrow of the spruce understory. In this paper, we summarize results from 18 stands measured 10 to 12 years after understory protection harvest. Diameter growth of spruce increased during the first five years after harvest while …

Climate Effects On Black Spruce And Trembling Aspen Productivity In Natural Origin Mixed Stands, Mahadev Sharma

Aspen Bibliography

Forest managers need site productivity estimates for tree species growing in mixed stands. Models developed in the past are generally for pure stands and don’t factor in the effects of climate change on site productivity. Therefore, site index (SI) models were developed for black spruce (Picea mariana Mill. B.S.P.) and trembling aspen (Populus tremuloides Michx.) trees grown in natural origin mixed stands. For this, 186 trees (93 black spruce and trembling aspen each) were sampled from 31 even-aged natural mixed stands (sites) (3 trees/species/site) across Ontario, Canada. Stand height growth models were developed by incorporating climate variables during …

Characterization Of Streptomyces Nymphaeiformis Sp. Nov., And Its Taxonomic Relatedness To Other Polyhydroxybutyrate-Degrading Streptomycetes, Gary R. Hix, Muhammad S. Khan, Mikayla T. Miller, Elisha C. Napier, Allison L. O'Brien, Roger P. White, Stephen F. Baron Ph.D.

Biology Faculty Scholarship

A polyhydroxybutyrate (PHB)-degrading actinomycete, strain SFB5A^T, was identified as a species of Streptomyces based on its membrane fatty acid profile and the presence of LL-diaminopimelic acid in the cell wall. It formed sporulating mycelia on most agar media, but flat or wrinkled, moist colonies on trypticase soy agar. Spores were smooth, cylindrical, and borne on long, straight to flexuous chains. It produced a light brown diffusible pigment, but not melanin. Comparison of genomic digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values indicated that strain SFB5A^T was related to Streptomyces litmocidini JCM 4394^T , Streptomyces …

Facilitation Differentially Affects Competitive Responses Of Aspen And Subalpine Fir Through Stages Of Stand Development, Rebecca Lee Molinari, Matthew F. Bekker, Benjamin D. St. Clair, Jason Bartholomew, R. Justin Derose, Stanley G. Kitchen, Samuel B. St. Clair

Aspen Bibliography

Spatial interactions between trees influence forest community succession. The objective of this study was to investigate how shifts in forest composition and proximity between tree species affect stand development over time in mixed forest systems. At six locations across the Fishlake National Forest, Utah, USA, in stands where facilitation has been documented previously, tree-ring samples were collected from aspen and subalpine fir trees. Basal area increment was calculated to characterize the effects of the proximity of overstory trees on multidecadal growth responses of aspen and subalpine fir in aspen-dominant and mixed aspen–conifer stands. Subalpine fir seedlings were established next to …

Phylogenomic Discordance Suggests Polytomies Along The Backbone Of The Large Genus Solanum, Edeline Gagnon, Rebeccca Hilgenhof, Andrés Orejuela, Angela J. Mcdonnell, Gaurav Sablok, Xavier Aubriot, Leandro Giacomin, Yuri Gouvêa, Thamyris Bragionis, João Renato Stehmann, Lynn Bohs, Steven Dodsworth, Christopher T. Martine, Péter Poczai, Sandra Knapp, Tiina Särkinen

Faculty Journal Articles

Premise of the study

Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants.

Methods

A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) …

Bottom-Up Drivers Of Future Fire Regimes In Western Boreal North America, Adrianna C. Foster, Jacquelyn K. Shuman, Brendan M. Rogers, Xanthe J. Walker, Michelle C. Mack, Laura L. Bourgeau-Chavez, Sander Veraverbeke, Scott J. Goetz

Aspen Bibliography

Forest characteristics, structure, and dynamics within the North American boreal region are heavily influenced by wildfire intensity, severity, and frequency. Increasing temperatures are likely to result in drier conditions and longer fire seasons, potentially leading to more intense and frequent fires. However, an increase in deciduous forest cover is also predicted across the region, potentially decreasing flammability. In this study, we use an individual tree-based forest model to test bottom-up (i.e. fuels) vs top-down (i.e. climate) controls on fire activity and project future forest and wildfire dynamics. The University of Virginia Forest Model Enhanced is an individual tree-based forest model …

Identifying Conifer Tree Vs. Deciduous Shrub And Tree Regeneration Trajectories In A Space-For-Time Boreal Peatland Fire Chronosequence Using Multispectral Lidar, Humaira Enayetullah, Laura Chasmer, Christopher Hopkinson, Dan Thompson, Danielle Cobbaert

Aspen Bibliography

Wildland fires and anthropogenic disturbances can cause changes in vegetation species composition and structure in boreal peatlands. These could potentially alter regeneration trajectories following severe fire or through cumulative impacts of climate-mediated drying, fire, and/or anthropogenic disturbance. We used lidar-derived point cloud metrics, and site-specific locational attributes to assess trajectories of post-disturbance vegetation regeneration in boreal peatlands south of Fort McMurray, Alberta, Canada using a space-for-time-chronosequence. The objectives were to (a) develop methods to identify conifer trees vs. deciduous shrubs and trees using multi-spectral lidar data, (b) quantify the proportional coverage of shrubs and trees to determine environmental conditions driving …

Increased Signal Complexity Is Associated With Increased Mating Success, Noori Choi, Matt Adams, Kasey Fowler-Finn, Elise Knowlton, Malcolm Rosenthal, Aaron Rundus, Roger D. Santer, Dustin J. Wilgers, Eileen Hebets

Eileen Hebets Publications

The evolution of complex signals has often been explored by testing multiple functional hypotheses regarding how independent signal components provide selective benefits to offset the costs of their production. In the present study, we take a different approach by exploring the function of complexity per se. We test the hypothesis that increased vibratory signal complexity— based on both proportional and temporal patterning—provides selective benefits to courting male Schizocosa stridulans wolf spiders. In support of this hypothesis, all of our quantified metrics of vibratory signal complexity predicted the mating success of male S. stridulans. The rate of visual signalling, which is …

Description Of The Courtship And Copulation Behaviours Of The Wall Spider Oecobius Concinnus (Oecobiidae), Diego Solano-Brenes, Laura Segura-Hernández, Gilbert Barrantes

Eileen Hebets Publications

Courtship and copulation behaviours are yet scantily described in many spider families, and this lack of information limits our understanding of the evolution of such behaviours within and across families. Here, we provide a detailed description of both courtship and copulation behaviour for Oecobius concinnus Simon, 1893. A striking characteristic of the male courtship is the construction of a tubular web (mating web) in which most courtship and copulation occurs. This web likely functions to restrain the female in a reduced space and as a substrate for male pheromones. The courtship consists of a complex web of interactions between both …

Effects Of Buried Wood On The Development Of Populus Tremuloides On Various Oil Sands Reclamation Soils, Kaitlyn E. Trepanier, Laura Manchola-Rojas, Bradley D. Pinno

Aspen Bibliography

Buried wood is an important but understudied component of reclamation soils. We examined the impacts of buried wood amounts and species on the growth of the common reclamation tree species trembling aspen (Populus tremuloides). In a greenhouse study, aspen seedlings were planted into four soil types, upland derived fine forest floor-mineral mix (fFFMM), coarse forest floor-mineral mix (cFFMM), and lowland derived peat and peat-mineral mix (PMM), that were mixed with either aspen or pine wood shavings at four concentrations (0%, 10%, 20% and 50% of total volume). Height and diameter growth, chlorophyll concentration, and leaf and stem biomass were measured. …