Genetics and Genomics Commons^™

Harnessing Population Genetics For Pest Management: Theory And Application For Urban Rats, Matthew Combs, Kaylee Byers, Chelsea Himsworth, Jason Munshi-South

Human–Wildlife Interactions

Effective management of rodent pests requires an ecological understanding of how they move through their environment and how those movements influence the invasion, persistence, or reinvasion of problematic colonies. Traditional methodologies used to describe rodent movement patterns, such as mark-recapture, are hindered by their time-consuming nature and limited geographic scope. As such, our understanding of how rodents interact with urban environments remains limited. Population genetic principles and tools have the capacity to greatly increase our understanding of rodent population dynamics, ecological relationships, and movements across space, but this field is often unapproachable to non-scientist pest management professionals (PMPs). In this …

The New Natural Distribution Area Of Aspen (Populus Tremula L.) Marginal Populations In Pasinler In The Erzurum Province, Turkey, And Its Stand Characteristics, Halil Bariş Özel, Sezgin Ayan, Serdar Erpay, Bojan Simovski

Aspen Bibliography

Background and Purpose: Genetic diversity is the basis for adaptation and survival of tree species under changing environmental conditions, representing the key issue of stability and productivity of forest ecosystems. This paper studies the marginal population characteristics and stand dynamics of aspen tree (Populus tremula L.) in natural, pure and mixed forest stands with Scots pine (Pinus sylvestris L.). These populations were observed on founding sites between Timarli Valley and Timan Plateau located in Pasinler in the Erzurum Province in Turkey.
Materials and Methods: Three replicated sample sites were established according to a randomised block design …

Power In Pairs: Assessing The Statistical Value Of Paired Samples In Tests For Differential Expression, John R. Stevens, Jennifer S. Herrick, Roger K. Wolff, Martha L. Slattery

Mathematics and Statistics Faculty Publications

Background: When genomics researchers design a high-throughput study to test for differential expression, some biological systems and research questions provide opportunities to use paired samples from subjects, and researchers can plan for a certain proportion of subjects to have paired samples. We consider the effect of this paired samples proportion on the statistical power of the study, using characteristics of both count (RNA-Seq) and continuous (microarray) expression data from a colorectal cancer study.

Results: We demonstrate that a higher proportion of subjects with paired samples yields higher statistical power, for various total numbers of samples, and for various strengths of …

Dependence Of Aspen Stands On A Subsurface Water Subsidy: Implications For Climate Change Impacts, D. M. Love, M. D. Venturas, J. S. Sperry, P. D. Brooks, J. L. Pettit, Y. Wang, W. R. L. Anderegg, X. Tai, D. S. Mackay

Aspen Bibliography

The reliance of 10 Utah (USA) aspen forests on direct infiltration of growing season rain versus an additional subsurface water subsidy was determined from a trait- and process-based model of stomatal control. The model simulated the relationship between water supply to the root zone versus canopy transpiration and assimilation over a growing season. Canopy flux thresholds were identified that distinguished nonstressed, stressed, and dying stands. We found growing season rain and local soil moisture were insufficient for the survival of 5 of 10 stands. Six stands required a substantial subsidy (31–80% of potential seasonal transpiration) to avoid water stress and …

Phylogeographic Analyses Of A Widely Distributed Populus Davidiana: Further Evidence For The Existence Of Glacial Refugia Of Cool‐Temperate Deciduous Trees In Northern East Asia, Zhe Hou, Zhaoshan Wang, Zhanyang Ye, Shuhui Du, Shuya Liu, Jianguo Zhang

Aspen Bibliography

Despite several phylogeographic studies had provided evidence to support the existence of glacial refugia of cool‐temperate deciduous trees in northeast China, the species used in these studies were limited by the species ranges, which could not exclude the possibility that northern populations were the colonists from southern refugial populations during the last glacial maximum (LGM). Here, we estimated the nucleotide variation in Populus davidiana, a widespread species distributed in Eurasia. Three groups in northeast, central, and southwest China were constructed according to the simulation results from SAMOVA, composition of chloroplast haplotypes and structure results. We revealed that the northeast …

Phylogeny And Population Genetic Analyses Reveals Cryptic Speciation In The Bombus Fervidus Species Complex (Hymenoptera: Apidae), Jonathan B. Koch, Juanita Rodriguez, James P. Pitts, James P. Strange

Ecology Center Publications

Bumble bees (Bombus Latrielle) are significant pollinators of flowering plants due to their large body size, abundant setae, and generalist foraging strategies. However, shared setal coloration patterns among closely and distantly related bumble bee species makes identification notoriously difficult. The advent of molecular genetic techniques has increased our understanding of bumble bee evolution and taxonomy, and enables effective conservation policy and management. Individuals belonging to the North American Bombus fervidus species-complex (SC) are homogenous in body structure but exhibit significant body color phenotype variation across their geographic distribution. Given the uncertainty of the genealogical boundaries within the SC, some …

South American Leaf-Cutter Bees (Genus Megachile) Of The Subgenera Rhyssomegachile And Zonomegachile, With Two New Subgenera (Hymenoptera: Megachilidae), Víctor H. González, Terry Griswold, Michael S. Engel

All PIRU Publications

Leaf-cutter bees (genus Megachile Latreille) are among the most common and diverse group of bees. However, the identity and taxonomic placement of many species are problematic and species identification is often difficult. Some species are known only from a single specimen or from one of the sexes, and identification keys are not available for many groups. We address these taxonomic issues for the subgenera Rhyssomegachile Mitchell and Zonomegachile Mitchell, two poorly known South American lineages of leaf-cutter bees. We provide comparative diagnoses, redescriptions, illustrated identification keys, new geographical records, and designate needed neotypes for Megachile cara Mitchell, M. gigas Schrottky, …

Genetic Variants In The Sirt6 Transcriptional Regulatory Region Affect Gene Activity And Carcass Quality Traits In Indigenous Chinese Beef Cattle (Bos Taurus), Lin-Sheng Gui, Sayed Haidar Abbas Raza, Matthew Garcia, Yong-Gang Sun, Irfan Ullah, Yin-Cang Han

Animal, Dairy, and Veterinary Science Faculty Publications

Background: The aim of this study was to analyze potential influences of polymorphisms within the regulatory region of the bovine SIRT6 gene on carcass quality traits. Expression analyses suggested that SIRT6 gene is predominately expressed in kidney, compared with other tissues. In 535 indigenous Chinese beef cattle, two novel single nucleotide polymorphisms (SNPs) were identified within the promoter region of the SIRT6 gene.

Results: Association analysis indicated that G allele of the c.-1100 A > G had a positive effect on fat deposition, and the Hap4/4 diplotype had more favourable results than other dipoltypes with respect to the evaluation of carcass …

Identification And Heterologous Reconstitution Of A 5-Alk(En)Ylresorcinol Synthase From Endophytic Fungus Shiraia Sp. Slf14, Huiwen Yan, Lei Sun, Jinge Huang, Yixing Qiu, Fuchao Xu, Riming Yan, Du Zhu, Wei Wang, Jixun Zhan

Biological Engineering Faculty Publications

A new type III polyketide synthase gene (Ssars) was discovered from the genome of Shiraia sp. Slf14, an endophytic fungal strain from Huperzia serrata. The intron-free gene was cloned from the cDNA and ligated to two expression vectors pET28a and YEpADH2p-URA3 for expression in Escherichia coli BL21(DE3) and Saccharomyces cerevisiae BJ5464, respectively. SsARS was efficiently expressed in E. coli BL21(DE3), leading to the synthesis of a series of polyketide products. Six major products were isolated from the engineered E. coli and characterized as 1,3-dihydroxyphenyl-5-undecane, 1,3-dihydroxyphenyl-5-cis-6'-tridecene,1,3-dihydroxyphenyl-5-tridecane, 1,3-dihydroxyphenyl-5-cis-8'-pentadecene, 1,3-dihydroxyphenyl-5-pentadecane and 1,3-dihydroxyphenyl-5-cis-10'-heptadecene, respectively, …

How Behavior Of Nontarget Species Affects Perceived Accuracy Of Scat Detection Dog Surveys, Karen E. Dematteo, Linsey W. Blake, Julie K. Young, Barbara Davenport

Wildland Resources Faculty Publications

Detection dogs, specially trained domestic dogs (Canis familiaris), have become a valuable, noninvasive, conservation tool because they remove the dependence of attracting species to a particular location. Further, detection dogs locate samples independent of appearance, composition, or visibility allowing researchers to collect large sets of unbiased samples that can be used in complex ecological queries. One question not fully addressed is why samples from nontarget species are inadvertently collected during detection dog surveys. While a common explanation has been incomplete handler or dog training, our study aimed to explore alternative explanations. Our trials demonstrate that a scat’s genetic …

Dietary Docosahexaenoic Acid Prevents Silica-Induced Development Of Pulmonary Ectopic Germinal Centers And Glomerulonephritis In The Lupus-Prone Nzbwf1 Mouse, Melissa A. Bates, Peyman Akbari, Kristen N. Gilley, James G. Wagner, Ning Li, Anna K. Kopec, Kathryn A. Wierenga, Daven Jackson-Humbles, Christina Brandenberger, Andrij Holian, Abby D. Benninghoff, Jack R. Harkema, James J. Pestka

Animal, Dairy, and Veterinary Science Faculty Publications

Ectopic lymphoid structures (ELS) consist of B-cell and T-cell aggregates that are initiated de novo in inflamed tissues outside of secondary lymphoid organs. When organized within follicular dendritic cell (FDC) networks, ELS contain functional germinal centers that can yield autoantibody-secreting plasma cells and promote autoimmune disease. Intranasal instillation of lupus-prone mice with crystalline silica (cSiO₂), a respirable particle linked to human lupus, triggers ELS formation in the lung, systemic autoantibodies, and early onset of glomerulonephritis. Here we tested the hypothesis that consumption of docosahexaenoic acid (DHA), an ω-3 polyunsaturated fatty acid with anti-inflammatory properties, influences the temporal profile …

Aspen Recruitment In The Yellowstone Region Linked To Reduced Herbivory After Large Carnivore Restoration, Luke E. Painter, Robert L. Beschta, Eric J. Larsen, William J. Ripple

Aspen Bibliography

Quaking aspen (Populus tremuloides) recruitment during the 1980s–90s was suppressed by Rocky Mountain elk (Cervus canadensis) herbivory on winter ranges in the Yellowstone region, and saplings (young aspen taller than 2 m) were rare. Following the 1995–96 reintroduction of gray wolves (Canis lupus), browsing decreased and sapling recruitment increased in Yellowstone National Park. We compared aspen data from inside the park to data collected in three winter ranges outside the park. For most areas, the percentage of young aspen browsed annually was 80–100% in 1997–98, decreasing to 30–60% in 2011–15. Sapling recruitment was inversely …

Effects Of Stand Structure, Browsing, And Biophysical Conditions On Regeneration Following Mountain Pine Beetle In Mixed Lodgepole Pine And Aspen Forests Of The Southern Rockies, Kristen A. Pelz, Frederick W. Smith

Aspen Bibliography

Aspen (Populus tremuloides) and lodgepole pine (Pinus contorta var. latifolia) co-occur in the southern Rocky Mountains (USA), where mountain pine beetle (MPB, Dendroctonus ponderosae) has caused extensive lodgepole pine mortality since the late 1990s. Both species excel in post-disturbance high-light environments, but lodgepole pine has generally been thought to establish poorly on undisturbed seedbeds, and aspen suckering may be inhibited by intact aspen overstory. We ask whether lodgepole pine and aspen will regenerate in sufficient quantities to revegetate these forests. We visited a random sample of aspen and lodgepole pine stands across the affected landscape …

Genome-Wide Association Study For Variants That Modulate Relationships Between Cerebrospinal Fluid Amyloid-Beta 42, Tau, And P-Tau Levels, Taylor J. Maxwell, Chris Corcoran, Jorge L. Del-Aguila, John P. Budde, Yuetiva Deming, Carlos Cruchaga, Alison M. Goate, John S. K. Kauwe, Alzheimer's Disease Neuroimaging Initiative

Mathematics and Statistics Faculty Publications

Background: A relationship quantitative trait locus exists when the correlation between multiple traits varies by genotype for that locus. Relationship quantitative trait loci (rQTL) are often involved in gene-by-gene (G×G) interactions or gene-by-environmental interactions, making them a powerful tool for detecting G×G.

Methods: We performed genome-wide association studies to identify rQTL between tau and Aβ42 and ptau and Aβ42 with over 3000 individuals using age, gender, series, APOE ε2, APOE ε4, and two principal components for population structure as covariates. Each significant rQTL was separately screened for interactions with other loci for each trait in the rQTL model. Parametric bootstrapping …

Mobile Elements Shape Plastome Evolution In Ferns, Tanner A. Robison, Amanda L. Grusz, Paul G. Wolf, Jeffrey P. Mower, Blake D. Fauskee, Karla Sosa, Eric Schuettpelz

Biology Faculty Publications

Plastid genomes display remarkable organizational stability over evolutionary time. From green algae to angiosperms, most plastid genomes are largely collinear, with only a few cases of inversion, gene loss, or, in extremely rare cases, gene addition. These plastome insertions are mostly clade-specific and are typically of nuclear or mitochondrial origin. Here, we expand on these findings and present the first family-level survey of plastome evolution in ferns, revealing a novel suite of dynamic mobile elements. Comparative plastome analyses of the Pteridaceae expose several mobile open reading frames that vary in sequence length, insertion site, and configuration among sampled taxa. Even …

Role Of Nucleotide Identity In Effective Crispr Target Escape Mutations, Tim Künne, Yifan Zhu, Fausia Da Silva, Nico Konstantinides, Rebecca E. Mckenzie, Ryan N. Jackson, Stan J.J. Brouns

Chemistry and Biochemistry Faculty Publications

Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped CRISPR interference through mutations in their protospacer target site. We previously observed a trend that nucleotide-dependent mismatches between crRNA and the protospacer strongly influence the efficiency of primed CRISPR adaptation. Here we show that guanine-substitutions in the target strand of the protospacer are highly detrimental to CRISPR interference and interference-dependent priming, while cytosine-substitutions are more readily tolerated. Furthermore, we show that this effect is based on strongly decreased binding affinity of the effector complex Cascade for guanine-mismatched targets, while cytosine-mismatched targets …

Molecular Adaptations For Sensing And Securing Prey And Insight Into Amniote Genome Diversity From The Garter Snake Genome, Blair W. Perry, Daren C. Card, Joel W. Mcglothlin, Giulia I.M. Pasquesi, Richard H. Adams, Drew R. Schield, Nicole R. Hales, Andrew B. Corbin, Jeffery P. Demuth, Federico G. Hoffmann, Michael W. Vandewege, Ryan K. Schott, Nihar Bhattacharyya, Belinda S.W. Chang, Nicholas R. Casewell, Gareth Whiteley, Jacobo Reyes-Velasco, Stephen P. Mackessy, Tony Gamble, Kenneth B. Storey, Kyle K. Biggar, Courtney N. Passow, Chih-Horng Kuo, Suzanne E. Mcgaugh, Anne M. Bronikowski, A.P. Jason De Koning, Scott V. Edwards, Michael E. Pfrender, Patrick Minx, Edmund D. Brodie Jr., Edmund D. Brodie Jr., Wesley C. Warren, Todd A. Castoe

Biology Faculty Publications

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile …

Fitness Consequences Of Interspecific Nesting Associations Among Cavity-Nesting Birds, James C. Mouton, Thomas E. Martin

Aspen Bibliography

Interspecific aggregations of prey may provide benefits by mitigating predation risk, but they can also create costs if they increase competition for resources or are more easily detectable by predators. Variation in predation risk and resource availability may influence the occurrence and fitness effects of aggregating in nature. Yet tests of such possibilities are lacking. Cavity-nesting birds provide an interesting test case. They compete aggressively for resources and experience low nest predation rates, which might predict dispersion, but across 19 years of study we found that they commonly aggregate by sharing nest trees. Tree sharing was more common when aspen …

Removal Of Invasive Plants From Pando Exclosure 2018, Marc Coles-Ritchie

Aspen Bibliography

On July 10-11, 2018 volunteers and staff from Great Old Broads for Wilderness and Grand Canyon Trust removed invasive plants from the Pando exclosure, a fenced portion of the Pando Clone aspen forest adjacent to Fish Lake, in Central Utah. This area has been fenced to restore a portion of the Pando Clone that has been lacking recruitment for decades, by protecting young aspen from browsing by deer and cattle. We have been removing invasive species for five years from this exclosure.

The 2018 trip included 10 women and one staffer of Great Old Broads for Wilderness, from the states …

Phytochemical Screening Of Quaking Aspen (Populus Tremuloides) Extracts By Uplc-Qtof-Ms And Evaluation Of Their Antimicrobial Activity, Annabelle St-Pierre, Dorian Blondeau, André Lajeunesse, Julien Bley, Nathalie Bourdeau, Isabel Desgagné-Penix

Aspen Bibliography

The continual emergence of pathogen resistance is a recurring challenge and pushes for the development of antimicrobial compounds. Here, we investigated compounds from quaking aspen trees (Populus tremuloides) as potential antimicrobial agents. Several extractions using different solvents were realized, and corresponding antimicrobial activity was tested against eight microorganisms. Results revealed that polar extraction solvents including water, ethanol and methanol gave the best extraction yields (>15.07%). Minimal inhibition concentration (MIC) and minimal bactericidal/fungicidal concentration (MBC/MFC) demonstrated that water extracts had the best antimicrobial activity by a weak to moderate inhibition of growth of all eight tested microorganisms in addition to …

Characterization Of An N-Terminal Non-Core Domain Of Rag1 Gene Disrupted Syrian Hamster Model Generated By Crispr Cas9, Jinxin Miao, Baoling Ying, Rong Li, Ann E. Tollefson, Jacqueline F. Spencer, William S.M. Wold, Seok-Hwan Song, Il-Keun Kong, Karoly Toth, Yaohe Wang, Zhongde Wang

Animal, Dairy, and Veterinary Science Faculty Publications

The accumulating evidence demonstrates that Syrian hamsters have advantages as models for various diseases. To develop a Syrian hamster (Mesocricetus auratus) model of human immunodeficiency caused by RAG1 gene mutations, we employed the CRISPR/Cas9 system and introduced an 86-nucleotide frameshift deletion in the hamster RAG1 gene encoding part of the N-terminal non-core domain of RAG1. Histological and immunohistochemical analyses demonstrated that these hamsters (referred herein as RAG1-86nt hamsters) had atrophic spleen and thymus, and developed significantly less white pulp and were almost completely devoid of splenic lymphoid follicles. The RAG1-nt86 hamsters had barely detectable CD3+ and CD4+ T cells. The …

Rapid Regeneration Offsets Losses From Warming-Induced Tree Mortality In An Aspen-Dominated Broad-Leaved Forest In Northern China, Pengwu Zhao, Chongyang Xu, Mei Zhou, Bo Zhang, Peng Ge, Nan Zeng, Hongyan Liu

Aspen Bibliography

Worldwide tree mortality as induced by climate change presents a challenge to forest managers. To successfully manage vulnerable forests requires the capacity of regeneration to compensate for losses from tree mortality. We observed rapid regeneration and the growth release of young trees after warming-induced mortality in a David aspen-dominated (Populus davidiana) broad-leaved forest in Inner Mongolia, China, as based on individual tree measurements taken in 2012 and 2015 from a 6-ha permanent plot. Warming and drought stress killed large trees 10–15 m tall with a total number of 2881 trees during 2011–2012, and also thinned the upper crowns. …

Salvinia Radseq, Carol A. Rowe, Donald Hauber, Paul G. Wolf

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No abstract provided.

Genetic Differentiation Between Two Species Of Buckwheat (Eriogonum), Paul G. Wolf, Jenessa B. Lemon

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Discovering the extent of genetic differentiation between closely related taxa facilitates decisions regarding species protection under the Endangered Species Act. Here, we analyze genotype data to explore the relatedness of two buckwheat species: Eriogonum soredium Reveal- a narrow endemic under consideration for protection, and a widespread close relative, Eriogonum shockleyi S. Watson. Eriogonum soredium grows only on Ordovician limestone outcroppings in west central Utah, whereas the range of E. shockleyi is broad, spanning the western United States from Colorado to California, and Idaho to Arizona. Eriogonum shockleyi is suspected of hybridizing with other buckwheats throughout this range. We detected higher …

Large Effect Quantitative Trait Loci For Salicinoid Phenolic Glycosides In Populus: Implications For Gene Discovery, Scott A. Woolbright, Brian J. Rehill, Richard L. Lindroth

Aspen Bibliography

Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, genes for salicinoid phenolic glycosides (SPGs)—ecologically important compounds with significant commercial, cultural, and medicinal applications—remain largely undescribed. We used a linkage map derived from a full‐sib population of hybrid cottonwoods (Populus spp.) to search for quantitative trait loci (QTL) for the SPGs salicortin and HCH‐salicortin. SSR markers and primer sequences were used to anchor the map to the V3.0 P. trichocarpa genome. We discovered 21 QTL for the two traits, including a major QTL for HCH‐salicortin (R2 = .52) that colocated …

The Impact Of Reconstructed Soils Following Oil Sands Exploitation On Aspen And Its Associated Belowground Microbiome, Franck Stefani, Nathalie Isabel, Marie-Josee Morency

Aspen Bibliography

Oil sands surface mining in the Athabasca region of northern Alberta (Canada) is a significant anthropogenic disturbance that resets boreal forest development and succession to early stages. During surface mining, the vegetation is cleared, the topsoil is salvaged, and the overburden (the layer of sand and clay in between the topsoil and the oil sands) is piled (see Fig. 2 in Audet et al.1 for an explanation of the land-reclamation procedure). After mining is finished, the landforms (composed of overburden and tailings sand) are capped with organic matter-rich soil covers made of either upland-derived forest floor-mineral mix (FFMM) or a …

Hart Prairie Preserve Site Visit To Assess Aspen Health Nature Conservancy, Flagstaff, Az, Amanda Grady

Aspen Bibliography

On June 11, 2018, Amanda Grady, Entomologist, Arizona Zone, Forest Health Protection, performed a site visit to evaluate aspen health on the Nature Conservancy lands at Heart Prairie Preserve (HPP) near Flagstaff. Specifically, the evaluation was to determine whether or not the aspen within exclosures on Fern Mountain have symptoms or signs of Oystershell scale (OSS), an emergent forest pest contributing to aspen decline in northern Arizona.

Effects Of Climate Change On Forest Vegetation In The Northern Rockies Region, Robert E. Keane, Mary Frances Mahalovich

Aspen Bibliography

No abstract provided.

Climate-Induced Gradients Of Populus Sp. Forest Biomass On The Territory Of Eurasia, Usoltev Vladimir Andreevich, Omid Shobairi, Chasovskikh Viktor Petrovich

Aspen Bibliography

On the basis of the compiled database in a number of 413 sample plots with determinations of forest biomass of the genus Populus sp. on the territory of Eurasia from France to southern China and Japan statistically significant transcontinental decreasing of stem, above ground and total biomass as in the direction from northern temperate to subequatorial zonal belt and in the direction from the Atlantic and Pacific coasts to the continentality pole in Siberia is established. Unlike wood story, understory biomass in these directions has not decreased, and increasing. The root: shoot ratio increases in the range between northern temperate …

Data From: Target Sequence Capture Of Nuclear-Encoded Genes For Phylogenetic Analysis In Ferns, Paul G. Wolf, Tanner A. Robison, Matthew G. Johnson, Michael A. Sundue, Weston L. Testo, Carl J. Rothfels

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Premise of the study: Until recently, most phylogenetic studies of ferns were based on chloroplast genes. Evolutionary inferences based on these data can be incomplete because the characters are from a single linkage group and are uniparentally inherited. These limitations are particularly acute in studies of hybridization, which is prevalent in ferns; fern hybrids are common and ferns are able to hybridize across highly diverged lineages, up to 60 million years since divergence in one documented case. However, it not yet clear what effect such hybridization has on fern evolution, in part due to a paucity of available biparentally inherited …