Biology Commons^™

Contemporaneous Radiations Of Fungi And Plants Linked To Symbiosis, François Lutzoni, Michael D. Nowak, Michael E. Alfaro, Valérie Reeb, Jolanta Miadlikowska, Michael Krug, A. Elizabeth Arnold, Louise A. Lewis, David L. Swofford, David Hibbett, Khidir Hilu, Timothy Y. James, Dietmar Quandt, Susana Magallón

Biology

Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma), likely facilitating terrestriality through endomycorrhizal and possibly endophytic symbioses. The largest radiation of fungi (Leotiomyceta), the origin of arbuscular mycorrhizae, and the diversification of extant …

Genomics And Development Of Lentinus Tigrinus: A White-Rot Wood-Decaying Mushroom With Dimorphic Fruiting Bodies, Baojun Wu, Zhangyi Xu, Alicia Knudson, Alexis Carlson, Naiyao Chen, Sam Kovaka, Kurt Labutti, Anna Lipzen, Christa Pennachio, Robert Riley, Wendy Schakwitz, Kiwamu Umezawa, Robin A. Ohm, Igor V. Grigoriev, Laszlo G. Nagy, John Gibbons, David Hibbett

Biology

Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has an agaricoid form (a gilled mushroom) and a secotioid form (puffball-like, with enclosed spore-bearing structures). Previous studies suggested that the secotioid form is conferred by a recessive allele of a single locus. We sequenced the genomes of one agaricoid (Aga) strain and one secotioid (Sec) strain (39.53–39.88 Mb, with 15,581–15,380 genes, respectively). We mated the Sec and Aga monokaryons, geno-typed the progeny, and performed bulked segregant analysis (BSA). We also fruited three Sec/Sec and three Aga/Aga dikaryons, and sampled transcriptomes at four developmental stages. Using BSA, we identified 105 …

Technology And Grieving: A Relationship, James Nichols

Biology

No abstract provided.

Bone Morphogenetic Protein Signaling Is Required For Rad51-Mediated Maintenance Of Genome Integrity In Vascular Endothelial Cells, Sanna Vattulainen-Collanus, Mark Southwood, Xu Dong Yang, Stephen Moore, Prajakta Ghatpande, Nicholas W. Morrell, Giorgio Lagna, Akiko Hata

Biology

The integrity of blood vessels is fundamental to vascular homeostasis. Inactivating mutations in the bone morphogenetic protein (BMP) receptor type II (BMPR2) gene cause hereditary vascular disorders, including pulmonary arterial hypertension and hereditary hemorrhagic telangiectasia, suggesting that BMPR2 and its downstream signaling pathway are pivotal to the maintenance of vascular integrity through an unknown molecular mechanism. Here we report that inactivation of BMPR2 in pulmonary vascular endothelial cells results in a deficit of RAD51, an enzyme essential for DNA repair and replication. Loss of RAD51, which causes DNA damage and cell death, is also detected in animal models and human …

A Student’S Perspective On Engagement In Ecological Research During Their First Semester In College, Natalie M. Aguirre, Karagan L. Smith, Cristian M. Garcia, Cheryl Swift, Stephen D. Davis

Biology

Pepperdine University and Whittier College jointly initiated a new first-year seminar series in the fall of 2016 that engaged students in authentic research, their first semester on campus. The goals are listed below. Assessment of these goals included both qualitative focus groups and quantitative survey questionnaires administered by an outside assessment agency, WestEd.org.

Ninety-two percent of students reported that their first-year seminar improved learning in concurrent courses and ninety to ninety-three percent of students said their first-year seminar increased their interest in STEM. In addition, students self-reported a significant improvement in all aspects of their ability to plan and conduct …

Evolutionary Dynamics Of Host Specialization In Wood-Decay Fungi, Franz Sebastian Krah, Claus Bässler, Christoph Heibl, John Soghigian, Hanno Schaefer, David S. Hibbett

Biology

Background: The majority of wood decomposing fungi are mushroom-forming Agaricomycetes, which exhibit two main modes of plant cell wall decomposition: white rot, in which all plant cell wall components are degraded, including lignin, and brown rot, in which lignin is modified but not appreciably removed. Previous studies suggested that brown rot fungi tend to be specialists of gymnosperm hosts and that brown rot promotes gymnosperm specialization. However, these hypotheses were based on analyses of limited datasets of Agaricomycetes. Overcoming this limitation, we used a phylogeny with 1157 species integrating available sequences, assembled decay mode characters from the literature, and coded …

Post Drought Recovery In Malosma Laurina After Severe Dieback During California’S Historic Drought Of 2012-2016, Karagan L. Smith, Guinevere X. Mesh, Natalie M. Aguirre, Gabriella N. Palmeri, Helen I. Holmlund, Stephen D. Davis

Biology

Malosma laurina is a species of chaparral shrub that dominates coastal exposures of the Santa Monica Mountains of southern California. Between 2012 and 2016, protracted drought with half normal rainfall over a five-year period (175 mm), led to severe dieback, exceeding 50% whole plant mortality at some sites. The drought dissipated in 2017 with an annual rainfall that exceeded the 140-yr normal by 108 mm. As a result of this elevated annual rainfall in 2017, we were interested in documenting the potential for full recovery of Malosma laurina as a keystone species of coastal chaparral shrub communities. We tested the …

Proposals For Consideration At Imc11 To Modify Provisions Related Solely To Fungi In The International Code Of Nomenclature For Algae, Fungi, And Plants, Luis A. Parra, Juan C. Zamora, David L. Hawksworth, David S. Hibbett, Paul M. Kirk, Robert Lücking, Gerhard Rambold, Konstanze Bensch, Yi Jian Yao, Vincent Robert, Dagmar Triebel

Biology

Seven proposals to modify the provisions of the International Code of Nomenclature for algae, fungi, and plants (ICN) at the 11th International Mycological Congress (IMC11) in July 2018 had been received by the proscribed date of 1 March 2018. These proposals are formally presented together here. The topics addressed relate to the clarification of the meaning of “original material” in relation to the typification of sanctioned names, the indication of the nomenclatural status of sanctioned names in author citations, the use of DNA sequences as nomenclatural types, and the possibility of including repository identifiers as an alternative to author citations. …

Phenotypic Plasticity In Light-Induced Flavonoids Varies Among Tissues In Silene Littorea (Caryophyllaceae), José Carlos Del Valle, Mª Luisa Buide, Justen B. Whittall, Eduardo Narbona

Biology

Plants respond to environmental stimuli in a diversity of ways including the production of secondary metabolites. Biosynthesis of plant phenolics, including flavonoids, is frequently activated in response to a variety of abiotic and biotic stressors (e.g. extreme temperatures, high radiation, pathogens, etc.). This induced reaction is typically assumed to be a plastic response, but the components attributable to plasticity vs genetic variance in these components are poorly understood. Here, we investigate the variation in flavonoid production (anthocyanins and flavones) in petals and in photosynthetic tissues (calyces, leaves and stems) of Silene littorea. We performed a common garden experiment with …

Digital Photography Provides A Fast, Reliable, And Noninvasive Method To Estimate Anthocyanin Pigment Concentration In Reproductive And Vegetative Plant Tissues, José C. Del Valle, Antonio Gallardo-López, Mª Luisa Buide, Justen B. Whittall, Eduardo Narbona

Biology

Anthocyanin pigments have become a model trait for evolutionary ecology as they often provide adaptive benefits for plants. Anthocyanins have been traditionally quantified biochemically or more recently using spectral reflectance. However, both methods require destructive sampling and can be labor intensive and challenging with small samples. Recent advances in digital photography and image processing make it the method of choice for measuring color in the wild. Here, we use digital images as a quick, noninvasive method to estimate relative anthocyanin concentrations in species exhibiting color variation. Using a consumer‐level digital camera and a free image processing toolbox, we extracted RGB …

Regressed But Not Gone: Patterns Of Vision Gene Loss And Retention In Subterranean Mammals, Christopher A. Emerling

Biology

Regressive evolution involves the degradation of formerly useful traits as organisms invade novel ecological niches. In animals, committing to a strict subterranean habit can lead to regression of the eyes, likely due to a limited exposure to light. Several lineages of subterranean mammals show evidence of such degeneration, which can include decreased organization of the retina, malformation of the lens, and subcutaneous positioning of the eye. Advances in DNA sequencing have revealed that this regression co-occurs with a degradation of genomic loci encoding visual functions, including protein-coding genes. Other dim light-adapted vertebrates with normal ocular anatomy, such as nocturnal and …

Chitinase Genes (Chias) Provide Genomic Footprints Of A Post-Cretaceous Dietary Radiation In Placental Mammals, Christopher A. Emerling, Frédéric Delsuc, Michael W. Nachman

Biology

The end-Cretaceous extinction led to a massive faunal turnover, with placental mammals radiating in the wake of nonavian dinosaurs. Fossils indicate that Cretaceous stem placentals were generally insectivorous, whereas their earliest Cenozoic descendants occupied a variety of dietary niches. It is hypothesized that this dietary radiation resulted from the opening of niche space, following the extinction of dinosaurian carnivores and herbivores. We provide the first genomic evidence for the occurrence and timing of this dietary radiation in placental mammals. By comparing the genomes of 107 placental mammals, we robustly infer that chitinase genes (CHIAs), encoding enzymes capable of digesting insect …

From Ground Pools To Treeholes: Convergent Evolution Of Habitat And Phenotype In Aedes Mosquitoes, John Soghigian, Theodore G. Andreadis, Todd P. Livdahl

Biology

Background: Invasive mosquito species are responsible for millions of vector-borne disease cases annually. The global invasive success of Aedes mosquitoes such as Aedes aegypti and Aedes albopictus has relied on the human transport of immature stages in container habitats. However, despite the importance of these mosquitoes and this ecological specialization to their widespread dispersal, evolution of habitat specialization in this group has remained largely unstudied. We use comparative methods to evaluate the evolution of habitat specialization and its potential influence on larval morphology, and evaluate whether container dwelling and invasiveness are monophyletic in Aedes. Results: We show that habitat specialization …

Draft Genome Sequence Of A Monokaryotic Model Brown-Rot Fungus Postia (Rhodonia) Placenta Sb12, Jill Gaskell, Phil Kersten, Luis F. Larrondo, Paulo Canessa, Diego Martinez, David Hibbett, Monika Schmoll, Christian P. Kubicek, Angel T. Martinez, Jagjit Yadav, Emma Master, Jon Karl Magnuson, Debbie Yaver, Randy Berka, Kathleen Lail, Cindy Chen, Kurt Labutti, Matt Nolan, Anna Lipzen, Andrea Aerts, Robert Riley, Kerrie Barry, Bernard Henrissat, Robert Blanchette, Igor V. Grigoriev, Dan Cullen

Biology

We report the genome of Postia (Rhodonia) placenta MAD-SB12, a homokaryotic wood decay fungus (Basidiomycota, Polyporales). Intensively studied as a representative brown rot decayer, the gene complement is consistent with the rapid depolymerization of cellulose but not lignin.

A Comparison Of Water Potential, Photosynthetic Rate, Electron Transport Rate, And Stomatal Conductance Between Native Malosma Laurina And Exotic Schinus Molle, Karagan L. Smith, Agatha C. Heng, Viridiana Hernandez-Lopez, Stephen D. Davis

Biology

Schinus molle is a relatively new invasive chaparral shrub in the Santa Monica Mountains and has only recently been observed to displace native shrubs like Malosma laurina. To investigate the probable cause of S. molle’s competitive displacement of M. laurina, we compared their water status, photosynthetic rates, electron transport rates, and stomatal conductance to water vapor diffusion during the fall months of 2016. We hypothesized that S. molle would physiologically outperform M. laurina indicated by higher photosynthetic rates, electron transport rates, stomatal conductance rates, and less negative water potential. We found that there was no significant difference between dry …

The Effect Of Drought On The Comparative Fitness Of Purple Needle Grass (Stipa Pulchra) In The Presence Of An Invasive Weed, Grace M. Palmer, Taylor M. Purdy, Stephen D. Davis

Biology

Studies on the relative health of Stipa pulchra, a California native perennial bunchgrass, were conducted at the transplant garden on the Drescher campus of Pepperdine University in the Spring semesters of 2016 and 2017. Following the trend of other perennial native grasses, Stipa pulchra is dwindling due to competition with Avena fatua and other invasive species introduced by human activities. In 2016, in the midst of historic five-year drought in California, stomatal conductance, dark adapted fluorescence, water potential, and height of S. pulchra and A. fatua were recorded and compared. As hypothesized, the wild S. pulchra exhibited greater overall fitness-- …

Assessment Of Intra And Interregional Genetic Variation In The Eastern Red-Backed Salamander, Plethodon Cinereus, Via Analysis Of Novel Microsatellite Markers, Alexander C. Cameron

Biology

The red-backed salamander (Plethodon cinereus) has long-served as a model system in ecology, evolution, and behavior, and studies surveying molecular variation in this species have become increasingly common over the past decade. However, difficulties are commonly encountered when extending microsatellite markers to populations that are unstudied from a genetic perspective due to high levels of genetic differentiation across this species’ range. To ameliorate this issue, we used 454 pyrosequencing to identify hundreds of microsatellite loci. We then screened 40 of our top candidate loci in populations in Virginia, Pennsylvania, and Ohio—including an isolated island population ~ 4.5 km off the …

The Folded K-Spectrum Kernel: A Machine Learning Approach To Detecting Transcription Factor Binding Sites With Gapped Nucleotide Dependencies, Abdulkadir Elmas, Xiaodong Wang, Jacqueline M. Dresch

Biology

Understanding the molecular machinery involved in transcriptional regulation is central to improving our knowledge of an organism’s development, disease, and evolution. The building blocks of this complex molecular machinery are an organism’s genomic DNA sequence and transcription factor proteins. Despite the vast amount of sequence data now available for many model organisms, predicting where transcription factors bind, often referred to as ‘motif detection’ is still incredibly challenging. In this study, we develop a novel bioinformatic approach to binding site prediction. We do this by extending pre-existing SVM approaches in an unbiased way to include all possible gapped k-mers, representing different …

There’S More Than One Way To Climb A Tree: Limb Length And Microhabitat Use In Lizards With Toe Pads, Travis J. Hagey, Scott Hart, Matthew Vickers, Luke J. Harmon, Lin Schwarzkopf

Biology

Ecomorphology links microhabitat and morphology. By comparing ecomorphological associations across clades, we can investigate the extent to which evolution can produce similar solutions in response to similar challenges. While Anolis lizards represent a well-studied example of repeated convergent evolution, very few studies have investigated the ecomorphology of geckos. Similar to anoles, gekkonid lizards have independently evolved adhesive toe pads and many species are scansorial. We quantified gecko and anole limb length and microhabitat use, finding that geckos tend to have shorter limbs than anoles. Combining these measurements with microhabitat observations of geckos in Queensland, Australia, we observed geckos using similar …

Differential Response To Mosquito Host Sex And Parasite Dosage Suggest Mixed Dispersal Strategies In The Parasite Ascogregarina Taiwanensis, John Soghigian, Todd Livdahl

Biology

Mixed dispersal strategies are a form of bet hedging in which a species or population utilizes different dispersal strategies dependent upon biotic or abiotic conditions. Here we provide an example of a mixed dispersal strategy in the Aedes albopictus / Ascogregarina taiwanensis host/parasite system, wherein upon host emergence, the gregarine parasite is either carried with an adult mosquito leaving the larval habitat, or released back into the larval habitat. We show that the parasite invests a larger proportion of its dispersing (oocyst) life stage into adult female mosquitoes as opposed to adult male mosquitoes at low parasite exposure levels. However, …

Swing Boat: Inducing And Recording Locomotor Activity In A Drosophila Melanogaster Model Of Alzheimer’S Disease, Johannes Berlandi, Fang Ju Lin, Oliver Ambrée, Dirk Rieger, Werner Paulus, Astrid Jeibmann

Biology

Recent studies indicate that physical activity can slow down progression of neurodegeneration in humans. To date, automated ways to induce activity have been predominantly described in rodent models. To study the impact of activity on behavior and survival in adult Drosophila melanogaster, we aimed to develop a rotating tube device “swing boat” which is capable of monitoring activity and sleep patterns as well as survival rates of flies. For the purpose of a first application, we tested our device on a transgenic fly model of Alzheimer’s disease (AD). Activity of flies was recorded in a climate chamber using the Drosophila …

Conflicting Evolutionary Histories Of The Mitochondrial And Nuclear Genomes In New World Myotis Bats, Thomas Lee Jr.

Biology

The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred fromnuclear markers lackedresolution. Our current understanding of relationships withinMyotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this,we sequenced the full mitochondrial genomes of 37 representativeMyotis, primarily fromtheNewWorld, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic …

Spatiotemporal Regulation Of Nervous System Development In The Annelid Capitella Teleta, Abhinav Sur, Craig R. Magie, Elaine C. Seaver, Néva P. Meyer

Biology

Background: How nervous systems evolved remains an unresolved question. Previous studies in vertebrates and arthropods revealed that homologous genes regulate important neurogenic processes such as cell proliferation and differentiation. However, the mechanisms through which such homologs regulate neurogenesis across different bilaterian clades are variable, making inferences about nervous system evolution difficult. A better understanding of neurogenesis in the third major bilaterian clade, Spiralia, would greatly contribute to our ability to deduce the ancestral mechanism of neurogenesis. Results: Using whole-mount in situ hybridization, we examined spatiotemporal gene expression for homologs of soxB, musashi, prospero, achaete-scute, neurogenin, and neuroD in embryos and …

Resistance To Xylem Cavitation In Evergreen Ferns Correlates With Seasonal Dehydration Levels, Not Mechanical Strength, Helen I. Holmlund, Kaitlyn E. Sauer, Breahna M. Gillespie, Jarmila Pittermann, Stephen D. Davis

Biology

Ferns in the Santa Monica Mountains of southern California display a range of responses to severe drought. In this study, we further characterized the traits that may contribute to fern survival in a mediterranean-type climate. Due to anatomical differences between ferns and angiosperms, we predicted that ferns would exhibit no correlation between stipe mechanical strength and vulnerability to water stress-induced cavitation of stipe xylem. However, we predicted that ferns would show a correlation between seasonal water stress (minimum water potential) and cavitation resistance. Our results support these hypotheses; however, we must increase our sample size of evergreen fern species in …

Let-7 Microrna-Dependent Control Of Leukotriene Signaling Regulates The Transition Of Hematopoietic Niche In Mice, Xuan Jiang, John S. Hawkins, Jerry Lee, Carlos O. Lizama, Nicholas S. Hill, Matthew D. Layne, Akiko Hata, Giorgio Lagna

Biology

Hematopoietic stem and progenitor cells arise from the vascular endothelium of the dorsal aorta and subsequently switch niche to the fetal liver through unknown mechanisms. Here we report that vascular endothelium-specific deletion of mouse Drosha (Drosha cKO), an enzyme essential for microRNA biogenesis, leads to anemia and death. A similar number of hematopoietic stem and progenitor cells emerge from Drosha-deficient and control vascular endothelium, but Drosha cKO-derived hematopoietic stem and progenitor cells accumulate in the dorsal aorta and fail to colonize the fetal liver. Depletion of the let-7 family of microRNAs is a primary cause of this defect, as it …

Tempo And Mode Of Performance Evolution Across Multiple Independent Origins Of Adhesive Toe Pads In Lizards, Travis J. Hagey, Josef C. Uyeda, Kristen E. Crandell, Jorn A. Cheney, Kellar Autumn, Luke J. Harmon

Biology

Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics. Here, we ask whether convergent evolution of pad-bearing lizards has followed similar evolutionary dynamics, or whether independent origins are accompanied by unique constraints and selective …

Mycophagous Rove Beetles Highlight Diverse Mushrooms In The Cretaceous, Chenyang Cai, Richard A.B. Leschen, David S. Hibbett, Fangyuan Xia, Diying Huang

Biology

Agaricomycetes, or mushrooms, are familiar, conspicuous and morphologically diverse Fungi. Most Agaricomycete fruiting bodies are ephemeral, and their fossil record is limited. Here we report diverse gilled mushrooms (Agaricales) and mycophagous rove beetles (Staphylinidae) from mid-Cretaceous Burmese amber, the latter belonging to Oxyporinae, modern members of which exhibit an obligate association with soft-textured mushrooms. The discovery of four mushroom forms, most with a complete intact cap containing distinct gills and a stalk, suggests evolutionary stasis of body form for ∼99 Myr and highlights the palaeodiversity of Agaricomycetes. The mouthparts of early oxyporines, including enlarged mandibles and greatly enlarged apical labial …

Competition From Bromus Tectorum Removes Differences Between Perennial Grasses In N Capture And Conservation Strategies, Rebecca E. Drenovsky, Jeffrey T. Walker, J. J. James

Biology

Background and aims

Competition from the annual grass Bromus tectorum threatens aridland perennial bunchgrass communities. Unlike annuals, perennials must allocate part of their first year nitrogen (N) budget to storage rather than growth, potentially placing them at a competitive disadvantage.

Methods

We evaluated N acquisition and conservation for two perennial bunchgrasses, Agropyron desertorum and Pseudoroegneria spicata, at the seedling stage to investigate potential trade-offs between storage and growth when grown with and without B. tectorum under two levels of soil N.

Results

Agropyron desertorum had higher growth rates, N uptake, and N productivity than P. spicata when grown without …

A Parasite's Modification Of Host Behavior Reduces Predation On Its Host, John Soghigian, Linda R. Valsdottir, Todd P. Livdahl

Biology

Parasite modification of host behavior is common, and the literature is dominated by demonstrations of enhanced predation on parasitized prey resulting in transmission of parasites to their next host. We present a case in which predation on parasitized prey is reduced. Despite theoretical modeling suggesting that this phenomenon should be common, it has been reported in only a few host–parasite–predator systems. Using a system of gregarine endosymbionts in host mosquitoes, we designed experiments to compare the vulnerability of parasitized and unparasitized mosquito larvae to predation by obligate predatory mosquito larvae and then compared behavioral features known to change in the …

Do The Shuffle: Changes In Symbiodinium Consortia Throughout Juvenile Coral Development, Hannah G. Reich, Deborah L. Robertson, Gretchen Goodbody-Gringley

Biology

Previous studies of symbiotic associations between scleractinians corals and Symbiodinium have demonstrated that the consortium of symbionts can change in response to environmental conditions. However, less is known about symbiont shuffling during early coral development, particularly in brooding species. This study examined whether Symbiodinium consortia (1) varied in Porites astreoides on shallow (10m) and upper mesophotic (30m) reefs, (2) changed during coral development, and (3) influenced growth of juveniles in different environments. Symbiodinium ITS2 sequences were amplified using universal primers and analyzed using phylotype-specific primers designed for phylotypes A, B, and C. Adults from both depths were found to host …