10 Works

Data from: A whole-transcriptome approach to evaluating reference genes for quantitative gene expression studies: a case study in Mimulus

Kimmy A. Stanton, Patrick P. Edger, Joshua R. Puzey, Taliesin Kinser, Philip Cheng, Daniel M. Vernon, Nancy R. Forsthoefel & Arielle M. Cooley
While quantitative PCR (qPCR) is widely recognized as being among the most accurate methods for quantifying gene expression, it is highly dependent on the use of reliable, stably expressed reference genes. With the increased availability of high-throughput methods for measuring gene expression, whole-transcriptome approaches may be increasingly utilized for reference gene selection and validation. In this study, RNA-seq was used to identify a set of novel qPCR reference genes and evaluate a panel of traditional...

Data from: Timber harvest and tree size near nests explains variation in nest site occupancy but not productivity in northern goshawks (Accipiter gentilis)

Sabrina A. Rodriguez, Patricia L. Kennedy & Timothy H. Parker
Conservation concern for the northern goshawk (Accipiter gentilis) reflects evidence that goshawks may abandon nest sites or suffer from reduced nesting success in response to some forms of timber harvest. However, this evidence is mixed and has yet to be reviewed systemically and quantitatively. Therefore, we conducted a meta-analysis to assess the extent to which timber harvest and tree size explain variation in goshawk productivity and site occupancy. Goshawk productivity was not significantly explained by...

Melanic pigmentation and light preference within and between two Drosophila species

Arielle Cooley, Suzanne Schmitz, Eduardo Cabrera, Mitchell Cutter, Maxwell Sheffield, Ian Gingerich, Gabriella Thomas, Calvin Lincoln, Virginia Moore, Alexandra Moore, Sarah Davidson, Nikhil Lonberg, Eli Fournier, Sophia Love, Galen Posch, Matthew Bihrle, Spencer Mayer, Kuenzang Om, Lauren Wilson, Casey Doe, Chantalle Vincent, Elizabeth Wong, Ilona Wall, Jarred Wicks & Stephon Roberts
Environmental adaptation and species divergence often involve suites of co-evolving traits. Pigmentation in insects presents a variable, adaptive, and well-characterized class of phenotypes for which correlations with multiple other traits have been demonstrated. In Drosophila, the pigmentation genes ebony and tan have pleiotropic effects on flies’ response to light, creating the potential for correlated evolution of pigmentation and vision. Here we investigate differences in light preference within and between two sister species, Drosophila americana and...

Neurophysiological coordination of duet singing

Melissa J Coleman, Nancy F Day, Pamela Rivera-Parra & Eric S Fortune
Cooperation is critical for survival and reproduction in many animal species. Coordination of behavior for cooperative performances often relies on linkages mediated by sensory cues exchanged between participants. How neurophysiological responses to sensory information affect motor programs to coordinate behavior between individuals is not known. We investigated how plain-tailed wrens (Pheugopedius euophrys) use acoustic feedback to coordinate extraordinary duet performances in which females and males rapidly take turns singing. We made simultaneous neurophysiological recordings in...

Data from: Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower

Patrick P. Edger, Ronald D. Smith, Michael R. McKain, Arielle M. Cooley, Mario Vallejo-Marin, Yao-Wu Yuan, Adam J. Bewick, Lexiang Ji, Adrian E. Platts, Megan J. Bowman, Kevin Childs, Jacob D. Washburn, Robert Schmitz, Gregory D. Smith, J. Chris Pires & Joshua R. Puzey
Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant - having both retained more genes and being more highly expressed - a phenomenon termed subgenome dominance. The genomic features that determine how quickly and which subgenome dominates within a newly formed polyploid remain poorly understood. To investigate the rate of subgenome dominance emergence, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural,...

Data from: Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor

Mario Vallejo-Marin, Arielle M. Cooley, Michelle Yuequi Lee, Madison Folmer, Michael R. McKain & Joshua Robert Puzey
PREMISE OF THE STUDY: Hybridization between diploids and tetraploids can lead to new allopolyploid species, often via a triploid intermediate. Viable triploids are often produced asymmetrically, with greater success observed for “maternal-excess” crosses where the mother has a higher ploidy than the father. Here we investigated the evolutionary origins of Mimulus peregrinus, an allohexaploid recently derived from the triploid M. ×robertsii, to determine whether reproductive asymmetry has shaped the formation of this new species. METHODS:...

Data from: Reduced skin bacterial diversity correlates with increased pathogen infection intensity in an endangered amphibian host

Silas Ellison, Roland A. Knapp, Wesley Sparagon, Andrea Swei & Vance T. Vredenburg
The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects the skin of amphibians, and has caused severe declines and extinctions of amphibians globally. In this study, we investigate the interaction between Bd and the bacterial skin microbiome of the endangered Sierra Nevada yellow-legged frog, Rana sierrae, using both culture-dependent and culture-independent methods. Samples were collected from two populations of R. sierrae that likely underwent Bd epizootics in the past, but that continue to persist with Bd in...

Data from: Speciation by genome duplication: repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus

Mario Vallejo-Marin, Richard J. A. Buggs, Arielle M. Cooley & Joshua R. Puzey
Whole genome duplication (polyploidisation) is a mechanism of “instantaneous” species formation that has played a major role in the evolutionary history of plants. Much of what we know about the early evolution of polyploids is based upon studies of a handful of recently formed species. A new polyploid hybrid (allopolyploid) species Mimulus peregrinus, formed within the last 140 years, was recently discovered on the Scottish mainland and corroborated by chromosome counts. Here, using targeted, high-depth...

Data from: Long-term persistence of wildlife populations in a pastoral area

Christian Kiffner, John Kioko, Jack Baylis, Camille Beckwith, Craig Brunner, Christine Burns, Vasco Chavez-Molina, Sara Cotton, Laura Glazik, Ellen Loftis, Megan Moran, Caitlin O’Neill, Ole Theisinger & Bernard Kissui
Facilitating coexistence between people and wildlife is a major conservation challenge in East Africa. Some conservation models aim to balance the needs of people and wildlife, but the effectiveness of these models is rarely assessed. Using a case-study approach, we assessed the ecological performance of a pastoral area in northern Tanzania (Manyara Ranch) and established a long-term wildlife population monitoring programme (carried out intermittently from 2003-2008 and regularly from 2011-2019) embedded in a distance sampling...

Endosperm-based incompatibilities in hybrid monkeyflowers

Taliesin Kinser, Ronald Smith, Amelia Lawrence, Arielle Cooley, Mario Vallejo-Marín, Gregory Conradi Smith & Joshua Puzey
The sexual endosperm is an angiosperm innovation central to flowering plant reproduction. Genomic interactions between parental alleles control its development and help determine seed viability. These interactions are characterized by genomic imprinting, where expression from certain genes is parent-specific. Unsuccessful imprinting has been linked to failed hybridization between plants of different species or ploidies. Here, we describe an endosperm-based barrier between Mimulus guttatus, a diploid, and M. luteus, an allotetraploid. Hybrid seeds suffer from underdeveloped...

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