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A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)
The proliferation of genomic sequencing approaches has significantly impacted the field of phylogenetics. Target capture approaches provide a cost-effective, fast and easily applied strategy for phylogenetic inference of non-model organisms. However, several existing target capture processing pipelines are incapable of incorporating whole genome sequencing (WGS). Here, we develop a new pipeline fo
Authors
André Gomes-dos-Santos, Elsa Froufe, John M. Pfeiffer, Nathan Johnson, Chase H. Smith, André M. Machado, L. Filipe C. Castro, Van Tu Do, Akimasa Hattori, Nicole Garrison, Nathan V. Whelan, Ivan N. Bolotov, Ilya V. Vikhrev, Alexander V. Kondakov, Mohamed Ghamizi, Vincent Prié, Arthur E. Bogan, Manuel Lopes Lima
Strength recovery in quartzite is controlled by changes in friction in experiments at hydrothermal conditions up to 200°C
The rate of fault zone restrengthening between earthquakes can be influenced by both frictional and cohesive healing processes. Friction is dependent on effective normal stress while cohesion is independent of normal stress, potentially explaining—in part—the lack of depth dependence of earthquake stress drops. Although amenable to laboratory testing, few studies have systematically addressed the
Authors
Tamara Nicole Jeppson, David A. Lockner, Nicholas M. Beeler, Stephen H. Hickman
Kings of the North: Bridging disciplines to understand the effects of changing climate on Chinook salmon in the Arctic-Yukon-Kuskokwim Region
Understanding how species are responding to environmental change is a central challenge for stewards and managers of fish and wildlife who seek to maintain harvest opportunities for communities and Indigenous peoples. This is a particularly daunting but increasingly important task in remote, high-latitude regions where environmental conditions are changing rapidly and data collection is logistical
Authors
Megan L. Feddern, Erik R. Schoen, Rebecca Shaftel, Curry J. Cunningham, Craig Chythlook, Brendan M. Connors, Alyssa D. Murdoch, Vanessa R. von Biela, Brooke Woods
Contributions to uncertainty in runup forecasts
The U.S. Geological Survey (USGS) provides operational forecasts of total water levels (TWL) and coastal change. Uncertainties around forecast TWL are based on the temporal and spatial range of observed beach slopes near the forecast site. This paper investigates other sources of uncertainty that are not accounted for, focusing on four beaches where the USGS has deployed remote cameras, and on out
Authors
Christopher R. Sherwood, Alfredo Aretxabaleta, Peter A. Traykovski, Jin-Si R. Over, Erin Lyons, David S. Foster, Jennifer L. Miselis, Timothy Nelson, Erdinc Sogut
A coupled human and natural systems framework to characterize emerging infectious diseases: The case of fibropapillomatosis in marine turtles
Emerging infectious diseases of wildlife have markedly increased in the last few decades. Unsustainable, continuous, and rapid alterations within and between coupled human and natural systems have significantly disrupted wildlife disease dynamics. Direct and indirect anthropogenic effects, such as climate change, pollution, encroachment, urbanization, travel, and trade, can promote outbreaks of in
Authors
Costanza Manes, Raymond Carthy, Vanessa Hull
Exploring the relevance of the multidimensionality of wildlife recreationists to conservation behaviors: A case study in Virginia
Wildlife recreationists' participation in conservation behaviors could provide key support to the conservation efforts of state fish and wildlife agencies. However, little is known about how identifying with multiple forms of wildlife recreation (i.e., hunters, anglers, birders, wildlife viewers) may influence participation in conservation behaviors, specifically for supporting state fish and wild
Authors
Bennett Grooms, Ashley A. Dayer, Jessica Barnes, Ashley Peele, Jonathan D. Rutter, Nicholas Cole
Estimating the impact of climate and vegetation changes on runoff risk across the Hawaiian landscape
In Hawai’i, ecosystem conservation practitioners are increasingly considering the potential ecohydrological benefits from applied conservation action to mitigate the degrading impacts of runoff on native and restored ecosystems. One determinant of runoff is excess rainfall events where rainfall rates exceed the infiltration capacity of soils. To help understand runoff risks, we calculated the prob
Authors
Lucas Fortini, Lauren R. Kaiser, Kimberlie Perkins, Lulin Xue, Yaping Wang
The energy–water limitation threshold explains divergent drought responses in tree growth, needle length, and stable isotope ratios
Predicted increases in extreme droughts will likely cause major shifts in carbon sequestration and forest composition. Although growth declines during drought are widely documented, an increasing number of studies have reported both positive and negative responses to the same drought. These divergent growth patterns may reflect thresholds (i.e., nonlinear responses) promoted by changes in the domi
Authors
Joan Dudney, Andrew M. Latimer, Phillip J. van Mantgem, Harold S. Zald, Claire E Willing, Jonathan C.B. Nesmith, Jennifer E Cribbs, Elizabeth R Milano
Geoelectric monitoring of the electric potential field of the Lower Rio Grande before, during, and after Intermittent Streamflow, May–October, 2022
Understanding the intermittent hydraulic connectivity between ephemeral streams and alluvial aquifers is a key challenge for managing water resources in arid environments. The lower Rio Grande flows for short, discontinuous periods during the irrigation season through the Mesilla Basin in southeastern New Mexico and southwestern Texas. Hydraulic connections between the Rio Grande and the Rio Grand
Authors
Scott Ikard, Kenneth C. Carroll, Dale F. Rucker, Andrew Teeple, Jason D. Payne, Chia-Hsing Tsai, Erek H. Fuchs, Ahsan Jamil
Improving ecological data science with workflow management software
Pressing environmental research questions demand the integration of increasingly diverse and large-scale ecological datasets as well as complex analytical methods, which require specialized tools and resources.Computational training for ecological and evolutionary sciences has become more abundant and accessible over the past decade, but tool development has outpaced the availability of specialize
Authors
Matthew R. Brousil, Alessandro Filazzola, Michael Frederick Meyer, Sapna Sharma, Stephanie E. Hampton
Quantifying uncertainty in coastal salinity regime for biological application using quantile regression
Salinity regimes in coastal ecosystems are highly dynamic and driven by complex geomorphic and hydrological processes. Estuarine biota are generally adapted to salinity fluctuation, but are vulnerable to salinity extremes. Characterizing coastal salinity regime for ecological studies therefore requires representing extremes of salinity ranges at time scales relevant to ecology (e.g., daily, monthl
Authors
Simeon Yurek, Micheal S Allen, Mitchell Eaton, David Chagaris, Nathan Reaver, Julien Martin, Peter C Frederick, Mark Dehaven
The effects of management practices on grassland birds—Dickcissel (Spiza americana)
Keys to Dickcissel (Spiza americana) management include providing dense, moderate-to-tall vegetation, particularly with a well-developed forb component, and moderately deep litter. Dickcissels have been reported to use grassland habitats with 4–166 centimeters (cm) average vegetation height, 6–85 cm visual obstruction reading, 11–68 percent grass cover, 1–86 percent forb cover, less than or equal
Authors
Jill A. Shaffer, Lawrence D. Igl, Douglas H. Johnson, Marriah L. Sondreal, Christopher M. Goldade, Amy L. Zimmerman, Betty R. Euliss