1,041 Works

Data from: Spatial and temporal dynamics and value of nature-based recreation, estimated via social media

Laura J. Sonter, Keri B. Watson, Spencer A. Wood & Taylor H. Ricketts
Conserved lands provide multiple ecosystem services, including opportunities for nature-based recreation. Managing this service requires understanding the landscape attributes underpinning its provision, and how changes in land management affect its contribution to human wellbeing over time. However, evidence from both spatially explicit and temporally dynamic analyses is scarce, often due to data limitations. In this study, we investigated nature-based recreation within conserved lands in Vermont, USA. We used geotagged photographs uploaded to the photo-sharing website...

Data from: Genetic signatures of ecological diversity along an urbanization gradient

Ryan P. Kelly, James L. O'Donnell, Natalie C. Lowell, Andrew O. Shelton, Jameal F. Samhouri, Shannon M. Hennessey, Blake E. Feist & Gregory D. Williams
Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore...

Data from: Use of glacial fronts by narwhals (Monodon monoceros) in West Greenland

Kristin L. Laidre, Twila Moon, Donna D.W. Hauser, Richard McGovern, Mads Peter Heide-Joergensen, Rune Dietz, Benjamin Hudson, Donna D. W. Hauser & Ben Hudson
Glacial fronts are important summer habitat for narwhals (Monodon monoceros), however, no studies have quantified which glacial properties attract whales. We investigated the importance of glacial habitats using telemetry data from n=15 whales in September 1993-1994 and 2006-2007 in Melville Bay, West Greenland. For 41 marine-terminating glaciers, we estimated 1) narwhal presence/absence, 2) number of 24 h periods spent at glaciers, and 3) the fraction of narwhals that visited each glacier (at 5, 7, and...

Data from: Quantifying the effect of gape and morphology on bite force: biomechanical modeling and in vivo measurements in bats

Sharlene E. Santana
Maximum bite force is an important metric of feeding performance that defines the dietary ecology of many vertebrates. In mammals, theoretical analyses and empirical studies suggest a trade-off between maximum bite force and gape at behavioural and evolutionary scales; in vivo bite force is expected to decrease at wide gapes, and cranial morphologies that enable high mechanical advantage are thought to have a lower ability to generate high bite forces at wide gapes, and vice...

Data from: A submersible, off-axis holographic microscope for detection of microbial motility and morphology in aqueous and icy environments

Christian A. Lindensmith, Stephanie Rider, Manuel Bedrossian, J. Kent Wallace, Eugene Serabyn, Gordon M. Showalter, Jody W. Deming & Jay L. Nadeau
Sea ice is an analog environment for several of astrobiology’s near-term targets: Mars, Europa, Enceladus, and perhaps other Jovian or Saturnian moons. Microorganisms, both eukaryotic and prokaryotic, remain active within brine channels inside the ice, making it unnecessary to penetrate through to liquid water below in order to detect life. We have developed a submersible digital holographic microscope (DHM) that is capable of resolving individual bacterial cells, and demonstrated its utility for immediately imaging samples...

Data from: Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae)

Charles W. Linkem, Vladimir N. Minin & Adam D. Leaché
The anomaly zone, defined by the presence of gene tree topologies that are more probable than the true species tree, presents a major challenge to the accurate resolution of many parts of the Tree of Life. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data via loci concatenation will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies...

Data from: Individual marking of soft-bodied subtidal invertebrates in situ - a novel staining technique applied to the giant plumose anemone Metridium farcimen (Tilesius, 1809)

Christopher D. Wells & Kenneth P. Sebens
The ability to recognize individuals and track growth over time is crucial to population dynamics research as well as studies of animal behavior. Invertebrates are particularly difficult to track as they often molt, have regenerative capabilities, or lack hard parts to attach markers. We tested, in laboratory and field studies, a new way of marking sea anemones (order Actiniaria) by injection of three vital stains (i.e., neutral red, methylene blue, and fluorescein). Neutral red and...

Data from: Contrasting genetic metrics and patterns among naturalized rainbow trout (Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture

Cristian B. Canales-Aguirre, Lisa W. Seeb, James E. Seeb, Maria I. Cadiz, Selim S. Musleh, Ivan Arismendi, Gonzalo Gajardo, Ricardo Galleguillos & Daniel Gomez-Uchida
Different pathways of propagation and dispersal of non-native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setting to contrast these two pathways. Using a panel of single nucleotide polymorphisms, we found contrasting genetic metrics and patterns among naturalized trout in Lake Llanquihue, Chile’s largest producer of...

Data from: 2D or Not 2D? Testing the utility of 2D vs. 3D landmark data in geometric morphometrics of the sculpin subfamily Oligocottinae (Pisces; Cottoidea)

Thaddaeus J. Buser, Brian L. Sidlauskas & Adam P. Summers
We contrast 2D vs. 3D landmark‐based geometric morphometrics in the fish subfamily Oligocottinae by using 3D landmarks from CT‐generated models and comparing the morphospace of the 3D landmarks to one based on 2D landmarks from images. The 2D and 3D shape variables capture common patterns across taxa, such that the pairwise Procrustes distances among taxa correspond and the trends captured by principal component analysis are similar in the xy plane. We use the two sets...

Data from: Taxonomy-based hierarchical analysis of natural mortality: polar and sub-polar phocid seals

Irina S. Trukhanova, Paul B. Conn & Peter L. Boveng
Knowledge of life‐history parameters is frequently lacking in many species and populations, often because they are cryptic or logistically challenging to study, but also because life‐history parameters can be difficult to estimate with adequate precision. We suggest using hierarchical Bayesian analysis (HBA) to analyze variation in life‐history parameters among related species, with prior variance components representing shared taxonomy, phenotypic plasticity, and observation error. We develop such a framework to analyze U‐shaped natural mortality patterns typical...

Data from: The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life

Walter Jetz & R. Alexander Pyron
Human activities continue to erode the tree of life, requiring us to prioritize research and conservation. Amphibians represent key victims and bellwethers of global change, and the need for action to conserve them is drastically outpacing knowledge. We provide a phylogeny incorporating nearly all extant amphibians (7,238 species). Current amphibian diversity is composed of both older, depauperate lineages and extensive, more recent tropical radiations found in select clades. Frog and salamander diversification increased strongly after...

Data from: Geometric morphometrics reveal altered corpus callosum shape in pyridoxine-dependent epilepsy

Gabriela Oesch, A. Murat Maga, Seth D. Friedman, Sandra L. Poliachik, Christopher B. Budech, Jason N. Wright, Levinus A. Bok & Sidney M. Gospe
Objective: To evaluate the features and maturational changes in overall callosal shape in patients with pyridoxine-dependent epilepsy (PDE). Methods: Measurements were conducted through landmark based geometric morphometrics applied on cerebral MRIs of PDE patients and age-matched control subjects. The outline of the corpus callosum was manually traced in the midsagittal plane. 300 semi-landmarks along the outline were collected and underwent statistical generalized Procrustes analysis. An allometric regression was applied to evaluate the callosal shape due...

Data from: Genetic signals of artificial and natural dispersal linked to colonization of South America by non-native Chinook salmon (Oncorhynchus tshawytscha)

Daniel Gomez-Uchida, Diego Cañas-Rojas, Carla M. Riva-Rossi, Javier E. Ciancio, Miguel A. Pascual, Billy Ernst, Eduardo Aedo, Selim S. Musleh, Francisca Valenzuela-Aguayo, Thomas P. Quinn, James E. Seeb & Lisa W. Seeb
Genetics data have provided unprecedented insights into evolutionary aspects of colonization by non-native populations. Yet, our understanding of how artificial (human-mediated) and natural dispersal pathways of non-native individuals influence genetic metrics, evolution of genetic structure, and admixture remains elusive. We capitalize on the widespread colonization of Chinook salmon Oncorhynchus tshawytscha in South America, mediated by both dispersal pathways, to address these issues using data from a panel of polymorphic SNPs. First, genetic diversity and the...

Data from: A practical introduction to random forest for genetic association studies in ecology and evolution

Marine S.O. Brieuc, Charles D. Waters, Daniel P. Drinan, Kerry Ann Naish & Marine S. O. Brieuc
Large genomic studies are becoming increasingly common with advances in sequencing technology, and our ability to understand how genomic variation influences phenotypic variation between individuals has never been greater. The exploration of such relationships first requires the identification of associations between molecular markers and phenotypes. Here we explore the use of Random Forest (RF), a powerful machine learning algorithm, in genomic studies to discern loci underlying both discrete and quantitative traits, particularly when studying wild...

Data from: Genomewide association analyses of fitness traits in captive-reared Chinook salmon: applications in evaluating conservation strategies

Charles D. Waters, Jeffrey J. Hard, Marine S.O. Brieuc, David E. Fast, Kenneth I. Warheit, Curtis M. Knudsen, William J. Bosch, Kerry A. Naish & Marine S. O. Brieuc
A novel application of genome-wide association analyses is to use trait-associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive- and wild-origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon (Oncorhynchus...

Data from: Accounting for observation processes across multiple levels of uncertainty improves inference of species distributions and guides adaptive sampling of environmental DNA

Amy J. Davis, Kelly E. Williams, Nathan P. Snow, Kim M. Pepin & Antoinette J. Piaggio
Understanding factors that influence observation processes is critical for accurate assessment of underlying ecological processes. When indirect methods of detection, such as environmental DNA, are used to determine species presence, additional levels of uncertainty from observation processes need to be accounted for. We conducted a field trial to evaluate observation processes of a terrestrial invasive species (wild pigs- Sus scrofa) from DNA in water bodies. We used a multi-scale occupancy analysis to estimate different levels...

Data from: High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

James Starrett, Shahan Derkarabetian, Marshal Hedin, , John E. McCormack, Brant C. Faircloth & Robert W. Bryson
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic...

Data from: Forty years of seagrass population stability and resilience in an urbanizing estuary

Andrew Olaf Shelton, Tessa B. Francis, Blake E. Feist, Gregory D. Williams, Adam Lindquist, Phillip S. Levin & Philip S. Levin
Coasts and estuaries contain among the most productive and ecologically important habitats in the world and face intense pressure from current and projected human activities, including coastal development. Seagrasses are a key habitat feature in many estuaries perceived to be in widespread decline owing to human actions. We use spatio-temporal models and a 41-year time series from 100s of km of shoreline which includes over 160 000 observations from Puget Sound, Washington, USA, to examine...

Data from: Phylogeny and new taxonomy of the Booted Eagles (Accipitriformes: Aquilinae)

Heather R. L. Lerner, Les Christidis, Anita Gamauf, Carole Griffiths, Elisabeth Haring, Christopher J. Huddleston, Sonia Kabra, Annett Kocum, Meade Krosby, Kirsti Kvaloy, David Mindell, Pamela Rasmussen, Nils Rov, Rachel Wadleigh, Michael Wink & Jan Ove Gjershaug
We present a phylogeny of all booted eagles (38 extant and one extinct species) based on analysis of published sequences from seven loci. We find molecular support for five major clades within the booted eagles: Nisaetus (10 species), Spizaetus (4 species), Clanga (3 species), Hieraaetus (6 species) and Aquila (11 species), requiring generic changes for 14 taxa. Additionally, we recommend that the Long-crested Eagle (Lophaetus occipitalis) and the Black Eagle (Ictinaetus malaiensis) remain in their...

Data from: Multiple natural enemies cause distance-dependent mortality at the seed-to-seedling transition

Evan C. Fricke, Joshua J. Tewksbury & Haldre S. Rogers
Specialised natural enemies maintain forest diversity by reducing tree survival in a density- or distance-dependent manner. Fungal pathogens, insects and mammals are the enemy types most commonly hypothesised to cause this phenomenon. Still, their relative importance remains largely unknown, as robust manipulative experiments have generally targeted a single enemy type and life history stage. Here, we use fungicide, insecticide and physical exclosure treatments to isolate the impacts of each enemy type on two life history...

Data from: A phylogenomic perspective on the biogeography of skinks in the Plestiodon brevirostris group inferred from target enrichment of ultraconserved elements

, Charles W. Linkem, Carlos J. Pavón-Vázquez, Adrián Nieto-Montes De Oca, John Klicka, John E. McCormack & Robert W. Bryson
Aim: The aim of our study was to reconstruct ancestral geographic distributions from time-calibrated phylogenies generated from phylogenomic data to answer three broad questions about the biogeography of skinks in the Plestiodon brevirostris group: (1) Are biogeographic patterns correlated with the formation of the Trans-Mexican Volcanic Belt? (2) Do different methods of phylogenetic estimation result in different topologies? If so, (3) are biogeographic reconstructions impacted by the use of different phylogenetic trees? Location: Mexico. Methods:...

Data from: A major shift in diversification rate helps explain macroevolutionary patterns in primate species diversity

Jessica H. Arbour & Sharlene E. Santana
Primates represent one of the most species rich, wide ranging and ecologically diverse clades of mammals. What major macroevolutionary factors have driven their diversification and contributed to the modern distribution of primate species remains widely debated. We employed phylogenetic comparative methods to examine the role of clade age and evolutionary rate heterogeneity in the modern distribution of species diversity of Primates. Primate diversification has accelerated since its origin, with decreased extinction leading to a shift...

Data from: Tracing the dynamics of gene transcripts after organismal death

Alexander E. Pozhitkov, Rafik Neme, Tomislav Domazet-Lošo, Brian G. Leroux, Shivani Soni, Diethard Tautz & Peter A. Noble
In life, genetic and epigenetic networks precisely coordinate the expression of genes—but in death, it is not known if gene expression diminishes gradually or abruptly stops or if specific genes and pathways are involved. We studied this by identifying mRNA transcripts that apparently increase in relative abundance after death, assessing their functions, and comparing their abundance profiles through postmortem time in two species, mouse and zebrafish. We found mRNA transcript profiles of 1063 genes became...

Data from: A new Late Cretaceous iguanomorph from North America and the origin of New World Pleurodonta (Squamata, Iguania)

David G. DeMar, Jack L. Conrad, Jason J. Head, David J. Varricchio & Gregory P. Wilson
Iguanomorpha (stem + crown Iguania) is a diverse squamate clade with members that predominate many modern American lizard ecosystems. However, the temporal and palaeobiogeographic origins of its constituent crown clades (e.g. Pleurodonta (basilisks, iguanas, and their relatives)) are poorly constrained, mainly due to a meagre Mesozoic-age fossil record. Here, we report on two nearly complete skeletons from the Late Cretaceous (Campanian) of North America that represent a new and relatively large-bodied and possibly herbivorous iguanomorph...

Data from: Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome

Morten T. Limborg, Wesley A. Larson, Lisa W. Seeb & James E. Seeb
A whole-genome duplication (WGD) doubles the entire genomic content of a species and is thought to have catalysed adaptive radiation in some polyploid-origin lineages. However, little is known about general consequences of a WGD because gene duplicates (i.e., paralogs) are commonly filtered in genomic studies; such filtering may remove substantial portions of the genome in data sets from polyploid-origin species. We demonstrate a new method that enables genome-wide scans for signatures of selection at both...

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