Marlon E. Cobos
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View article: Field+Genomics Workshop: an initiative to build Nanopore sequencing capacity in field-based host-pathogen research
Field+Genomics Workshop: an initiative to build Nanopore sequencing capacity in field-based host-pathogen research Open
Wildlife disease surveillance has received considerable attention following recent emergence of high-consequence zoonotic pathogens in humans. Increased portability and affordability of sequencing technologies over the last decade have mad…
View article: Natural history biorepositories are critical infrastructure for pandemic preparedness
Natural history biorepositories are critical infrastructure for pandemic preparedness Open
View article: Spatiotemporal dynamics of questing activity by four tick species in the central Great Plains
Spatiotemporal dynamics of questing activity by four tick species in the central Great Plains Open
In this study, we explore a suite of new ecological niche modeling approaches to illuminate the distributional potential and distributional dynamics of questing individuals of four tick species in the central Great Plains region. Specifica…
View article: ArctosR: An Interface to the 'Arctos' Database
ArctosR: An Interface to the 'Arctos' Database Open
View article: Harnessing historical sampling to substantiate range shifts: southward movement of North American least weasels (Mustela nivalis)
Harnessing historical sampling to substantiate range shifts: southward movement of North American least weasels (Mustela nivalis) Open
Contemporary climate change is rapidly affecting species’ ranges and distributions. While there is a general trend of poleward movement, there are exceptions. For example, despite the North American least weasel’s ( Mustela nivalis ) elusi…
View article: Achieving higher standards in species distribution modeling by leveraging the diversity of available software
Achieving higher standards in species distribution modeling by leveraging the diversity of available software Open
The increasing online availability of biodiversity data and advances in ecological modeling have led to a proliferation of open‐source modeling tools. In particular, R packages for species distribution modeling continue to multiply without…
View article: Modeling spatiotemporal dynamics of Amblyomma americanum questing activity in the central Great Plains
Modeling spatiotemporal dynamics of Amblyomma americanum questing activity in the central Great Plains Open
Ticks represent important vectors of a number of bacterial and viral disease agents, owing to their hematophagous nature and their questing behavior (the process in which they seek new hosts). Questing activity is notably seasonal with spa…
View article: Detailed multivariate comparisons of environments with mobility oriented parity
Detailed multivariate comparisons of environments with mobility oriented parity Open
Multivariate model projections onto conditions that differ from those under which the models were calibrated can result in uncertainty owing to response extrapolation. Therefore, interpretations of models transferred to conditions not anal…
View article: Revisiting plant hardiness zones to include multiple climatic stress dimensions
Revisiting plant hardiness zones to include multiple climatic stress dimensions Open
View article: Broad-scale ecological niches of pathogens vectored by the ticks <i>Ixodes scapularis</i> and <i>Amblyomma americanum</i> in North America
Broad-scale ecological niches of pathogens vectored by the ticks <i>Ixodes scapularis</i> and <i>Amblyomma americanum</i> in North America Open
Environmental dimensions, such as temperature, precipitation, humidity, and vegetation type, influence the activity, survival, and geographic distribution of tick species. Ticks are vectors of various pathogens that cause disease in humans…
View article: Selecting sites for strategic surveillance of zoonotic pathogens: a case study in Panamá
Selecting sites for strategic surveillance of zoonotic pathogens: a case study in Panamá Open
Surveillance and monitoring of zoonotic pathogens is key to identifying and mitigating emerging public health threats. Surveillance is often designed to be taxonomically targeted or systematically dispersed across geography, however, those…
View article: enmpa: An R package for ecological niche modeling using presence-absence data and generalized linear models
enmpa: An R package for ecological niche modeling using presence-absence data and generalized linear models Open
Here, we present the new R package “enmpa,” which includes a range of tools for modeling ecological niches using presence-absence data via logistic generalized linear models. The package allows users to calibrate, select, project, and eval…
View article: Long-term antibiotic exposure landscapes and resistant Escherichia coli colonization in a densely populated setting
Long-term antibiotic exposure landscapes and resistant Escherichia coli colonization in a densely populated setting Open
Antibiotic exposure is associated with resistant bacterial colonization, but this relationship can be obscured in community settings owing to horizontal bacterial transmission and broad distributions. Locality-level exposure estimates cons…
View article: Correlative ecological niche model applications to predicting landscape-scale woody plant encroachment in Kansas tallgrass prairie systems
Correlative ecological niche model applications to predicting landscape-scale woody plant encroachment in Kansas tallgrass prairie systems Open
Woody plant encroachment (WPE) in grassland ecosystems has been a pervasive process across the Great Plains, yet a predictive understanding of where it will occur has been elusive. As an exploration of tools of potential utility in this ch…
View article: Spatiotemporal dynamic models of<i>Amblyomma americanum</i>questing activity in the Central Great Plains
Spatiotemporal dynamic models of<i>Amblyomma americanum</i>questing activity in the Central Great Plains Open
Ticks represent important vectors of a number of bacterial and viral disease agents, owing to their hematophagous nature and their questing behavior (the process in which they seek new hosts). Questing activity is notably seasonal with spa…
View article: Phenology of five tick species in the central Great Plains
Phenology of five tick species in the central Great Plains Open
The states of Kansas and Oklahoma, in the central Great Plains, lie at the western periphery of the geographic distributions of several tick species. As the focus of most research on ticks and tick-borne diseases has been on Lyme disease w…
View article: enmpa: An R package for ecological niche modeling using presence-absence data and generalized linear models
enmpa: An R package for ecological niche modeling using presence-absence data and generalized linear models Open
Here, we present the new R package “enmpa,” which includes a range of tools for modeling ecological niches using presence-absence data via logistic generalized linear models. The package allows users to calibrate, select, project, and eval…
View article: Relationships among cost, citation, and access in journal publishing by an ecology and evolutionary biology department at a U.S. university
Relationships among cost, citation, and access in journal publishing by an ecology and evolutionary biology department at a U.S. university Open
Background Optimizing access to high-quality scientific journals has become an important priority for academic departments, including the ability to read the scientific literature and the ability to afford to publish papers in those journa…
View article: Ecological restoration and protection of remnants are key to the survival of the critically endangered Araucaria tree under climate change
Ecological restoration and protection of remnants are key to the survival of the critically endangered Araucaria tree under climate change Open
Araucaria angustifolia – ‘araucaria’– is a critically endangered conifer tree of great ecological, economic, and cultural importance occurring in subtropical forests and grasslands in southern Brazil. Using ecological niche modeling we est…
View article: Effects of occurrence data density on conservation prioritization strategies
Effects of occurrence data density on conservation prioritization strategies Open
View article: Advancing the central role of non-model biorepositories in predictive modeling of emerging pathogens
Advancing the central role of non-model biorepositories in predictive modeling of emerging pathogens Open
The COVID-19 pandemic demonstrated the insufficiency of a reactive approach to emerging zoonotic pathogens. With spillover increasing in frequency as environments change and the human footprint continues to grow, pandemic prevention will r…
View article: Broad-scale factors shaping the ecological niche and geographic distribution of Spirodela polyrhiza
Broad-scale factors shaping the ecological niche and geographic distribution of Spirodela polyrhiza Open
The choice of appropriate independent variables to create models characterizing ecological niches of species is of critical importance in distributional ecology. This set of dimensions in which a niche is defined can inform about what fact…
View article: Global ecological niche conservatism and evolution in Olea species
Global ecological niche conservatism and evolution in Olea species Open
View article: Broad-scale factors shaping the ecological niche and geographic distribution of<i>Spirodela polyrhiza</i>
Broad-scale factors shaping the ecological niche and geographic distribution of<i>Spirodela polyrhiza</i> Open
The choice of appropriate independent variables to create models characterizing ecological niches of species is of critical importance in distributional ecology. This set of dimensions in which a niche is defined can inform about what fact…
View article: Ecological niche and potential geographic distributions of <i>Dermacentor marginatus</i> and <i>Dermacentor reticulatus</i> (Acari: Ixodidae) under current and future climate conditions
Ecological niche and potential geographic distributions of <i>Dermacentor marginatus</i> and <i>Dermacentor reticulatus</i> (Acari: Ixodidae) under current and future climate conditions Open
Dermacentor marginatus is a vector disease of both humans and animals and transmits the causative agents of Q fever (Coxiella burnetii) and the spotted fever group (Rickettsia raoultii and R. slovaca), as well as of Crimean–Congo hemorrhag…
View article: rangemap: An R Package to Explore Species' Geographic Ranges
rangemap: An R Package to Explore Species' Geographic Ranges Open
Data exploration is a critical step in understanding patterns and biases in information about species’ geographic distributions. We present rangemap, an R package that implements tools to explore species’ ranges based on simple analyses an…
View article: Detecting Signals of Species’ Ecological Niches in Results of Studies with Defined Sampling Protocols: Example Application to Pathogen Niches
Detecting Signals of Species’ Ecological Niches in Results of Studies with Defined Sampling Protocols: Example Application to Pathogen Niches Open
Ecological niches are increasingly appreciated as a long-term stable constraint on the geographic and temporal distributions of species, including species involved in disease transmission cycles (pathogens, vectors, hosts). Although consid…
View article: ENM2020: A Free Online Course and Set of Resources on Modeling Species' Niches and Distributions
ENM2020: A Free Online Course and Set of Resources on Modeling Species' Niches and Distributions Open
The field of distributional ecology has seen considerable recent attention, particularly surrounding the theory, protocols, and tools for Ecological Niche Modeling (ENM) or Species Distribution Modeling (SDM). Such analyses have grown stea…
View article: Supplementary material: Effects of occurrence data density on conservation prioritization strategies
Supplementary material: Effects of occurrence data density on conservation prioritization strategies Open
Supplementary Material for the manuscript "Effects of occurrence data density on conservation prioritization strategies" Contents: Complete_process.R. Commented R script with code to reproduce all analyses. Data.zip. Compressed folder con…
View article: On the potential of documenting decadal-scale avifaunal change from before-and-after comparisons of museum and observational data across North America
On the potential of documenting decadal-scale avifaunal change from before-and-after comparisons of museum and observational data across North America Open
Studies of biodiversity dynamics have been cast on either long (systematics) or short (ecology) time scales, leaving a gap in coverage for moderate time scales of decades to centuries. Large-scale biodiversity information resources now ava…