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"Stuart, James N."
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Phylogenomic Analysis of Wide‐Ranging Least Shrews Refines Conservation Priorities and Supports a Paradigm for Evolution of Biota Spanning Eastern North America and Mesoamerica
2025
Anthropogenic global change is impacting the evolutionary potential of biodiversity in ways that have been difficult to predict. Distinct evolutionary units within species may respond differently to the same environmental trends, reflecting unique geography, ecology, adaptation, or drift. Least shrews (Cryptotis parvus group) have a widespread distribution across North America, yet systematic relationships and ongoing evolutionary processes remain unresolved. Westernmost peripheral populations have been prioritized for conservation, but little is known of their evolutionary histories or population trajectories. The broad range of this group of species is coincident with many other temperate taxa, presenting a hypothesis that diversification of least shrews follows a repeated process through the Pleistocene, leading to regionally diagnosable conservation units. We use genomic data and niche modeling to delimit species and conservation units of least shrews. Our results show that least shrews warrant recognition as multiple distinct species, along with geographically discrete infraspecific lineages of C. parvus (sensu stricto). Western peripheral populations are evolutionarily distinct based on nuclear, but not mitochondrial data, possibly reflecting mitochondrial capture during the last glacial phase. This population represents a relict conservation unit, consistent with both an “adaptive unit” and “management unit” based on non‐neutral and neutral divergence, respectively. Hindcast niche modeling supports growing evidence for a shared process of diversification among co‐distributed biota, and forecast modeling suggests continued future loss of suitable environmental niche in peripheral regions. Given mito‐nuclear discordance among samples of parapatric lineages, future environmental perturbation may continue to impact the genomic integrity of important conservation units, making ecological and genomic monitoring a critical need. Least shrews, distributed widely across North America and Mesoamerica, remain an enigmatic group in terms of their evolutionary history, biogeography, and ongoing responses to environmental change. Under a phylogenomic framework using reduced representation genome data, we investigated these dynamics across multiple scales of analysis. We found that the current taxonomy is in need of revision and provide updated nomenclature, systematic relationships, and conservation implications. This group provides a clear demonstration of diagnosable diversification across this vast study area.
Journal Article
Control of Tamarix in the Western United States: Implications for Water Salvage, Wildlife Use, and Riparian Restoration
by
Cleverly, James R.
,
Stuart, James N.
,
VAN Riper, Charles
in
Animals
,
Animals, Wild
,
Conservation of Natural Resources
2005
Non-native shrub species in the genus Tamarix (saltcedar, tamarisk) have colonized hundreds of thousands of hectares of floodplains, reservoir margins, and other wetlands in western North America. Many resource managers seek to reduce saltcedar abundance and control its spread to increase the flow of water in streams that might otherwise be lost to evapotranspiration, to restore native riparian (streamside) vegetation, and to improve wildlife habitat. However, increased water yield might not always occur and has been substantially lower than expected in water salvage experiments, the potential for successful revegetation is variable, and not all wildlife taxa clearly prefer native plant habitats over saltcedar. As a result, there is considerable debate surrounding saltcedar control efforts. We review the literature on saltcedar control, water use, wildlife use, and riparian restoration to provide resource managers, researchers, and policy-makers with a balanced summary of the state of the science. To best ensure that the desired outcomes of removal programs are met, scientists and resource managers should use existing information and methodologies to carefully select and prioritize sites for removal, apply the most appropriate and cost-effective control methods, and then rigorously monitor control efficacy, revegetation success, water yield changes, and wildlife use.
Journal Article
Use of Anecdotal Occurrence Data in Species Distribution Models: An Example Based on the White-Nosed Coati (Nasua narica) in the American Southwest
2013
Species distributions are usually inferred from occurrence records. However, these records are prone to errors in spatial precision and reliability. Although influence of spatial errors has been fairly well studied, there is little information on impacts of poor reliability. Reliability of an occurrence record can be influenced by characteristics of the species, conditions during the observation, and observer’s knowledge. Some studies have advocated use of anecdotal data, while others have advocated more stringent evidentiary standards such as only accepting records verified by physical evidence, at least for rare or elusive species. Our goal was to evaluate the influence of occurrence records with different reliability on species distribution models (SDMs) of a unique mammal, the white-nosed coati (Nasua narica) in the American Southwest. We compared SDMs developed using maximum entropy analysis of combined bioclimatic and biophysical variables and based on seven subsets of occurrence records that varied in reliability and spatial precision. We found that the predicted distribution of the coati based on datasets that included anecdotal occurrence records were similar to those based on datasets that only included physical evidence. Coati distribution in the American Southwest was predicted to occur in southwestern New Mexico and southeastern Arizona and was defined primarily by evenness of climate and Madrean woodland and chaparral land-cover types. Coati distribution patterns in this region suggest a good model for understanding the biogeographic structure of range margins. We concluded that occurrence datasets that include anecdotal records can be used to infer species distributions, providing such data are used only for easily-identifiable species and based on robust modeling methods such as maximum entropy. Use of a reliability rating system is critical for using anecdotal data.
Journal Article
Alternatives to genetic affinity as a context for within-species response to climate
2019
Accounting for within-species variability in the relationship between occurrence and climate is essential to forecasting species’ responses to climate change. Few climate-vulnerability assessments explicitly consider intraspecific variation, and those that do typically assume that variability is best explained by genetic affinity. Here, we evaluate how well heterogeneity in responses to climate by a cold-adapted mammal, the American pika (Ochotona princeps), aligns with subdivisions of the geographic range by phylogenetic lineage, physiography, elevation or ecoregion. We find that variability in climate responses is most consistently explained by an ecoregional subdivision paired with background sites selected from a broad spatial extent indicative of long-term (millennial-scale) responses to climate. Our work challenges the common assumption that intraspecific variation in climate responses aligns with genetic affinity. Accounting for the appropriate context and scale of heterogeneity in species’ responses to climate will be critical for informing climate-adaptation management strategies at the local (spatial) extents at which such actions are typically implemented.
Journal Article
Naturalist’s Big Bend: An Introduction to the Trees and Shrubs, Wildflowers, Cacti, Mammals, Birds, Reptiles and Amphibians, Fish, and Insects
2002
\"Naturalist's Big Bend: An Introduction to the Trees and Shrubs, Wildflowers, Cacti, Mammals, Birds, Reptiles and Amphibians, Fish, and Insects\" by Roland H. Wauer and Carl M. Fleming is reviewed.
Book Review
Avian species richness in different-aged stands of riparian forest along the middle Rio Grande, New Mexico
by
Ellis, Lisa M.
,
Farley, Greg H.
,
Stuart, James N.
in
ANIMAL SALVAJE
,
ANIMAL SAUVAGE
,
Animal, plant and microbial ecology
1994
Riparian forests are important for maintaining vertebrate species richness in the southwestern United States, but they have become restricted in distribution due to both historical and current management practices. In order to counteract continued loss of this habitat, several mitigation programs were developed in the middle Rio Grande Valley of New Mexico. Three areas ranging from 50 to 140 ha were revegetated with native trees using pole planting and cattle exclosures, and changes in vegetation structure were quantified after 2, 3, and 5 years of growth. As expected, the older site contained the most heterogeneous mix of plant species and the greatest structural diversity. We compared year-round avian use of the revegetated sites with a mature cottonwood forest site of approximately 30 years of age. As the revegetated sites matured and salient habitat features changed, the population dynamics of individual avian species and patterns of guild structure varied. The older revegetated sites showed a greater similarity to the mature cottonwood site, suggesting that reclamation efforts established quality riparian habitats for birds in as little as 5 years. The revegetated sites appeared especially important for Neotropical-migrant birds. We suggest that a mosaic of riparian woodlands containing mixtures of native tree and shrub species of different size classes is necessary to maintain avian species richness in the middle Rio Grande drainage, and probably throughout the southwestern United States.
Journal Article
Variation and Species Status of Slider Turtles (Emydidae: Trachemys) in the Southwestern United States and Adjacent Mexico
by
Stuart, James N.
,
Seidel, Michael E.
,
Degenhardt, William G.
in
Amphibians
,
Biological taxonomies
,
Ecological life histories
1999
Examination of specimens and locality data of Trachemys scripta elegans, T. s. gaigeae, and T. s. cataspila in the southwestern United States and northeastern Mexico indicates these three taxa are primarily allopatric. Morphometric analysis further indicates that these forms are distinct, without evidence of intergradation. Little or no overlap of diagnostic marking patterns was detected, except for variation in the supratemporal stripe of T. s. elegans in the lower Rio Grande and Pecos River. Hemoglobin (analyzed by isoelectric focusing) of sliders in those drainages was also variable. Although limited introgression between T. s. elegans and T. s. gaigeae or T. s. cataspila might be possible in the lower Rio Grande, specimens of T. s. elegans from the area are not intergrades, and therefore we do not consider them to be conspecific with the other forms. Six specimens from the upper Rio Grande are possibly hybrids of elegans and gaigeae but their status is problematic. The appropriate species designations of gaigeae and cataspila await a broad phylogenetic analysis, including all forms in the T. scripta complex.
Journal Article
Nesting Record of a Big Bend Slider Turtle (Trachemys gaigeae) in New Mexico, and Overwintering of Hatchlings in the Nest
by
Morjan, Carrie L.
,
Stuart, James N.
in
Animal nesting
,
Ecological life histories
,
Female animals
2001
We describe observations of a nesting female T. gaigeae, characteristics of the nest, and overwintering status of hatchlings in Socorro Co., New Mexico.
Journal Article