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Journal of Mammalogy, 2024, XX, 1–25
https://doi.org/10.1093/jmammal/gyae135
Advance access publication 12 December 2024
Research Article
© The Author(s) 2024. Published by Oxford University Press on behalf of the American Society of Mammalogists.
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Received: March 5, 2024; Editorial Decision: October 8, 2024; Accepted: October 16, 2024
Research Article
Integrative species delimitation reveals an Idaho-endemic
ground squirrel, Urocitellus idahoensis (Merriam 1913)
Bryan S. McLean1,*,, Eric A. Rickart2,, Joseph A. Cook3,, Robert P. Guralnick4,, Connor J. Burgin3,, Kristin Lohr5
1Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC 27402, United States
2Natural History Museum of Utah, University of Utah, 301 Wakara Way, Salt Lake City, UT 84108, United States
3Museum of Southwestern Biology and Biology Department, University of New Mexico, MSC03-2020, Albuquerque, NM 87131, United States
4Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, United States
5Idaho Fish and Wildlife Ofce, United States Fish and Wildlife Service, 1387 S. Vinnell Way, Boise, ID 83709, United States
*Corresponding author: Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC 27402, United States.
Email: b_mclean@uncg.edu
Version of Record, rst published online December 12, 2024, with xed content and layout in compliance with Art. 8.1.3.2 ICZN.
Nomenclatural statement.—A life science identier (LSID) number was obtained for this publication: urn:lsid:zoobank.org:pub:
353E92B4-7D95-4DAC-8929-FF0B9634E487
Associate Editor was Kevin Rowe
Abstract
The “small-eared” species group of Urocitellus ground squirrels (Sciuridae: Xerinae: Marmotini) is endemic to the Great Basin, United
States, and surrounding cold desert ecosystems. Most specic and subspecic lineages in this group occupy narrow geographic ranges,
and some are of signicant conservation concern; despite this, current taxonomy remains largely based on karyotypic or subtle pelage
and morphological characteristics. Here, we leverage 2 multilocus DNA sequence data sets and apply formal species delimitation tests
alongside morphometric comparisons to demonstrate that the most widespread small-eared species (U. mollis Kennicott, 1863 sensu
lato; Piute Ground Squirrel) is comprised of 2 nonsister and deeply divergent lineages. The 2 lineages are geographically separated by
the east-west owing Snake River in southern Idaho, with no sites of sympatry currently known. Based on robust support across the
nuclear genome, we elevate populations previously attributed to U. mollis from north of the Snake River to species status under the name
Urocitellus idahoensis (Merriam 1913) and propose the common name “Snake River Plains Ground Squirrel” for this taxon. We delimit 2 sub-
species within U. idahoensis; U. i. idahoensis (Merriam 1913) in western Idaho and U. i. artemesiae (Merriam 1913) in eastern Idaho. Urocitellus
idahoensis is endemic to Idaho and has a maximal range area of roughly 29,700 km2 spanning 22 counties but occurs discontinuously
across this area. Our work substantially expands knowledge of ground squirrel diversity in the northern Great Basin and Columbia Plateau
and highlights the difculty in delimiting aridland mammals whose morphological attributes are highly conserved.
Key words: Columbia Plateau, geometric morphometrics, Great Basin, Marmotini, mitonuclear discordance, Snake River, UCEs.
The genus Urocitellus Obolenskij, 1927 (Holarctic ground squirrels)
comprises 12 recognized species of small- to medium-bodied, fos-
sorial, and obligatorily heterothermic sciurids distributed across
temperate North America and Asia (Helgen et al. 2009; Kays and
Wilson 2010; Mammal Diversity Database 2023). Traditionally, the
genus has been conceptualized as containing 2 species groups—the
“big-eared” and “small-eared” groups—which appear reciprocally
monophyletic (McLean et al. 2016, 2019, 2022) and differ from one
another in aspects of body size, habitat preference, and ecology
(Howell 1938; Davis 1939; Durrant and Hansen 1954; Rickart 1987).
The big-eared group contains 7 larger-bodied and mesic-adapted
species widely distributed across western North America (5 spe-
cies), Beringia (1 species), and eastern Asia (1 species). Conversely,
the small-eared group contains 5 species of smaller-bodied, pale-
colored, and desert-dwelling squirrels endemic to the Great Basin
and adjacent Columbia Plateau, United States (Howell 1938; Helgen
et al. 2009; McLean et al. 2016, 2022).
Small-eared Urocitellus remain remarkably understudied from
phylogenetic and population genetic perspectives despite the nar-
row geographic ranges and conservation concerns of most lineages.
In his comprehensive treatment, Howell (1938) recognized 4 spe-
cies of small-eared squirrels based on pelage, external morpholog-
ical, and cranial characters: U. brunneus (Howell 1928); U. idahoensis
(Merriam 1913); U. townsendii (Bachman 1839); and U. washingtoni
(Howell 1938), including subspecic forms. Conversely, Nadler et al.
(1982) and Rickart (1985, 1987) allied idahoensis with the widespread
U. t. mollis and simultaneously demonstrated the distinctiveness of
U. t. canus. Hoffmann et al. (1993) later synthesized available data
to recognize 5 species: U. brunneus (Howell 1928); U. canus (Merriam
1898); U. mollis (Kennicott 1863); U. townsendii (Bachman 1839); and
U. washingtoni (Howell 1938).
The treatments of subsequent workers have generally fol-
lowed the 5-species scheme above (Thorington and Hoffmann
2005; Helgen et al. 2009; Thorington et al. 2012; Mammal Diversity
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2 | McLean et al.
Database 2023). Recently, Hoisington-Lopez et al. (2012) elevated
subspecies within U. brunneus, thereby recognizing a sixth species
(U. endemicus). These sister taxa are minimally diverged genetically
(Hoisington-Lopez et al. 2012; McLean et al. 2016, 2022) but exhibit
other differences (Yensen 1991; Hoisington-Lopez et al. 2012). For
the purposes of this study, we combine individuals assignable to the
brunneus and endemicus lineages under U. brunneus given our limited
sampling of morphological and genetic characters for either lineage
and thus inability to further test Hoisington-Lopez et al.’s (2012) tax-
onomic hypothesis. Similarly, the taxon U. nancyae (Nadler 1968), dis-
tributed between the Yakima and Columbia Rivers of Washington,
was recently listed as a distinct species by the International Union
for the Conservation of Nature Red List (Yensen 2019). Urocitellus
nancyae is generally considered either a synonym or subspecies of
U. townsendii, although chromosomal distinctions were documented
(U. townsendii with 2N = 36, U. nancyae with 2N = 38; Nadler 1968). As
with U. brunneus, we combine all individuals here under U. townsen-
dii as traditionally dened, pending additional genetic sampling and
integrative analysis. However, given the close relationship of popu-
lations within both U. brunneus and U. townsendii, we do not expect
that these decisions impact our conclusions.
Roughly 40 years after the publication of karyotypes for most
Urocitellus species, small-eared Urocitellus remain delimited taxo-
nomically primarily by karyotype, geographic range, or a combina-
tion of the 2 (Helgen et al. 2009; Kays and Wilson 2010; Kays et al.
2022; Mammal Diversity Database 2023), so delimitations based on
additional data are needed. The group does display signicant kar-
yotypic variation, with diploid numbers varying from 2N = 36 for U.
townsendii to 2N = 46 for U. canus (Nadler 1966, 1968; Nadler et al.
1982; Rickart et al. 1985). Nadler et al. (1982:208) stated: “The Nearctic
townsendii group proper [small-eared taxa] forms a cluster of its
own on both biochemical and morphological evidence. However,
chromosomal differentiation is considerable.” Nevertheless, a reli-
ance on karyotypic and allozyme electrophoretic approaches alone,
especially given some incongruence between them, suggests a more
integrative systematic revision of the whole group is warranted.
This study reviews the systematics and phylogenetic placement
of populations currently attributed to the Piute Ground Squirrel, U.
mollis (Kennicott 1863). Urocitellus mollis is the most widely distrib-
uted small-eared Urocitellus with 3 subspecies recognized (Fig. 1;
Howell 1938; Rickart 1987; Helgen et al. 2009). The most widespread
subspecies, U. m. mollis, occurs throughout a large part of the Great
Basin, United States—from the Snake River (Idaho) south to south-
ern Nevada and from the eastern foothills of the Sierra Nevada in
California and Nevada east to central Utah. Conversely, U. m. ida-
hoensis (Merriam 1913) and U. m. artemesiae (Merriam 1913) occupy
smaller, adjacent ranges in southwestern and southeastern Idaho,
respectively, in steppe habitats of the Snake River Plain north of the
Snake River (Fig. 1). All 3 subspecies share a common karyotype
across the range of U. mollis (2N = 38, FN = 66; Nadler 1966, 1968;
Rickart et al. 1985).
The taxonomic history of U. mollis offers a case-in-point for
how reliance on single character types may mislead taxonomic
inferences, especially in aridland mammals whose morphological
attributes may be conserved, and highlights the urgency of inte-
grating multiple data sources for delimitation (Padial et al. 2010).
Using morphology, Merriam (1913) described idahoensis as a distinct
species (Citellus idahoensis) based on larger body size and robustness
of the cranium and dentition relative to U. m. mollis and U. m. arte-
mesiae. He distinguished U. m. artemesiae (as C. m. artemesiae) from
U. m. mollis based on its relatively small body size and a smaller
and more-slender cranium along with dental distinctions (Merriam
1913). Merriam (1898, 1913) further described 1 species (leurodon)
and 3 subspecies (stephensi, pessimus, washoensis) from within the
range of modern U. mollis, but Howell (1938) subsumed all forms
except idahoensis within mollis, also based on pelage and morpho-
logical characters. Using karyotypic data, Nadler (1966) and Rickart
et al. (1985) documented a uniform karyotype across the geographic
range of U. mollis and failed to recover evidence of hybridization
between these forms and geographically adjacent but karyotypi-
cally distinctive species (i.e., U. canus; Merriam’s Ground Squirrel).
This body of information was used to redene U. mollis (including
mollis, idahoensis, and artemesiae) by Hoffmann et al. (1993).
Here, we leverage comprehensive taxon sampling and multiple
independent data sets to critically evaluate relationships of named
forms within U. mollis, both with each other and relative to other
small-eared taxa. We analyze (i) previously published genome-wide
sequence data, reorganized here for targeted species delimitation
tests; (ii) mitochondrial (mtDNA) genetic distances from a compi-
lation of previously published cytochrome b gene (CytB) sequences;
(iii) new two-dimensional geometric morphometric data from cra-
nia; (iv) new linear measurements from crania and dentitions; and
(v) a large compilation of external body measurements from digi-
tized museum specimens. This work renes our concepts of sciu-
rid diversity and endemicity in Idaho and expands knowledge of
mammalian diversication here and across the Great Basin and
Columbia Plateau more broadly.
Materials and methods.
Nuclear DNA data sets.
We used 2 independent, published nuclear DNA (nuDNA) data
sets to test species delimitation hypotheses in U. mollis within the
Fig. 1. Map of the western United States depicting geographic ranges
of subspecies of Urocitellus mollis. The Snake River in Idaho delimits the
northern range limit of U. m. mollis and the southern range limits of U.
m. idahoensis and U. m. artemesiae, and stippling represents the presumed
boundary of the latter 2 subspecies.
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Journal of Mammalogy, 2024, Vol, XX, Issue XX | 3
broader context of the small-eared group (summarized in Appendix
I). All delimitations other than within U. mollis followed the existing
taxonomy of the Mammal Diversity Database v1.11 (2023). The rst
data set was from McLean et al. (2016), who inferred the Urocitellus
phylogeny based a data set of 5 nuclear genes (listed with approved
symbol and unique identiers from HUGO gene nomenclature):
partial von Willebrand factor (Vwf, HGNC:12726), breast cancer 1
associated protein (Brap, HGNC:1099), brinogen beta chain (Fgb,
HGNC:3662), glucosylceramidase beta 1 (Gba1, HGNC:4177), and
growth hormone receptor (Ghr, HGNC:4263). Twelve species (and 33
of 36 subspecies) were represented in that study, including all sub-
species within U. mollis. However, that study did not perform formal
species delimitation and assumed an accurate taxonomy, including
a monotypic U. mollis. We reanalyzed this 5-gene data set under an
alternative taxonomic scheme that split northern and southern U.
mollis (see Species tree reconstruction below) and formally compared
the 2 delimitations (see Tests of species delimitation hypotheses below).
The second data set was from McLean et al. (2022), who analyzed
>3,000 ultraconserved element loci (UCEs) from across the genomes
of all 12 species of Urocitellus. Based on population clustering analy-
ses of individuals, those authors instead assumed a bitypic U. mollis
and modeled separate northern and southern lineages for species
tree analyses. The study evaluated several alternative taxonomic
schemes within small-eared species but not within U. mollis. Thus,
we reanalyzed the same single nucleotide polymorphism (SNP)
data derived from 2,733 original phased UCE loci, coding U. mollis
as monotypic and formally comparing this delimitation with the
previous one assuming 2 species-level lineages. We focus only on
the phased SNP data of McLean et al. (2022) because these yielded
a more precise resolution of species trees than unphased data
(McLean et al. 2022).
All prior studies using eld-collected specimens were con-
ducted in accordance with recommendations of the American
Society of Mammalogists Guidelines (Sikes et al. 2016) and through
an approved institutional animal care and use protocol at the
University of New Mexico.
Species tree reconstruction.
Since the analysis of McLean et al. (2016) assumed a monotypic U.
mollis, our delimitation approach required species tree reestimation
with all U. mollis individuals from north of the Snake River assigned
to a new taxon set, reecting their potentially unique species iden-
tity. For this analysis, we used hierarchical Bayesian inference in the
*BEAST module in BEAST v2.6.3 (Bouckaert et al. 2014) and included
all species of Urocitellus as well as 2 ground squirrel outgroup taxa.
The analysis was specied as in McLean et al. (2016). The MCMC
chains were run for 2 billion generations, sampling every 2,500
generations and discarding the rst 50% as burn-in. Convergence
was assessed by visualizing log les in Tracer v1.7.1 (Rambaut et al.
2018) and requiring ESS of >200 for parameters. Results were visu-
alized as a maximum clade credibility phylogram, which we esti-
mated using the maxCladeCred function in the phangorn package
v2.6.3 (Schliep 2011). We also visualized sets of 5,000 random trees
taken from each of these posterior distributions using the densiTree
function in phangorn.
Tests of species delimitation hypotheses.
Working separately with the 5-gene and UCE data sets, we com-
pared 2 delimitation hypotheses: one in which U. mollis encom-
passes populations north and south of the Snake River in Idaho
(i.e., the current taxonomic concept), and a second in which north-
ern and southern populations are distinct. We used path sampling
implemented in the BEAST family of software packages, allowing
us to approximate the marginal likelihoods of each hypothesis and
compare competing delimitation models. Path sampling routines
were performed separately for the 5-gene and UCE data sets.
Path sampling for the 5-gene data set was performed in *BEAST
v2.6.3 using 48 steps and running each MCMC until convergence (at
least 1 million generations each). The data set included representa-
tives of all Urocitellus species, which was computationally intensive
but facilitated more accurate parameter estimates. Convergence
was assessed based on trace plots and requiring effective sample
sizes (ESS) >200 for all parameters (in Tracer v1.7.2). Due to dif-
culty in estimating some parameters across steps, we simplied
the site models for all 5 genes from GTR to HKY85, a departure
from McLean et al. (2016) that was necessary to achieve MCMC
convergence.
Path sampling for the UCE data set was performed using the BFD*
approach (Leaché et al. 2014) as implemented within the SNAPP
(Bryant et al. 2012) module in BEAST v2.6.3. The data set used for
both analyses was an alignment of 299 biallelic SNPs represent-
ing all small-eared Urocitellus species; these were ltered from the
larger data set of 2,733 phased UCEs to a level of 100% character
matrix completeness to decrease computational burden. Runs were
set up as in McLean et al. (2022), with path sampling performed for
48 steps and chains of 1 million generations per step.
From each path sampling analysis, we calculated Bayes Factors
(2 × BF), where BF equaled the difference in marginal log-likelihood
between the 2 delimitation hypotheses being compared. Bayes
Factor values were evaluated as in Kass and Rafferty (1995), with
2lnBF greater than 10 taken as decisive support (following Leaché et
al. 2014). All analyses were run on the Longleaf computing cluster at
the University of North Carolina (https://its.unc.edu/).
Mitochondrial DNA comparisons.
To provide a mtDNA-based perspective on diversity in the group,
we compiled available sequences of the CytB gene from small-eared
Urocitellus published previously (Harrison et al. 2003; Hoisington-
Lopez et al. 2012; McLean et al. 2016, 2022; n = 41 individuals,
Appendix I). Mitonuclear discordance is documented in Urocitellus
(McLean et al. 2016, 2022), and for this reason we do not rely on
CytB for taxonomic recommendations. Nevertheless, CytB distances
are commonly used in mammalian systematics to support species
designations (Baker and Bradley 2006) and can provide a broader
context to stimulate future research on the evolutionary causes of
discordance. In the case of the Hoisington-Lopez et al. (2012) data
set, we selected 3 individuals each from the brunneus and endemi-
cus lineages, which we again combined as U. brunneus given their
close genetic relationship and monophyly in all analyses to date.
All CytB sequences were obtained from GenBank, aligned in MAFFT
v7.487 (Katoh and Standley 2013), and analyzed using scripts from
the “ape” package (Paradis and Schliep 2019) in R. We computed
average pairwise distances among 6 nuDNA lineages (considering
U. mollis samples from north of the Snake River as distinct). We also
computed pairwise genetic distances among individuals and pro-
vided average genetic distances within each lineage, thus providing
perspective on levels of intraspecic variation. Genetic distances
were calculated using a Felsenstein 1984 (Felsenstein 1989) model
of sequence evolution, and GenBank accession numbers are pro-
vided in Appendix I.
Cranial shape data sets.
To evaluate whether cranial variation in small-eared Urocitellus is
concordant with nuDNA-based species delimitations, we collected
and analyzed 2 cranial morphological data sets (Appendix II).
The rst was a set of 2D geometric morphometric (GMM) data
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4 | McLean et al.
representing all species and subspecies of small-eared Urocitellus.
We also analyzed GMM data for only the U. mollis group (artemesiae,
idahoensis, and mollis). The second craniometric data set was com-
prised of 14 traditional linear measurements taken for lineages in
the U. mollis group.
Geometric morphometric data were collected by one of us (BSM)
from 151 adult specimens of small-eared Urocitellus, including a
minimum of 19 adult specimens of each species (mean 25, range
19 to 36; Supplementary Data SD1 and SD2). Representatives of
the brunneus and endemicus lineages were pooled as U. brunneus
due to low sample sizes, as stated above. Our age criterion was
complete eruption and development of upper premolars 3 and 4
(P3 and P4, respectively). Both sexes were included in the analysis.
Data were collected using the following procedure. Crania were rst
photographed in ventral aspect using a mounted Nikon D90 DSLR
camera tted with a Nikon AF-S 60mm macro autofocus lens and
a standardized position. We then used Helicon Remote software
(http://www.heliconsoft.com/) to obtain 15 to 25 high-resolution
images throughout the depth of eld for each cranium and stacked
the images using Helicon Focus software, ensuring proper focus
and accurate landmark placement throughout the depth of eld.
Twenty-four 2D landmarks (Supplementary Data SD1) were digi-
tized on each stacked image using the software tpsDig v2.10 (Rohlf
2006). Landmarks were digitized on the left ventral side of the cra-
nium for most specimens (n = 83) or digitized on the right side of
other specimens (n = 68) where crania were damaged or incomplete.
Thus, we implicitly assume the asymmetric component of bilateral
shape variation to be small relative to interspecic variation. We
performed a Procrustes superimposition using the complete land-
mark data in the R package “geomorph” v4.0.5 (Baken et al. 2021;
Adams et al. 2022) using the function gpagen.
Traditional cranial measurement data were collected by one
of us (EAR) over a period of 2 days (Supplementary Data SD3).
The data set comprised 14 standard measurements (Table 4), and
each was recorded to the nearest 0.1 mm using digital calipers.
Measurements used here are dened in Helgen et al. (2009). We
measured 55 adult specimens from the U. mollis group, including
a minimum of 13 adult specimens for each subspecies (range 13 to
31). Both sexes were included in the analysis. Summary data for all
specimens are presented in Table 4, and a subset of 40 specimens
with intact or only slightly damaged skulls were used for further
statistical analysis.
Analysis of cranial shape.
Our rst objective in analyzing cranial shape was to isolate and test
the effects of lineage identity and body size (i.e., evolutionary allom-
etry) within and among 6 nuDNA groups. To answer this question,
we used GMM data and a series of Procrustes ANOVAs implemented
in the “geomorph” function procD.lm. We constructed a fully spec-
ied ANOVA considering the predictors of nuDNA group identity
(n = 6; northern U. mollis assigned to a separate lineage), cranial size
(logarithm of conguration centroid sizes), and their interaction
(which modeled group-specic allometries). We compared this full
model to reduced models that lacked either (i) the interaction term;
or (ii) the interaction term and the cranial size term (thus ignoring
allometry entirely). Comparisons were performed using analysis of
variance.
Our second objective was to quantify the classication accu-
racy of crania to the same 6 nuDNA groups (northern U. mollis
again assigned to a separate lineage), which is more relevant to
our delimitation tests and combines signals from both size and
shape. First, we performed canonical variates analysis (CVA) using
the CVA function in the R package “Morpho” v2.9 (Schlager 2017),
paired with jackknife cross-validation to compute probabilities of
group assignment in morphospace. The input for CVA was a prin-
cipal components analysis (PCA) transformation of the original
Procrustes landmark conguration, which we performed using the
“geomorph” function gm.prcomp to avoid including redundant shape
information in the CVA. Second, we estimated pairwise group differ-
ences in mean shape statistically using the pairwise function in the
“RRPP” package v1.3.1 (Collyer and Adams 2021) in R, which is a test
of differences between least-squares group means. The input was
the simplest Procrustes ANOVA from above, with species identity as
the sole predictor variable.
Our third objective was to probe cranial variation just within
U. mollis as it is currently dened (including subspecies artemesiae,
idahoensis, and mollis). This critical delimitation routine was per-
formed using both (i) GMM data and (ii) traditional linear meas-
urements. Analysis of GMM data for U. mollis was exactly as above
for the entire small-eared group, with congurations subset to
include U. mollis and realigned using Procrustes superimposition.
Analysis of linear measurement data was done using a PCA of the
correlation matrix of log10-transformed measurements, using the
prcomp function in R with the scale parameter set to TRUE. We vis-
ualized the spread and extent of nuDNA groups in cranial shape
space using plotting routines in the “ggplot2” package (Wickham
2016) in R.
External morphological data and analysis.
To evaluate concordance of external morphological variation with
nuDNA-based delimitations, we analyzed 3 external measure-
ments from small-eared Urocitellus that are traditionally recorded
for museum specimens: total body length (TL), tail vertebrae length
(TV), and hindfoot length (HF). We also computed a fourth meas-
urement: head and body length (HBL). To assemble measurement
data, we used a hybrid approach that leveraged biodiversity infor-
matic tools and in-person visits to museum collections holding
specimens spanning the geographic range of the small-eared clade
(Supplementary Data SD4).
External measurements assembled informatically were accessed
in the FuTRES trait data store (https://futres.org/), a resource for
reporting individual-level trait measurements that currently con-
tain data for modern, archaeological, and fossil mammal speci-
mens (Balk et al. 2022). Data accessed via FuTRES were originally
harvested from specimen records contained in VertNet (https://
vertnet.org/) using extensions of the traiter toolkit (Guralnick et al.
2016) and republished in the FuTRES v1.0 data shapshot (https://
doi.org/10.5281/zenodo.6569644, Guralnick et al. 2022). External
measurement data for additional specimens were assembled by 2
of us (BSM, EAR) during in-person visits to the National Museum of
Natural History (United States), the University of Kansas Natural
History Museum, and the Natural History Museum of Utah.
We curated the combined external measurement data by
removing all specimens with missing values for each of the
3 traits of interest. We investigated obvious outliers by visit-
ing their digital occurrence records on the Global Biodiversity
Information Facility or Arctos and correcting obvious trait extrac-
tion errors manually. For the remaining data, we used scripts
from the “OutlierDetection” package in R (Tinwari and Kashikar
2019) as in Balk et al. (2022) to identify additional putative outli-
ers. Specically, we used the univariate outlier detection method
based on Euclidean distances, with a cutoff of 95% for all traits.
The derived HBL metric was also subjected to outlier detection.
Following this routine, the nal database included 1,051 records,
with a mean of 131 (range 37 to 283) observations per species
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Journal of Mammalogy, 2024, Vol, XX, Issue XX | 5
in the combined TL, TV, and HBL data set (subspecies of U. mol-
lis considered separately) and a mean of 39 (range 37 to 307)
observations per species for the HF data set. Sample sizes are
reported separately here given the substantially lower amount
of HF measurements available, especially from older specimens.
Distributions of traits were plotted using routines in the “ggridges”
(Wilke 2024) and “ggplot2” packages in R.
Because age verication was not possible for all specimens in the
external measurement database, we reanalyzed a subset of U. mollis
specimens for the same external measurements and 2 additional
ratios (TV/HBL, HF/HBL). These specimens were originally collected
and measured by a total of 3 individuals at 2 institutions, and they
have associated age class information, making them useful for
comparing central tendencies and ranges of the U. mollis lineages
in question.
Results
Species trees and nuDNA-based delimitation.
Species trees based on different nuDNA data sets varied in their
support for the placement of northern and southern U. mollis (Fig.2).
Relationships among small-eared species were resolved by the
5-gene data set with a range of posterior probabilities. We recovered
U. brunneus (containing the brunneus and endemicus lineages) as sis-
ter to all other small-eared species with high support (PP = 0.96). We
recovered a clade containing canus, townsendii, and southern mol-
lis with moderate support (PP = 0.79; Fig. 2a). However, uncertainty
existed in the placement of northern U. mollis, which we recovered
as sister to the former 3-taxon clade with low support (PP = 0.41).
Relationships were better-resolved in the UCE-based species trees
(Fig. 2b; McLean et al. 2022), which supported a brunneus + northern
mollis clade (PP = 0.98) and placed it sister to a clade containing all
other small-eared species (including southern mollis; PP = 0.98; Fig.
2b). While placement of southern mollis also varied among different
UCE data sets and inference methods in McLean et al. (2022), none
supported monophyly of U. mollis as currently dened.
Tests of species delimitation hypotheses supported the distinc-
tiveness of U. mollis occurring north and south of the Snake River
(Table 1). There was decisive support (i.e., 2lnBF exceeding 10) for
distinct northern and southern U. mollis lineages based on the
5-gene data set (2lnBF = 78.40), despite the lack of topological res-
olution in species tree analysis of those data (Fig. 2a). Even more
decisive support was found for this same hypothesis (relative to
a hypothesis of U. mollis monophyly) based on the UCE data set
(2lnBF = 397.12). While the placement of northern and southern U.
mollis varied between the independent nuDNA data sets, both sup-
ported a taxonomic scheme where northern and southern U. mollis
were assigned to distinct lineages.
Aspects of mtDNA variation.
Pairwise genetic distances among all individual CytB gene
sequences analyzed here ranged from 0% to 9.09%. Average pair-
wise distances among the 6 nuDNA lineages (i.e., with northern
and southern mollis as distinct) ranged from 2.27% (canus–south-
ern mollis comparison) to 8.68% (brunneus [brunneus + endemi-
cus]–townsendii comparison; Table 2). The average CytB distance
between northern and southern mollis was 4.09%. This was lower
Fig. 2. Maximum clade credibility (MCC) phylograms of small-eared
Urocitellus inferred from Bayesian analysis of a) 5 nuclear genes in *BEAST
and b) 2,733 ultraconserved element loci in SNAPP. For each plot, the MCC
phylogram (single bold bifurcating tree) is plotted over 5,000 trees drawn
from the posterior distribution of each analysis (underlying shaded trees).
Outgroups (differing for each study) were trimmed for clarity. Shading on
nodes reects ranges of Bayesian posterior probability values as described
in the legend. Representatives of the brunneus and endemicus lineages were
pooled here as “U. brunneus” given their close genetic relationship.
Table 1. Bayes factor-based tests of species delimitation
hypotheses for U. mollis based on nuclear DNA sequence data.
Model Marginal L2lnBF
Five gene data set
6 spp (northern mollis distinct) −7,875.92 —
5 spp (northern + southern mollis) −7,836.72 78.40
Ultraconserved element data set
6 spp (northern mollis distinct) −4,135.14 —
5 spp (northern + southern mollis) −3,936.58 397.12
Two hypotheses were compared: a 5-species model reecting current taxonomy
and a 6-species model recognizing distinctiveness of U. mollis north of the Snake
River in Idaho. Tests were performed separately on a data set of 5 nuclear genes
(McLean et al. 2016) and 299 phased SNPs from ultraconserved element loci
(McLean et al. 2022). Both data sets included multiple representatives of each
species-level lineage. For each analysis are reported the delimitation hypothesis,
model rank (within sequence data sets), marginal log-likelihood from path
sampling analysis, and 2 × log Bayes Factor.
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6 | McLean et al.
than all other between-species comparisons except for the canus–
southern mollis comparison above (Table 2), and it corresponds
with mtDNA-based phylogenies, which differ from nuDNA in
suggesting a closer (though not reciprocally monophyletic) rela-
tionship of northern and southern U. mollis (Harrison et al. 2003;
Herron et al. 2004; McLean et al. 2016, 2022). Interestingly, the
greatest average within-lineage CytB distance was found in north-
ern U. mollis (2.61%), which included the idahoensis and artemesiae
subspecies (Table 2).
Aspects of cranial and external variation.
Ventral cranial shape in small-eared Urocitellus was best predicted
by a combination of nuDNA lineage identity (F = 8.04, P = 0.001)
and among-group allometry (F = 10.61, P = 0.001; Table 3). This top-
ranked Procrustes ANOVA outranked a simpler model containing
lineage as a sole factor (P = 0.044), as well as a more complex model
that included lineage-specic allometries (P = 0.068). As suggested
from the top model, group means were distinguishable, and all
pairwise lineage comparisons (n = 15) supported group differences,
except in 1 case (northern and southern U. mollis comparison;
P = 0.08).
While lineages were statistically distinguishable based on ven-
tral cranium shape, there was nevertheless a substantial overlap
in ordination space (Fig. 3). We found U. brunneus (including brun-
neus and endemicus lineages) to be most strongly differentiated on
canonical axis 1, which represented 53.2% of the total among-group
variation. All U. brunneus specimens were accurately classied as
that species. The remaining 5 nuDNA groups were incompletely
differentiated along this and subsequent canonical axes, with
classication accuracies ranging from 55% (southern U. mollis) to
86% (U. canus). As in the ANOVA above, northern and southern U.
mollis exhibited the least pairwise differentiation in cranial shape
and the lowest percentages of correct jackknife classications (70%
and 55%, respectively; Fig. 3). The highest pairwise misclassica-
tions that we observed were southern U. mollis incorrectly assigned
to northern U. mollis (4 of 20 specimens incorrect), and northern U.
mollis incorrectly assigned to either southern U. mollis or U. townsen-
dii (each 3 of 27 specimens incorrect).
Conversely, in analyses considering only the U. mollis group,
subspecies were more easily discriminated using GMM and tra-
ditional linear measurements. The latter were more useful in
discriminating subspecies, so we limit discussion to these. In a
PCA based on 14 log10-transformed measurements from 40 adult
specimens (including 9 U. m. artemesiae, 8 U. m. idahoensis, and 23
U. m. mollis), the rst 4 components accounted for 75.7% of the
total variance (Fig. 4). All variables had positive loadings on the
rst component, and most (12 of 14) were of moderate to high
magnitude (0.533 to 0.915) indicating that the rst component
reected size variation. Component 2 accounted for an addition
12.1% of the total variance, with the highest magnitude negative
loadings for the length of the bulla and maxillary toothrow and
positive loading for the length of the bony palate, thus separat-
ing individuals with long palates and small bullae and large teeth
from those with the opposite features. This axis separated U. m.
mollis from U. m. idahoensis + artemesiae. Component 3 (10% of the
variance) separated individuals with broad postorbital regions,
narrow breadth across auditory bullae, and smaller teeth from
those with the converse. Component 4 (8.6%) separated individ-
uals on the basis of anterior palatal breadth but otherwise was
uninterpretable.
External body proportions did not clearly separate lineages of
small-eared Urocitellus. Substantial overlap was observed in stand-
ard measures of TL, HBL, TV, and HF. Outside of U. mollis, the U.
brunneus lineage presented the greatest and most distinctive val-
ues for these measurements (Fig. 5), a nding similar to the cra-
nial shape data (Fig. 3). Interestingly, the magnitude of variation
observed across 3 lineages of U. mollis was comparable to that seen
across the entire small-eared group (Fig. 5). The U. m. idahoensis
lineage had the greatest mean HBL, TV, and HF, while the U. m.
artemesiae lineage had the smallest averages for all measurements.
Urocitellus m. mollis was typically intermediate for these same
measurements.
Discussion
Delimiting temperate mammal diversity.
New species of mammals have been described at a steady and
elevated rate over the past 2 decades, with a majority of cryptic
diversity emerging from tropical regions (Reeder et al. 2007; Burgin
et al. 2018). A global reanalysis (Parsons et al. 2022) likewise pre-
dicted that the highest densities of future new species delimitations
may be concentrated in low-latitude and tropical regions, although
Table 2. Average pairwise cytochrome b distances among 6
nuclear DNA genetic lineages of small-eared Urocitellus (N = 41
total sequences).
brunneus canus mollis
North
mollis
South
townsendii washingtoni
brunneus 0.34 (10)
canus 5.38 1.18 (8)
mollis North 6.33 4.23 2.61 (7)
mollis South 6 2.27 4.09 1.55 (3)
townsendii 8.68 7.55 8.19 7.75 1.07 (7)
washingtoni 7.99 6.88 8.17 7.1 7.45 0.19 (6)
Representatives of the brunneus and endemicus lineages were pooled here as
“U. brunneus” given their close genetic relationship. Distances were calculated
assuming a Felsenstein 1984 model of sequence evolution (Felsenstein 1989).
Average within-lineage genetic distances (with sample sizes in parentheses) are
shown on the diagonal.
Table 3. Summary of the top-ranked Procrustes Analysis of Variance relating ventral cranial shape to nuclear DNA lineage identity and
cranial size in small-eared Urocitellus.
Variable df SS F Z P
Log(centroid size) 1 0.010230 10.6087 5.4979 0.001
NuDNA lineage 5 0.038769 8.0409 8.8556 0.001
Residuals 144 0.138859
Total 150 0.187858
This model outranked a simpler model containing lineage identity alone, as well as a more complex model including an additional lineage × size term (species-specic
allometries). See the main text for further details about ANOVA construction.
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Journal of Mammalogy, 2024, Vol, XX, Issue XX | 7
variables of body mass, range area, and extent of prior research and
sampling were also predictive of undescribed diversity.
Despite its relatively high latitude, northwestern North
America has emerged as a nexus of cryptic diversity in some
temperate mammals (Hafner and Upham 2011; Riddle et al.
2014; Malaney et al. 2017; Colella et al. 2021), including the fam-
ily Sciuridae (Phuong et al. 2014; Arbogast et al. 2017; Herrera et
al. 2022; Mills et al. 2023), and spanning both coastal and interior
faunas. This overlooked diversity is perhaps unsurprising given
the dynamic tectonic, paleooceanic, and paleoclimatic history of
the region and its impacts on mammal diversity through deeper
time (Badgley 2010; Badgley et al. 2014). Unfortunately, accurate
delimitation in these faunas is often labor-intensive because
many lineages are morphologically conserved (including ground
squirrels; McLean et al. 2018), subsumed within widespread taxa
(requiring range-wide sampling), or most convincingly diag-
nosed with genome-scale data (i.e., cryptic species). Thus, inte-
grative taxonomic analyses are essential even in well-studied
taxa throughout North America to better dene biodiversity and
trends across the continent.
The highest species diversity in small-eared Urocitellus exists in
the northern Great Basin (especially southern Idaho) and Columbia
Plateau in Oregon and Washington, a region where recent studies
have uncovered some other distinctive mammal lineages. Herrera
et al. (2022) reported 2 cryptic, species-level lineages of chipmunk
(Neotamias) based on whole genome data: the Crater chipmunk
(N. cratericus), which is restricted to Craters of the Moon lava ows
and nearby mountain ranges of central Idaho north of the Snake
River; and the Coulee chipmunk (N. grisescens), which has a narrow
range in the Channeled Scablands of central Washington. Riddle
et al. (2014) restricted the pocket mouse Perognathus parvus sensu
lato to the Columbia Plateau in Washington and Oregon, elevating
the Great Basin population of that taxon (P. mollipilosus) to species
status. Strikingly, these sister species exhibit up to 18.8% mtDNA
divergence from one another based on the cytochrome oxidase sub-
unit 3 (coIII) gene. These studies further highlight the importance of
the Columbian Plateau and Great Basin in the deep biogeographic
history of some small mammals in the region.
Although molecular systematics of Urocitellus ground squirrels
was actively researched half a century ago (e.g., Nadler 1966, 1968;
Table 4. Cranial and dental measurements (X ± 1 SD and ranges in millimeters) of adult Urocitellus mollis sensu lato subspecies.
Measurement U. m. artemesiae U. m. idahoensis U. m. mollis
Condylobasal length (CBL) 34.3 ± 1.0
32.7–36.2 (10)
36.9 ± 0.9
36.2–39.0
(8)
36.0 ± 1.3
33.4–38.6
(31)
Zygomatic breadth (ZB) 23.9 ± 0.6
22.8–24.7 (11)
25.2 ± 0.8
24.1–26.7
(8)
24.7 ± 0.9
23.1–26.6
(31)
Breadth of braincase (BBC) 17.0 ± 0.4
16.2–17.9 (13)
17.8 ± 0.5
17.3–18.4
(8)
17.2 ± 0.4
16.5–18.0
(30)
Height of braincase (HBC) 12.4 ± 0.2
12.2–12.9 (12)
13.2 ± 0.3
12.7–13.5
(8)
13.1 ± 0.5
12.2–13.9 (29)
Interorbital breadth (IOB) 7.7 ± 0.4
7.0–8.4 (13)
8.0 ± 0.3
7.6–8.6
(9)
8.1 ± 0.5
7.2–9.4
(28)
Postorbital breadth (POB) 9.9 ± 0.5
8.7–10.6 (14)
10.3 ± 0.4
9.7–10.7
(9)
9.6 ± 0.5
8.6–10.4
(30)
Length of auditory bulla (LAB) 7.6 ± 0.3
7.1–8.1 (13)
8.7 ± 0.2
8.4–8.9
(8)
8.5 ± 0.3
8.0–9.1
(31)
Width across auditory bullae (WAAB) 20.2 ± 0.6
19.3–21.4 (12)
21.7 ± 0.7
20.8–23.2 (8)
21.0 ± 0.7
19.7–22.3 (28)
Length of bony palate (LBP) 13.7 ± 0.2
13.4–13.9 (14)
14.7 ± 0.5
14.0–15.9 (9)
14.7 ± 0.5
13.7–15.8 (30)
Postpalatal length (PPL) 13.6 ± 0.4
12.9–14.5 (12)
14.4 ± 0.2
13.8–14.6 (8)
13.8 ± 0.5
13.0–15.1 (30)
Palatal breadth at M1 5.2 ± 0.3
4.8–5.7 (15)
5.8 ± 0.3
5.4–6.2
(9)
5.2 ± 0.4
4.2–5.9 (30)
Palatal breadth at M3 4.6 ± 0.3
4.1–5.1 (15)
5.0 ± 0.2
4.7–5.3
(9)
5.0 ± 0.4
4.0–5.7
(3)
Length of maxillary toothrow (P3–M3) 7.9 ± 0.4
7.3–8.5 (15)
8.5 ± 0.2
8.3–8.9
(9)
8.5 ± 0.2
8.0–9.0
(30)
Width of M2 (WM2) 2.5 ± 0.1
2.3–2.7 (15)
2.7 ± 0.1
2.5–2.9
(9)
2.6 ± 0.1
2.4–3.0
(30)
Sample sizes in parentheses.
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8 | McLean et al.
Nadler et al. 1982, 1984), integrative tests of existing taxonomic
delimitations have been lacking apart from the work of Hoisington-
Lopez et al. (2012) on U. brunneus. We focused here on delimitation
in a single, widely distributed small-eared species (U. mollis; Piute
Ground Squirrel) distributed across much of the Great Basin as eco-
logically dened (Grayson 2011). Nuclear DNA data supported dis-
tinct evolutionary histories in U. mollis populations occurring north
and south of the Snake River in Idaho. We failed to recover these
geographic lineages of U. mollis sensu lato as reciprocally monophy-
letic in any analysis, and Bayes Factor-based species delimitation
tests decisively rejected their monophyly (Table 1) regardless of
exact topological resolution.
The clear and convincing nuDNA evidence for unrecognized
species- level diversity within U. mollis contrasts with more subtle dif-
ferentiation in cranial morphology, external morphology, pelage, and
even mtDNA sequences. Whereas GMM-based analyses of the ven-
tral cranium did not strongly discriminate northern and southern U.
mollis (Figs 3 and 4b), traditional linear measurements encompassing
the entire cranium did this when taxonomic sampling was limited to
just the focal taxa. Linear measurements also separated subspecies
idahoensis and artemesiae within the northern mollis lineage (Fig.4a).
Thus, evidence from morphology of the entire cranium supports
nuDNA-based delimitation hypotheses presented here.
Considering external morphology, we observed a high degree of
conservatism in the group. Even though some statistical differences
Fig. 3. Cranial shape variation in 6 nuclear DNA lineages of small-
eared Urocitellus based on 24 two-dimensional landmarks. a) Plots of
group-wide variation from canonical axes 1 and 2 (top), and 1 and 3
(bottom). b) Heatmap of classication accuracies among all pairwise
combinations of the 6 genetic lineages. Percent accurate classications
for each species are specied with numbers on the diagonal. b = brunneus,
c = canus, w = washingtoni, t = townsendii, m (North) = northern mollis, m
(South) = southern mollis. The cladogram at the bottom is the tree in Fig.
2b. Representatives of the brunneus and endemicus lineages were pooled
here due to low sample sizes.
Fig. 4. Principal component analysis of cranial morphology among
U. mollis sensu lato subspecies based on a) 14 traditional linear
measurements and b) 24 two-dimensional geometric morphometric
(GMM) landmarks. The GMM data are representative of the ventral
cranium only.
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Journal of Mammalogy, 2024, Vol, XX, Issue XX | 9
exist among small-eared species, most of them overlap substantially
in measurements of HBL, TV, and HF (Fig. 5). External morphology
does support recognition of the 2 existing forms within northern
U. mollis (subspecies idahoensis and artemesiae), with idahoensis being
larger in each external metric. However, southern U. mollis displays
intermediate values between U. m. idahoensis and U. m. artemesiae
for all metrics. External morphological characters therefore do not
predict the species-level differences suggested by our nuDNA-based
phylogenies, although they do support current delineations at the
subspecic level.
Finally, mtDNA data corroborated our major nuDNA-based con-
clusions but revealed discordant patterns as well. The mtDNA-based
phylogeny failed to recover a monophyletic U. mollis and is thus in
agreement with nuDNA. However, mtDNA trees placed northern U.
mollis sister to a clade containing southern U. mollis and U. canus
(Harrison et al. 2003; Herron et al. 2004; McLean et al. 2016, 2022),
suggesting a closer relationship than in nuDNA trees. Similarly,
the average CytB distance between northern and southern U. mollis
was 4.09%, which, while greater than some between-species com-
parisons in mammals, is lower than most other pairwise species
comparisons in the small-eared group (Table 2). Mitochondrial data
therefore suggest a closer afnity between northern and southern
U. mollis than does nuDNA. The cause(s) of this mitonuclear discord-
ance and whether there could be potential hybridization signatures
in regions of the nuclear genome beyond UCEs and in taxon pairs
beyond those examined by McLean et al. (2022), are important next
steps in future work.
Given decisive nuDNA evidence and support from multiple mor-
phological aspects, we re-elevate populations of U. mollis sensu lato
occurring north of the Snake River (referred to above as “north-
ern U. mollis”) to their own species, U. idahoensis (Merriam 1913),
which encompasses 2 subspecies: the larger-bodied U. i. idahoensis
in the west Snake River Plain and the smaller-bodied U. i. arteme-
siae in the east Snake River Plain (see the Nomenclature section for
further descriptive notes and synonymies). We restrict the nomen
U. mollis (Kennicott 1863) to populations occurring south of the
Snake River (referred to above as “southern U. mollis”) with priority
taken from the original type locality (“Camp Floyd, near Faireld,
[Utah County,] Utah”) of Kennicott (1863). Our inference that the
most recent common ancestor of northern and southern lineages
existed early in the history of the small-eared clade (i.e., Fig. 2b)
reects a substantially deeper history of diversication across the
Great Basin and Columbia Plateau for the entire group than previ-
ously appreciated.
Importance of the Snake River as a physiographic
barrier.
Population connectivity for many low-elevation, terrestrial ver-
tebrates is high in the interior Great Basin (Jezkova et al. 2011;
Mantooth et al. 2013; Riddle et al. 2014; but see, e.g., Hafner and
Upham 2011; Jezkova et al. 2015). This may be due to the general
discontinuity of physiographic barriers, including rivers, nearly all
of which drain inward rather than transecting basin boundaries.
An exception to this pattern is the Snake River, which ows in a
generally east-west direction across southern Idaho, thus dissecting
the northern Great Basin. The Snake River has been a prominent
and persistent landscape feature since the Miocene, draining the
Yellowstone hotspot and adjacent regions to the east and encom-
passing several intermittent paleolakes along its course in Idaho,
including Lake Idaho, a large paleolake in the western Snake River
Plain (Beranek et al. 2006; Grayson 2011; Staisch et al. 2022). It has
remained a major hydrological feature and drained the massive
Lake Bonneville as recently as the late Quaternary.
Merriam (1913) described 3 forms (species or subspecies) within
the U. mollis group from north of the Snake River in Idaho. Howell
(1938) and Davis (1939) retained 2 of these as species (idahoensis and
artemesiae). While neither Merriam (1913) nor Howell (1938) elabo-
rated on the possible role of the Snake River as a barrier to dispersal,
Davis (1939) wrote extensively about the antiquity of this feature
and its role in limiting the movements of Idahoan mammals. He
asserted that the Snake River placed greater dispersal limitations on
“hibernating, land-dwelling mammals which are closely restricted
to a denite home territory and… [are] burrowing” (p. 53). He did not
consider the Snake River impermeable to mammals, instead argu-
ing that a species potential to disperse across this feature varied
with its breadth, which increases along its course from southeast-
ern to southwestern Idaho.
Citing Urocitellus as one example, Davis (1939) hypothesized min-
imal trans-riverine dispersal in western Idaho where the Snake
reaches its greatest breadth, and the distributions of multiple lin-
eages are bounded by it (U. i. idahoensis to the north, U. mollis to the
southeast, and U. canus vigilis to the southwest). Conversely, in east-
ern Idaho, where the Snake River and its tributaries are narrower, he
hypothesized higher dispersal and intergradation between lineages
north and south of the drainage (e.g., U. i. artemesiae and U. mollis),
respectively. These assertions were based on previous morphology-
based concepts of relatedness between lineages (Merriam 1913;
Howell 1938), which our nuDNA-based phylogenies did not support.
Instead, the new phylogenetic hypotheses presented here support a
Fig. 5. Ridgeline plots showing distributions of 3 external body measurements in lineages of small-eared Urocitellus. Representatives of the brunneus and
endemicus lineages were pooled here due to low sample sizes. U. mollis artemesiae and U. m. idahoensis represent a single clade (e.g., Fig. 2) but are plotted
separately here.
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10 | McLean et al.
longstanding role for the Snake River in the diversication of small-
eared Urocitellus throughout its entire length, likely as a barrier that
promoted allopatric speciation or, minimally, reinforced isolation of
already-diverged lineages. Further work is needed to test the per-
meability of the Snake River as a biogeographic barrier for other
mammals, which may start with testing for gene ow at landscape
scales between populations of U. mollis south of the Snake River
with those of U. i. idahoensis and U. i. artemesiae to the north.
Conservation aspects.
Urocitellus idahoensis has a maximal bounded range area of roughly
29,700 km2 spread across 22 counties in Idaho. This gure is only
7.5% of the total range area of U. mollis, as redened here. However,
its distribution within this range polygon is highly discontinuous,
and the total area of occupied habitat is likely substantially less.
Given the restricted range of U. idahoensis and a myriad of possi-
ble threats to this taxon, renewed population censuses, monitor-
ing, and assessment of threats are sorely needed. Possible threats
faced by U. idahoensis include (i) habitat loss and fragmentation,
paired with accelerated re regime; (ii) broader climatic shifts,
including changing trends in seasonality, which could affect
hibernation phenology; and (iii) human interactions, especially
shooting and the application of rodenticide. A fourth threat of
intermittent disease outbreaks—especially sylvatic plague—is
known to place additional pressure on ground squirrel popula-
tions and can compound negative impacts from other threats (U.S.
Fish and Wildlife Service 2004; Steenhof et al. 2006; Goldberg et al.
2021; Idaho Department of Fish and Game 2024). Data supporting
actual population impacts of any of these factors on U. idahoensis
are extremely limited, however.
For example, a well-documented positive feedback loop between
the expansion of invasive annual grasses like Cheatgrass (Bromus
tectorum) and an accelerated re regime has led to signicant
sage-steppe landscape conversion in western North America
(Knick and Rotenberry 1997; Bradley et al. 2018; Crist et al. 2023).
The Snake River Plain is an epicenter of this phenomenon, hav-
ing experienced widespread conversion from a shrub and forb
mosaic dominated primarily by Sagebrush (Artemisia spp.) to one
of cheatgrass and other exotic annual grasses (Boyte and Wylie
2017), which can directly impact some ground squirrels (Yensen
et al. 1992; Steenhof et al. 2006; Lohr et al. 2013; Holbrook et al.
2016). Obligate heterotherms, like all small-eared Urocitellus, are
vulnerable to food availability in the active and breeding seasons
since they emerge in late winter and begin the estivation/hiberna-
tion phase in early summer (Davis 1939; Rickart 1987). Changes in
forage phenology coupled with potential earlier hibernation emer-
gence due to earlier snowmelt, which has been seen in U. brunneus
(Goldberg and Conway 2021), may result in suboptimal foraging
conditions. Impactful management actions could include enhanc-
ing the availability of spring forage through native plant diversity,
reduced coverage of invasive grasses, and suppression of acceler-
ated re regimes.
Negative human interactions could pose additional threats to U.
idahoensis, driven in part by the proclivity of this species for burrow-
ing in and adjacent to agricultural and ranching lands (Davis 1939;
Durrant and Hansen 1954; Rickart 1987). Shooting but not harvest-
ing ground squirrels (thus leaving the carcass on the landscape) is
also a popular activity in parts of the range, including on the Morley
Nelson Snake River Birds of Prey National Conservation Area in
southwest Idaho, where U. idahoensis is believed to be relatively
abundant (Katzner et al. 2020; Aberg 2023). Additional research is
needed to determine the population-level effects of shooting on
U. idahoensis, especially given the existing estimates of individual
ground squirrels killed (Pauli et al. 2019) and the current lack of
management focus relative to other Urocitellus endemic to Idaho
(Idaho Department of Fish and Game 2024).
Finally, disease outbreaks are known to cause temporary reduc-
tions in population densities in U. idahoensis and other ground-
dwelling squirrels. The most notable of these is sylvatic plague,
caused by the bacterium Yersinia pestis, a pathogen endemic to
Eurasia but introduced to the western United States in the early
1900s (Gage and Kosoy 2005; Morelli et al. 2010). Plague persists
in animal reservoirs in the western United States and is vectored
by infected eas. Accordingly, this pathogen thrives in social and
colonial reservoir species, such as some ground-dwelling sciurids
(Biggins and Kosoy 2001; Augustine et al. 2023). Within the range
of U. idahoensis, few studies have quantied the extent or impact of
plague on ground squirrels except in northern populations of the
Idaho Ground Squirrel (U. brunneus) and in the Columbian Ground
Squirrel (U. columbianus; Goldberg et al. 2021).
In conclusion, species delimitation integrating multiple DNA
sequence and morphological data sets supports specic rec-
ognition of the Idaho-endemic taxon U. idahoensis (Snake River
Plains Ground Squirrel), distinguishing it from U. mollis (Piute
ground squirrel) south of the Snake River. Our ndings sharpen
understanding of ground squirrel diversity and distributions in
the northern Great Basin and Columbia Plateau ecoregions and
reemphasize the importance of the Snake River as a biogeographic
barrier that also separates these 2 taxa. This new taxonomy also
provides essential knowledge for effective conservation. Given
the restricted geographic range of U. idahoensis, renewed conser-
vation and landscape connectivity assessments are critical given
a combination of potential threats that could place increasingly
inexible constraints on the maintenance of healthy popula-
tions. Modeling tools that provide range-wide measures of ecolog-
ical resilience in the sagebrush biome and resistance to threats
could aid in the prioritization of protective or restorative actions
(Chambers et al. 2023). Positive outcomes may require paradigm
shifts towards adaptive wildlife management encompassing mul-
tiple potential threats of changing seasonality, re regime, human
interactions, and disease.
Nomenclature
Family Sciuridae Fischer, 1814
Subfamily Xerinae Murray, 1866
Tribe Marmotini Pocock, 1923
Genus Urocitellus Obolenskiy, 1927
Urocitellus idahoensis comb. nov. (Merriam, 1913)
Snake River Plains Ground Squirrel
Urocitellus idahoensis idahoensis comb. nov. (Merriam, 1913)
Spermophilus townsendi Merriam, 1891:36. Not Spermophilus
townsendii Bachman, 1839.
Citellus idahoensis Merriam, 1913:135. Type locality “Payette, at
junction of Payette and Snake River, [Payette County,] Idaho,” United
States.
Citellus mollis idahoensis: Davis, 1939:184. Name combination.
Spermophilus townsendii idahoensis: Hall and Kelson, 1959:336.
Name combination.
S[permophilus]. idahoensis: Nadler, 1968:144. Name combination.
S[permophilus]. m[ollis]. idahoensis: Nadler et al., 1982:199. Name
combination.
U[rocitellus]. m[ollis]. idahoensis: Helgen et al., 2009:297. Name
combination.
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Journal of Mammalogy, 2024, Vol, XX, Issue XX | 11
Holotype
USNM 168290; adult female skin and skull with the following meas-
urements: total length 263 mm, tail length 61 mm, hindfoot length
35 mm. Collected 23 April 1910 by S. G. Jewett.
Urocitellus idahoensis artemesiae comb. nov. (Merriam, 1913)
Citellus mollis artemesiae Merriam, 1913:137. Type locality “Birch
Creek, [Clark County,] Idaho,” United States.
Citellus mollus [sic] pessimus Merriam, 1913:138. Type locality
“lower part of Big Lost River, [Butte County,] east central Idaho,”
United States.
Citellus townsendii artemesiae: Howell, 1938:65. Name
combination.
Spermophilus townsendii artemesiae: Hall and Kelson, 1959:336.
Name combination.
Spermophilus artemesiae: Rickart, 1989:532. Name combination.
S[permophilus]. m[ollis]. artemesiae: Wilson and Ruff, 1999:426.
Name combination.
S[permophilus]. mollis artemisiae Yensen and Sherman, 2001:74.
Incorrect subsequent spelling of Citellus mollis artemesiae Merriam,
1913.
U[rocitellus]. m[ollis]. artemesiae: Helgen et al., 2009:297. Name
combination.
Holotype
USNM 23489; adult male skin and skull with the following meas-
urements: total length 188 mm, tail length 43 mm, hindfoot length
31 mm, ear length 3 mm. Collected on 9 August 1890 by V. Bailey
and B. H. Dutcher.
General characteristics.
Includes both the smallest (U. i. artemesiae) and largest (U. i. idahoen-
sis) of the small-eared Urocitellus (see Table 5 for specic external
measurements and means for both subspecies). As in other small-
eared Urocitellus, members of the species have a shorter tail (gen-
erally <60 mm) and hindfoot length (<39 mm) relative to body size
in comparison to the long-eared clade and possess inconspicuous
external pinnae. General dorsal color variegated yellowish-brown
with pale yellow dappling that is most distinct on rump but extend-
ing to shoulders in some individuals. In subspecies artemesiae, dap-
pling less distinct (pale markings fewer and smaller), along with
in older individuals of idahoensis. Individual guard hairs dark gray
basally, pale yellow mid-length, and black distally. Lateral and
ventral surfaces grayish. Top of nose, outer surfaces of the lower
hind legs, and underside of the tail are reddish-brown. Tail with a
grayish- black subterminal patch (less distinct in artemesiae). The eye
ring and anterior edge of the pinna are white. Feet yellowish-white.
Bowing in the zygomatic arches varies in adults, being more out-
bowed in shorter skulls and inbowed in longer skulls (according to
Merriam 1913). Temporal ridges are lyrate, meeting in older indi-
viduals near the base of the skull. Postorbital process is long and
slender, curving downward towards the tip; supraorbital boundaries
are slightly elevated. Cheek teeth are hypsodont and robust. Dental
formula is 1/1, 0/0, 2/1, 3/3 = 22. See Table 5 for specic cranial
measurements and means for subspecies idahoensis and artemesiae.
Comparison
Present comparisons focus only on the formerly conspecic U. mol-
lis, U. i. idahoensis, and U. i. artemesiae. Consistent size differences
exist between subspecies artemesiae and idahoensis in length of head
and body (artemesiae 166.5 mm ± 5.7, 154 to 174; idahoensis 180.3
mm ± 3.1, 175 to 185; Table 5) and length of hind foot (artemesiae
32.7 mm ± 0.6, 30 to 33; idahoensis 36.4 mm ± 1.3, 34 to 39, Table 5).
Based on our sampling, idahoensis and artemesiae can be reliably
distinguished using only some external measures, with idahoensis
having a larger head and body (i.e., >174 mm) and hind foot length
(i.e., >34 mm) on average compared to artemesiae (although there is
considerable overlap in tail length). Urocitellus mollis is intermedi-
ate in most external measures. There are also some less consistent
distinctions in pelage coloration. A larger data set with more even
geographic sampling and accompanying age assignments is needed
to determine how reliable these differences are.
Craniodentally, subspecies idahoensis is larger than the arteme-
siae lineage and U. mollis in all measurements recorded here. Skulls
of idahoensis are short and broad with relatively wider zygomatic
arches, broader braincase, and larger, moderately inated auditory
bullae, whereas artemesiae is smaller on average than idahoensis in
these dimensions. Consistent craniodental measurement differ-
ences exist between artemesiae and idahoensis only in lengths and
widths of the auditory bullae and length of the bony palette (Table
4), with idahoensis larger in each. However, again, there is consider-
able overlap of combined U. idahoensis with U. mollis in individual
measurements of the cranium and dentition. These patterns are
evident in the ordinations of cranial morphological data as well (Fig.
4), which reveal nearly complete separation of the 2 subspecies arte-
mesiae and idahoensis along the rst component, reecting the sub-
stantial size differences between these taxa but substantial overlap
between them on component 2 indicating similarity in shape. In
contrast, U. mollis overlaps with both idahoensis and artemesiae on
component 1 reecting its intermediate position with respect to
size, whereas it is largely separated from both U. idahoensis subspe-
cies on component 2, indicating substantial differences in shape.
Principal component 2 is largely a composite of relative (but not
absolute) lengths of the bulla, maxillary toothrow, and bony palate.
Based on the PCA, U. idahoensis has relatively shorter bony palates
and larger auditory bullae than U. mollis, with longer toothrow pro-
portionate to skull size. Thus, although idahoensis and artemesiae
have distinct size differences, their cranial proportions are more
similar, reinforcing their conspecicity.
In the original description of U. idahoensis, Merriam (1913) men-
tions the following skull distinctions as compared to topotypical U.
mollis: “Skull larger and more massive; rostrum and nasals longer;
zygomata more spreading throughout; jugal much broader and
more massive; maxillary roots of zygomata (viewed from in front)
larger, broader, and more massive; anterior frontal region includ-
ing orbital shelf of frontal, more elevated; upper (superior) face of
premaxillary larger and usually reaching farther posteriorly; bullae
larger; teeth heavier, the toothrow longer (8.5 mm.).” Most of these
Table 5. External measurements (X ± 1 SD and ranges in
millimeters) and measurement ratios (expressed as percentages)
of known-age Urocitellus mollis sensu lato subspecies.
Measurements U. m. artemesiae U. m. idahoensis U. m. mollis
Length of head
and body (HBL)
166.5 ± 5.7
154–174 (15)
180.3 ± 3.1
175–185 (12)
175.5 ± 8.5
156–193 (31)
Length of tail
vertebrae (TV)
44.4 ± 4.4
40–53 (14)
53.4 ± 7.5
40–62 (12)
50.4 ± 4.4
45–60 (31)
Length of hind
foot (HF)
32.7 ± 0.6
30–33 (15)
36.4 ± 1.3
34–39 (13)
34.2 ± 1.2
32–37 (31)
TV/HBL (%) 27
24–31 (14)
30
23–34 (12)
30
24–38 (31)
HF/HBL (%) 19
19–21 (15)
20
19–22 (12)
20
18–22 (31)
Sample sizes in parentheses.
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12 | McLean et al.
characteristics are supported by our analyses based on idahoensis
having a generally larger size than U. mollis (component 1 of PCA,
Fig. 4). Key traits mentioned by Merriam (1913) that are corrobo-
rated here based on component 2 of our PCA are the larger bullae
and longer toothrow, although Merriam does not comment on the
full length of the bony palate, which was also an important trait for
distinguishing U. idahoensis from U. mollis.
Merriam (1913) also provided the following description for typical
artemesiae (which he considered a subspecies of mollis): “Skull small,
smaller and shorter than in mollis; rostrum rather short and slender;
zygomata moderately bowed; bullae small—as small as in canus;
molariform teeth decidedly smaller than in mollis (slightly larger
than in canus). Compared with typical mollis, the rostrum is shorter,
the zygomata more bowed, the bullae much smaller. Skull very like
that of canus but zygomata less outstanding anteriorly, braincase
slightly less broad posteriorly, and tooth row a little longer; bullae
of same size.” This aligns with our comparison to U. mollis here, but
Merriam did not highlight any afnities between idahoensis and
artemesiae in his description. Externally, artemesiae does tend to
resemble U. mollis; however, it shares some key characteristics with
idahoensis, including the more distinctly dappled pelage (albeit less
so than idahoensis) and a grayish-black subterminal patch on the
tail (again, less distinct than in idahoensis). The external similarities
between U. mollis and artemesiae, and less pronounced similarities to
idahoensis, initially led Merriam to place artemesiae as a subspecies
of mollis while including idahoensis as a distinct species, an arrange-
ment followed by only some subsequent authors and not supported
here.
Distribution
Endemic to the Snake River Plain in south-central Idaho between
the Snake River and the Sawtooth Range, extending from Payette
and Canyon counties east to Jefferson and Clark counties. The
nominate subspecies, U. i. idahoensis, is distributed in the western
Snake River Plain, from Payette County east to Elmore County.
The subspecies U. i. artemesiae is distributed in the eastern Snake
River Plain, from Clark County in the east to Gooding County in
the west. The exact distributional limit between the 2 subspe-
cies is currently uncertain, although it is likely in Elmore and
Gooding counties. The Snake River appears to be a major bioge-
ographic barrier for this species, separating it from U. mollis to
the south and U. canus to the west. The nominate subspecies is
also partially sympatric with the U. brunneus in Gem and Payette
Counties.
Urocitellus mollis (Kennicott, 1863)
Piute Ground Squirrel
Spermophilus mollis Kennicott, 1863:157. Type locality “Camp
Floyd, near Faireld, [Utah County,] Utah,” United States.
[Spermophilus townsendi] var. mollis: Allen, 1874:293. Name
combination.
Spermophilus mollis stephensi Merriam, 1898:69. Type locality
“Queen Station, near head of Owens Valley, [Esmeralda County,]
Nevada,” United States.
[Citellus] mollis: Trouessart, 1904:339. Name combination.
[Citellus mollis] stephensi: Trouessart, 1904:339. Name combination.
Citellus leurodon Merriam, 1913:136. Type locality “Murphy,
[Owyhee County,] in hills of southwestern Idaho west of Snake
River,” United States.
Citellus mollus Merriam, 1913:138. Incorrect subsequent spelling
of Spermophilus mollis Kennicott, 1863.
Citellus mollis washoensis Merriam, 1913:138. Type locality “Carson
Valley, [Douglas County,] western Nevada,” United States.
Citellus townsendii mollis: Howell, 1938:63. Name combination.
Urocitellus mollis: Helgen et al., 2009:297. First use of current name
combination.
Holotype
USNM 3777; age and sex unknown, skin and skull with the following
measurements: total length 188 mm, tail length 43 mm, hindfoot
length 31 mm, ear length 3 mm. Collected on 18 March 1859 by C.
S. McCarthy.
General characteristics.
As in other small-eared Urocitellus, including U. idahoensis, members
of the species have a short tail (generally <60 mm) and hindfoot
length (<39 mm) relative to body size and possess inconspicu-
ous external pinnae. The general dorsal color is yellowish- gray to
medium gray, occasionally with faint pale dappling conned to
back and rump. Lateral and ventral pelage grayish- white. Faint
reddish-brown on top of nose and above eyes. The dorsal surface
of tail bright reddish-brown to dark gray, undersurface reddish-
brown or gray. The tail lacks subterminal black spot. The eye ring
and anterior edge of the pinna are pale gray or white. Feet grayish-
or yellowish-white. General skull morphology is similar to that of
U. idahoensis described above, but see Comparison section below.
Comparison
Despite the consistent size differences that separate subspecies of
U. idahoensis, U. mollis is intermediate in most external measures
and thus external proportions alone do not consistently distin-
guish it from the former species. The relative tail and hind foot
lengths of U. mollis are closer to those of U. i. idahoensis than U. i.
artemesiae (Table 5), so these relative lengths combined with geog-
raphy may serve to distinguish the 2 species. Mean cranial meas-
urements of U. mollis are also intermediate in comparison to the
smaller U. i. artemesiae and larger U. i. idahoensis (Tables 4 and 5),
and U. mollis overlaps with both idahoensis and artemesiae on princi-
pal component 1 reecting its intermediate position with respect to
size. However, the former species is separated from the other taxa
on component 2 indicating substantial differences in cranial shape.
Component 2 is largely a composite of lengths of the bulla and
maxillary toothrow and the length of the bony palate. Based on the
PCA, U. mollis has relatively longer bony palates, shorter auditory
bullae, and a shorter tooth row proportionate to skull size than U.
idahoensis.
Kennicott’s (1863) original description of U. mollis focuses pri-
marily on the external appearance of the species, stating: “Form
rather stout, with the head small and the muzzle short and com-
pressed. Ears rudimentary, the auricle only about one-twentieth
of an inch high, and scarcely distinguishable in dried specimens.
Feet rather large with the claws very weak, much compressed and
considerably curved. Tail much attened, the central hairs above
and below short and closely appressed, the outer ones longer and
distended laterally. The hair clothing and the body are remarkably
ne and soft. The upper parts are nely variegated silvery-gray,
light yellowish-brown, and black; these colors intimately and uni-
formly mixed throughout, without any indication of spots what-
ever. Under parts silvery-gray, with a slight wash of dirty creamy
yellow. Tail above yellowish-brown, slightly mixed with black,
with a distinct and prominent border and tip of white; beneath
reddish- brown within the white border.” This description provides
few details pertinent to distinguishing U. mollis from U. idahoensis,
but the lack of spots is a key external feature highlighted here.
Urocitellus mollis can be distinguished from both subspecies of U.
idahoensis based on subtle pelage traits, including having no dap-
pling (spotting) on their back and not having a subterminal patch
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Journal of Mammalogy, 2024, Vol, XX, Issue XX | 13
on the tail. Both of these traits are less distinct in U. i. artemesiae,
but are generally still present.
Distribution
Widely distributed throughout much of the Great Basin, including
southern Idaho, southeastern Oregon, Nevada, northeastern and
east-central California, and the western half of Utah. The northern
limit of its distribution is marked by the Snake River, which sepa-
rates the species from U. idahoensis in the north. U. mollis may con-
tact U. canus in the northeastern portion of its distribution (Cole and
Wilson 2009), where the 2 species may be parapatrically distributed
in northeastern Nevada, southeastern Oregon, and southwestern
Idaho, but more surveys in this region are necessary. In Oregon, U.
mollis extends at least as far as Malheur County in the northwestern
portion of its distribution, although the exact distributional limits
where this species meets U. canus are uncertain. In the west, the spe-
cies extends to Lassen and Plumas Counties in northeast California
and Mono County, California, in the southeast of its range. In the
south, U. mollis has been recorded as far as northern Clark County at
the north end of the Spring Mountains of Nevada. In Utah, U. mollis
extends east to Sanpete County and southeast to Iron County and
is limited to the west and south of the Great Salt Lake. The species
extends north into Idaho at least as far as Bannock County in the
northeast and Owyhee County in the northwest.
Supplementary data
Supplementary data are available at Journal of Mammalogy online.
Supplementary Data SD1. Locations of geometric morphometric
landmarks on ventral crania.
Supplementary Data SD2. Raw (nonsuperimposed) geometric
morphometric landmark data.
Supplementary Data SD3. Linear measurement data from cra-
nia of known-age Urocitellus mollis.
Supplementary Data SD4. Extremal measurement data for
small-eared Urocitellus.
Acknowledgments
Bill Bosworth and Jamie Utz (Idaho Department of Fish and Game)
provided logistical support for some portions of this work. We
thank the curators and collection managers who facilitated access
to important specimens, especially Kristofer Helgen (Australian
Museum Research Institute), Chris Conroy (Museum of Vertebrate
Zoology), Jonathan Dunnum (Museum of Southwestern Biology),
and Robert Timm (University of Kansas Biodiversity Institute). We
also acknowledge the generations of mammalogists, museum pro-
fessionals, and informaticians whose collective work has made trait
data from mammal specimens increasingly discoverable on the
internet for biodiversity description.
Author contributions
BSM conceptualized the study; BSM, EAR, RPG, and CJB collected
and curated the data; BSM and EAR analyzed and visualized the
data; BSM, JAC, and RPG acquired the funding; BSM, CJB, and EAR
wrote the original draft; all authors contributed to review and edit-
ing of subsequent drafts.
Funding
This work was partially funded by a U.S. National Science
Foundation Postdoctoral Research Fellowship in Biology to BSM
(NSF DBI 1812152), ABI Innovation grant to RPG (NSF DBI 1759898),
Predictive Intelligence for Pandemic Prevention (PIPP) grant to JAC
(NSF CCF 2155252), and a U.S. Fish and Wildlife Service Candidate
Conservation Fund grant to BSM and JAC (F17AC0031).
Conict of interest
None declared.
Data availability
GenBank accession numbers for genetic data are provided in
Appendix I. Raw morphometric data are provided in Supplementary
Data les.
References
Aberg MC. 2023. A coupled human and natural systems approach to
studying recreation on public lands [doctoral dissertation]. Boise
(ID, USA): Boise State University. https://www.proquest.com/
docview/2835521427
Adams DC, Collyer ML, Kaliontzopoulou A, Baken EK. 2022.
Geomorph: software for geometric morphometric analyses.
Version 4.0.4. [Computer software]. https://cran.r-project.org/
package=geomorph
Allen JA. 1874. On geographical variation in color among North
American squirrels; with a list of the species and varieties of the
American Sciuridae occurring north of Mexico. Proceedings of the
Boston Society of Natural History 16(1873-1874):276–294. https://
www.biodiversitylibrary.org/item/130707
Arbogast BS, Schumacher KI, Kerhoulas NJ, Bidlack AL, Cook JA, Kenagy
GJ. 2017. Genetic data reveal a cryptic species of New World ying
squirrel: Glaucomys oregonensis. Journal of Mammalogy 98(4):1027–
1041. https://doi.org/10.1093/jmammal/gyx055
Augustine DJ, Smith JE, Davidson AD, Stapp P. 2023. Burrowing rodents.
In: McNew LB, Dahlgren DK, Beck JL, editors. Rangeland wildlife
ecology and conservation. Cham (Switzerland): SpringerLink;
p.505–548.
Bachman J. 1839. Description of several new species of American quad-
rupeds. Journal of the Academy of Natural Sciences of Philadelphia
8(1):57–74. https://www.biodiversitylibrary.org/item/79280
Badgley C. 2010. Tectonics, topography, and mammalian diversity.
Ecography 33(2):220–231. https://doi.org/10.1111/j.1600-0587.
2010.06282.x
Badgley C, Smiley TM, Finarelli JA. 2014. Great Basin mammal diversity
in relation to landscape history. Journal of Mammalogy 95(6):1090–
1106. https://doi.org/10.1644/13-mamm-s-088
Baken EK, Collyer ML, Kaliontzopoulou A, Adams DC. 2021. Geomorph
v4.0 and gmShiny: enhanced analytics and a new graphi-
cal interface for a comprehensive morphometric experience.
Methods in Ecology and Evolution 12(12):2355–2363. https://doi.
org/10.1111/2041-210x.13723
Baker RJ, Bradley RD. 2006. Speciation in mammals and the genetic
species concept. Journal of Mammalogy 87(4):643–662. https://doi.
org/10.1644/06-MAMM-F-038R2.1
Balk MA, Deck J, Emery KF, Walls RL, Reuter D, LaFrance R, Arroyo-
Cabrales J, Barrett P, Blois J, Boileau A, et al. 2022. A solution to
the challenges of interdisciplinary aggregation and use of
specimen-level trait data. iScience 25(10):105101. https://doi.
org/10.1016/j.isci.2022.105101
Beranek LP, Link PK, Fanning CM. 2006. Miocene to Holocene land-
scape evolution of the western Snake River Plain region, Idaho:
using the SHRIMP detrital zircon provenance record to track
Downloaded from https://academic.oup.com/jmammal/advance-article/doi/10.1093/jmammal/gyae135/7922595 by guest on 30 December 2024
14 | McLean et al.
eastward migration of the Yellowstone hotspot. Geological Society
of America Bulletin 118(9–10):1027–1050. https://doi.org/10.1130/
b25896.1
Biggins DE, Kosoy MY. 2001. Inuences of introduced plague on
North American mammals: implications from ecology of plague
in Asia. Journal of Mammalogy 82(4):906–916. https://doi.
org/10.1644/1545-1542(2001)082<0906:ioipon>2.0.co;2
Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA,
Rambaut A, Drummond AJ. 2014. BEAST 2: a software platform
for Bayesian evolutionary analysis. PLoS Computational Biology
10(4):e1003537. https://doi.org/10.1371/journal.pcbi.1003537
Boyte SP, Wylie BK. 2017. Estimates of herbaceous annual cover in
the sagebrush ecosystem. (May 1, 2017). Sioux Falls (SD, USA):
U.S. Geological Survey Data Release. https://doi.org/10.5066/
F7445JZ9
Bradley BA, Curtis CA, Fusco EJ, Abatzoglou JT, Balch JK, Dadashi S,
Tuanmu MN. 2018. Cheatgrass (Bromus tectorum) distribution in
the intermountain Western United States and its relationship
to re frequency, seasonality, and ignitions. Biological Invasions
20(6):1493–1506. https://doi.org/10.1007/s10530-017-1641-8
Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, Roychoudhury A.
2012. Inferring species trees directly from biallelic genetic mark-
ers: bypassing gene trees in a full coalescent analysis. Molecular
Biology and Evolution 29(8):1917–1932. https://doi.org/10.1093/
molbev/mss086
Burgin CJ, Colella JP, Kahn PL, Upham NS. 2018. How many species of
mammals are there? Journal of Mammalogy 99(1):1–14. https://
doi.org/10.1093/jmammal/gyx147
Chambers JC, Brown JL, Bradford JB, Doherty KE, Crist MR, Schlaepfer
DR, Urza AK, Short KC. 2023. Combining resilience and resist-
ance with threat‐based approaches for prioritizing management
actions in sagebrush ecosystems. Conservation Science and
Practice 5(11):e13021. https://doi.org/10.1111/csp2.13021
Cole FR, Wilson DE. 2009. Urocitellus canus (Rodentia: Sciuridae).
Mammalian Species (834):1–8. https://doi.org/10.1644/834.1
Colella JP, Frederick LM, Talbot SL, Cook JA. 2021. Extrinsically rein-
forced hybrid speciation within Holarctic ermine (Mustela spp.)
produces an insular endemic. Diversity and Distributions
27(4):747–762. https://doi.org/10.1111/ddi.13234
Collyer ML, Adams DC. 2021. RRPP: linear model evaluation with ran-
domized residuals in a permutation procedure. Version 1.1.2.
[Computer software] (https://cran.r-project.org/package=RRPP).
Crist MR, Belger R, Davies KW, Davis DM, Meldrum JR, Shinneman DJ,
Remington TE, Welty J, Mayer KE. 2023. Trends, impacts, and cost
of catastrophic and frequent wildres in the sagebrush biome.
Rangeland Ecology and Management 89(July 2023):3–19. https://
doi.org/10.1016/j.rama.2023.03.003
Davis WB. 1939. The Recent Mammals of Idaho. Caldwell (ID, USA): The
Caxton Printers, Ltd.
Durrant SD, Hansen RM. 1954. Distribution patterns and phylogeny of
some western ground squirrels. Systematic Zoology 3(2):82–85.
https://doi.org/10.2307/2411841
Felsenstein J. 1989. PHYLIP – phylogeny inference package. Version 3.2.
Cladistics 5:164–166.
Fischer G. 1814. Zoognosia. Volumen III. Quadrupeda reliqua. Ceti.
Monotrymata. Moscow (Russia): Nicolai Sergeidis Vsevolozsky.
Gage KL, Kosoy MY. 2005. Natural history of plague: perspec-
tives from more than a century of research. Annual Review of
Entomology 50(2005):505–528. https://doi.org/10.1146/annurev.
ento.50.071803.130337
Grayson D. 2011. The Great Basin: a natural prehistory. Berkeley and
Los Angeles (CA, USA): University of California Press.
Goldberg AR, Conway CJ. 2021. Hibernation behavior of a federally
threatened ground squirrel: climate change and habitat selection
implications. Journal of Mammalogy 102(2):574–587. https://doi.
org/10.1093/jmammal/gyab021
Goldberg AR, Conway CJ, Biggins DE. 2021. Effects of experimental ea
removal and plague vaccine treatments on survival of northern
Idaho ground squirrels and two coexisting sciurids. Global Ecology
and Conservation 26(April 2021):e01489. https://doi.org/10.1016/j.
gecco.2021.e01489
Guralnick RP, Balk MA, Deck J, Emery K, Davis E, Sewnath N,
Bernor R, Walls R. 2022. FuTRES (Functional Trait Resource for
Environmental Studies) data store archival copy – 5/21/2022,
Version 1.0. [accessed 5 Dec 2023]. Zenodo. https://doi.
org/10.5281/zenodo.6569644
Guralnick RP, Zermoglio PF, Wieczorek J, LaFrance R, Bloom D, Russell L.
2016. The importance of digitized biocollections as a source of trait
data and a new VertNet resource. Database 2016(2016):baw158.
https://doi.org/10.1093/database/baw158
Hafner JC, Upham NS. 2011. Phylogeography of the dark kangaroo
mouse, Microdipodops megacephalus: cryptic lineages and dispersal
routes in North America’s Great Basin. Journal of Biogeography
38(6):1077–1097. https://doi.org/10.1111/j.1365-2699.2010.02472.x
Hall ER, Kelson KR. 1959. The mammals of North America. 1st ed. New
York (NY, USA): Ronald Press Co.
Harrison RG, Bogdanowicz SM, Hoffmann RS, Yensen E, Sherman PW.
2003. Phylogeny and evolutionary history of the ground squir-
rels (Rodentia: Marmotinae). Journal of Mammalian Evolution
10(3):249–276. https://doi.org/10.1023/b:jomm.0000015105.96065.
f0
Helgen KM, Cole FR, Helgen LE, Wilson DE. 2009. Generic revision in the
Holarctic ground squirrel genus Spermophilus. Journal of Mammalogy
90(2):270–305. https://doi.org/10.1644/07-mamm-a-309.1
Herrera ND, Bell KC, Callahan CM, Nordquist E, Sarver BAJ, Sullivan J,
Demboski JR, Good JM. 2022. Genomic resolution of cryptic species
diversity in chipmunks. Evolution 76(9):2004–2019. https://doi.
org/10.1111/evo.14546
Herron MD, Castoe TA, Parkinson CL. 2004. Sciurid phylogeny and the
paraphyly of Holarctic ground squirrels (Spermophilus). Molecular
Phylogenetics and Evolution 31(3):1015–1030. https://doi.
org/10.1016/j.ympev.2003.09.015
Hoffmann RS, Anderson CG, Thorington RW, Heaney LR. 1993. Family
Sciuridae. In: Wilson DE, Reeder DM., editors. Mammal species
of the world: a taxonomic and geographic reference. 2nd ed.
Washington (DC, USA): Smithsonian Institution Press; p. 419–466.
Hoisington-Lopez JL, Waits LP, Sullivan J. 2012. Species limits and inte-
grated taxonomy of the Idaho ground squirrel (Urocitellus brunneus):
genetic and ecological differentiation. Journal of Mammalogy
93(2):589–604. https://doi.org/10.1644/11-mamm-a-021.1
Holbrook JD, Arkle RS, Rachlow JL, Vierling KT, Pilliod DS, Wiest MM.
2016. Occupancy and abundance of predator and prey: impli-
cations of the re-cheatgrass cycle in sagebrush ecosystems.
Ecosphere 7(6):e01307. https://doi.org/10.1002/ecs2.1307
Howell AH. 1928. Descriptions of six new North American ground
squirrels. Proceedings of the Biological Society of Washington 41:211–
214. https://doi.org/10.5281/zenodo.13446982
Howell AH. 1938. Revision of the North American ground squirrels,
with a classication of the North American Sciuridae. North
American Fauna 56:1–256. https://doi.org/10.3996/nafa.56.0001
Idaho Department of Fish and Game. 2024. Idaho State wildlife action
plan. 2023 rev. ed. Boise (ID, USA): Idaho Department of Fish and
Game. https://idfg.idaho.gov/
Jezkova T, Jaeger JR, Oláh-Hemmings V, Jones KB, Lara-Resendiz RA,
Mulcahy DG, Riddle BR. 2015. Range and niche shifts in response
to past climate change in the desert horned lizard Phrynosoma
platyrhinos. Ecography 39(5):437–448. https://doi.org/10.1111/
ecog.01464
Downloaded from https://academic.oup.com/jmammal/advance-article/doi/10.1093/jmammal/gyae135/7922595 by guest on 30 December 2024
Journal of Mammalogy, 2024, Vol, XX, Issue XX | 15
Jezkova T, Olah-Hemmings V, Riddle BR. 2011. Niche shifting in response
to warming climate after the last glacial maximum: inference from
genetic data and niche assessments in the chisel-toothed kanga-
roo rat (Dipodomys microps). Global Change Biology 17(11):3486–
3502. https://doi.org/10.1111/j.1365-2486.2011.02508.x
Kass RE, Raftery AE. 1995. Bayes factors. Journal of the American
Statistical Association 90(430):773–795. https://doi.
org/10.2307/2291091
Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment
software version 7: improvements in performance and usabil-
ity. Molecular Biology and Evolution 30(4):772–780. https://doi.
org/10.1093/molbev/mst010
Katzner TE, Carlisle JD, Poessel SA, Thomason EC, Pauli BP, Pilliod DS,
Belthoff JR, Heath JA, Parker KJ, Warner KS, et al. 2020. Illegal kill-
ing of nongame wildlife and recreational shooting in conservation
areas. Conservation Science and Practice 2(11):e279. https://doi.
org/10.1111/csp2.279
Kays RW, Wilson DE. 2010. Mammals of North America. 2nd ed.
Princeton (NJ, USA): Princeton University Press.
Kays R, Lasky M, Allen ML, Dowler RC, Hawkins MTR, Hope AG, Kohli BA,
Mathis VL, McLean BS, Olson LE, et al. 2022. Which mammals can
be identied from camera traps and crowdsourced photographs?
Journal of Mammalogy 103(4):767–775. https://doi.org/10.1093/
jmammal/gyac021
Kennicott R. 1863. Descriptions of four new species of Spermophilus, in
the collections of the Smithsonian Institution. Proceedings of the
Academy of Natural Sciences of Philadelphia 15:157–158. https://
www.biodiversitylibrary.org/part/84767
Knick ST, Rotenberry JT. 1997. Landscape characteristics of dis-
turbed shrubsteppe habitats in southwestern Idaho
(USA). Landscape Ecology 12(1997):287–297. https://doi.
org/10.1023/A:1007915408590
Leaché AD, Fujita MK, Minin VN, Bouckaert RR. 2014. Species delimita-
tion using genome-wide SNP data. Systematic Biology 63(4):534–
542. https://doi.org/10.1093/sysbio/syu018
Lohr K, Yensen E, Munger JC, Novak SJ. 2013. Relationship between hab-
itat characteristics and densities of southern Idaho ground squir-
rels. The Journal of Wildlife Management 77(5):983–993. https://
doi.org/10.1002/jwmg.541
Malaney JL, Demboski JR, Cook JA. 2017. Integrative species
delimitation of the widespread North American jumping
mice (Zapodinae). Molecular Phylogenetics and Evolution
114(September 2017):137–152. https://doi.org/10.1016/j.
ympev.2017.06.001
Mammal Diversity Database. 2023. Mammal Diversity Database v1.11
[Data Set]. Zenodo. https://doi.org/10.5281/zenodo.7830771
Mantooth SJ, Hafner DJ, Bryson RW, Riddle BR. 2013. Phylogeographic
diversication of antelope squirrels (Ammospermophilus) across
North American deserts. Biological Journal of the Linnean Society
109(4):949–967. https://doi.org/10.1111/bij.12084
McLean BS, Bell KC, Allen JM, Helgen KM, Cook JA. 2019. Impacts of
inference method and data set ltering on phylogenomic resolu-
tion in a rapid radiation of ground squirrels (Xerinae: Marmotini).
Systematic Biology 68(2):298–316. https://doi.org/10.1093/sysbio/
syy064
McLean BS, Bell KC, Cook JA. 2022. SNP-based phylogenomic inference
in Holarctic ground squirrels (Urocitellus). Molecular Phylogenetics
and Evolution 169(April 2022):107396. https://doi.org/10.1016/j.
ympev.2022.107396
McLean BS, Helgen KM, Goodwin HT, Cook JA. 2018. Trait-specic pro-
cesses of convergence and conservatism shape ecomorphological
evolution in ground-dwelling squirrels. Evolution 72(3):473–489.
https://doi.org/10.1111/evo.13422
McLean BS, Jackson DJ, Cook JA. 2016. Rapid divergence and gene
ow at high latitudes shape the history of Holarctic ground
squirrels (Urocitellus). Molecular Phylogenetics and Evolution
102(September 2016):174–188. https://doi.org/10.1016/j.
ympev.2016.05.040
Merriam CH. 1891. Results of a biological reconnaissance of south
central Idaho, south of latitude 45° and east of the thirty-eighth
meridian, made during the summer of 1890, with annotated lists
of the mammals and birds, and descriptions of new species. North
American Fauna 5:1–30. https://doi.org/10.3996/nafa.5.0001
Merriam CH. 1898. Descriptions of six new ground squirrels from
the western United States. Proceedings of the Biological Society
of Washington 12(March 1898):69–71. http://doi.org/10.5281/
zenodo.13441805
Merriam CH. 1913. Six new ground squirrels of the Citellus mollis group
from Idaho, Oregon, and Nevada. Proceedings of the Biological
Society of Washington 26(May 1913):135–138. https://doi.
org/10.5281/zenodo.13676614
Mills KK, Everson KM, Hildebrandt KB, Brandler OV, Steppan SJ, Olson
LE. 2023. Ultraconserved elements improve resolution of marmot
phylogeny and offer insights into biogeographic history. Molecular
Phylogenetics and Evolution 184(July 2023):107785. https://doi.
org/10.1016/j.ympev.2023.107785
Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner
DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, et al. 2010. Yersinia
pestis genome sequencing identies patterns of global phyloge-
netic diversity. Nature Genetics 42(12):1140–1143. https://doi.
org/10.1038/ng.705
Murray A. 1866. The geographical distribution of mammals. London
(UK): Day and Son.
Nadler CF. 1966. Chromosomes and systematics of American ground
squirrels of the subgenus Spermophilus. Journal of Mammalogy
47(4):579–596. https://doi.org/10.2307/1377889
Nadler CF. 1968. The serum proteins and transferrins of the ground squirrel
subgenus Spermophilus. Comparative Biochemistry and Physiology
27(2):487–503. https://doi.org/10.1016/0010-406x(68)90246-6
Nadler CF. 1968. The chromosomes of Spermophilus townsendi (Rodentia:
Sciuridae) and report of a new subspecies. Cytogenetics 7(2):144–
157. https://doi.org/10.1159/000129978
Nadler CF, Hoffmann RS, Vorontsov NN, Koeppl JW, Deutsch L, Sukernik
RI. 1982. Evolution in ground squirrels: II. Biochemical compar-
isons in Holarctic populations of Spermophilus. Zeitschrift für
Säugetierkunde 47A(4):198–215. https://www.biodiversitylibrary.
org/part/191595
Nadler CF, Lyapunova EA, Hoffmann RS, Vorontsov NN, Shaitarova LL,
Borisov YM. 1984. Chromosomal evolution in holarctic ground
squirrels (Spermophilus). II: Giemsa-band homologies of chromo-
somes and the tempo of evolution. Zeitschrift für Säugetierkunde
49(2):78–90. https://www.biodiversitylibrary.org/part/191696
Obolenskiy S. 1927. A preliminary review of the Palaearctic sousliks
(Citellus and Spermophilopsis). Compe Rendu de l’Academie des
Sciences de l’USSR 12:188–193.
Padial JM, Miralles A, De la Riva I, Vences M. 2010. The integrative
future of taxonomy. Frontiers in Zoology 7(2010):16. https://doi.
org/10.1186/1742-9994-7-16
Paradis E, Schliep K. 2019. Ape 5.0: an environment for modern
phylogenetics and evolutionary analyses in R. Bioinformatics
35(3):526–528. https://doi.org/10.1093/bioinformatics/bty633
Parsons DJ, Pelletier TA, Wieringa JG, Duckett DJ, Carstens BC. 2022.
Analysis of biodiversity data suggests that mammal species are
hidden in predictable places. Proceedings of the National Academy
of Sciences of the United States of America 119(14):e2103400119.
https://doi.org/10.1073/pnas.2103400119
Downloaded from https://academic.oup.com/jmammal/advance-article/doi/10.1093/jmammal/gyae135/7922595 by guest on 30 December 2024
16 | McLean et al.
Pauli BP, Sun ER, Tinkle ZK, Forbey JS, Demps KE, Heath JA. 2019.
Human habitat selection: using tools from wildlife ecology to
predict recreation in natural landscapes. Natural Areas Journal
39(2):142–149. https://doi.org/10.3375/043.039.0202
Phuong MA, Lim MCW, Wait DR, Rowe KC, Moritz C. 2014. Delimiting
species in the genus Otospermophilus (Rodentia: Sciuridae), using
genetics, ecology, and morphology. Biological Journal of the Linnean
Society 113(4):1136–1151. https://doi.org/10.1111/bij.12391
Pocock RI. 1923. The classication of the Sciuridæ. Proceedings of
the Zoological Society of London 93(2):209–246. https://doi.
org/10.1111/j.1096-3642.1923.tb02184.x
Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. 2018. Posterior
summarization in Bayesian phylogenetics using Tracer 1.7.
Systematic Biology 67(5):901–904. https://doi.org/10.1093/sysbio/
syy032
Reeder DM, Helgen KM, Wilson DE. 2007. Global trends and biases
in new mammal species discoveries. Occasional Papers of the
Museum of Texas Tech University 269:1–35.
Rickart EA. 1987. Spermophilus townsendii. Mammalian Species 268:1–6.
https://doi.org/10.2307/0.268.1
Rickart EA. 1989. Variation in renal structure and urine concentrating
capacity among ground squirrels of the Spermophilus townsendii com-
plex (Rodentia: Sciuridae). Comparative Biochemistry and Physiology
92(4):531–534. https://doi.org/10.1016/0300-9629(89)90360-5
Rickart EA, Hoffmann RS, Roseneld M. 1985. Karyotype of Spermophilus
townsendii artemesiae (Rodentia: Sciuridae) and chromosomal
variation in the Spermophilus townsendii complex. Mammalian
Chromosomes Newsletter 26(3-4):94–102.
Riddle BR, Jezkova T, Eckstut ME, Oláh-Hemmings V, Carraway LN.
2014. Cryptic divergence and revised species taxonomy within
the Great Basin pocket mouse, Perognathus parvus (Peale, 1848),
species group. Journal of Mammalogy 95(1):9–25. https://doi.
org/10.1644/12-mamm-a-252
Rohlf FJ. 2006. tpsDig. Version 2.10. [Computer software]. Stony Brook
(NY, USA): Department of Ecology and Evolution, State University
of New York https://www.sbmorphometrics.org/
Schlager S. 2017. Morpho and Rvcg – shape analysis in R. In: Zheng G,
Li S, Szekely G, editors. Statistical shape and deformation analysis.
London (UK): Academic Press; p. 217–256.
Schliep KP. 2011. Phangorn: phylogenetic analysis in R. Bioinformatics
27(4):592–593. https://doi.org/10.1093/bioinformatics/btq706
Sikes RS, The Animal Care and Use Committee of the American Society
of Mammalogists. 2016. 2016 Guidelines of the American Society
of Mammalogists for the use of wild mammals in research and
education. Journal of Mammalogy 97(3):663–688. https://doi.
org/10.1093/jmammal/gyw078
Staisch LM, O’Connor JE, Cannon CM, Holm-Denoma C, Link PK,
Lasher J, Alexander JA. 2022. Major reorganization of the Snake
River modulated by passage of the Yellowstone Hotspot. Bulletin
of the Geological Society of America 134(7-8):1834–1844. https://
doi.org/10.1130/b36174.1
Steenhof K, Yensen E, Kochert MN, Gage KL. 2006. Populations and hab-
itat relationships of Piute ground squirrels in southwestern Idaho.
Western North American Naturalist 66(4):482–491. https://doi.
org/10.3398/1527-0904(2006)66[482:pahrop]2.0.co;2
Thorington RW, Hoffmann RS. 2005. Family Sciuridae. In: Wilson DE,
Reeder DM, editors. Mammal species of the world: a taxonomic
and geographic reference. 3rd ed. Baltimore (MD, USA): The Johns
Hopkins University Press; p. 754–818.
Thorington RW, Koprowski JL, Steele ML, Whatton JF. 2012. Squirrels
of the world. Baltimore (MD, USA): The Johns Hopkins University
Press.
Tinwari V, Kashikar A. 2019. Outlier detection. Version 0.1.0. [Computer
software]. https://cran.r-project.org/package=OutlierDetection.
Trouessart E-L. 1904. Catalogus mammalium tam viventium quam
fossilium. Berlin (Germany): R. Friedlander and Sohn.
U.S. Fish and Wildlife Service. 2004. Species assessment and list-
ing priority assignment form. Spermophilus brunneus endemi-
cus, southern Idaho ground squirrel. Boise (ID, USA): U.S. Fish
and Wildlife Service. https://downloads.regulations.gov/FWS-
HQ-ES-2015-0143-0022/content.pdf
Wickham H. 2016. ggplot2: elegant graphics for data analysis. New
York (NY, USA): Springer-Verlag.
Wilke CO. 2024. ggridges: Ridgeline plots in ggplot2.” Version
0.5.6. [Computer software]. https://cran.r-project.org/
package=ggridges
Wilson DE, Ruff S. 1999. The Smithsonian book of North American
Mammals. Washington (DC, USA): Smithsonian Institution Press.
Yensen E. 1991. Taxonomy and distribution of the Idaho ground squir-
rel, Spermophilus brunneus. Journal of Mammalogy 72(3):583–600.
https://doi.org/10.2307/1382142
Yensen E, Quinney DL, Johnson K, Timmerman K, Steenhof K. 1992. Fire,
vegetation changes, and population uctuations of Townsend’s
ground squirrels. American Midland Naturalist 128(2):299–312.
https://doi.org/10.2307/2426464
Yensen E. 2019. Urocitellus nancyae. The IUCN red list of threatened
species 2019: e.T116989724A116989738 [accessed 22 Dec 2023]
https://www.iucnredlist.org/species/116989724/116989738.
Yensen E, Sherman PW. 2001. Demise of the small-eared ground squir-
rels (Abstracts from the Symposium on Conservation Biology of
Ground Squirrels and the Shrub-Steppe Ecosystem). Journal of the
Idaho Academy of Science 37(1):74–77.
Downloaded from https://academic.oup.com/jmammal/advance-article/doi/10.1093/jmammal/gyae135/7922595 by guest on 30 December 2024
Journal of Mammalogy, 2024, Vol, XX, Issue XX | 17
Appendix I
Specimens examined for molecular analysis.
sample Code Genus specic
Epithet
subspecic
epithet
state
Province
County institution
Code
catalog
Number
tissue
Identier
tissue
Number
GenBank
Accessions
mtDNA
GenBank
Accessions
nuDNA_5gene
GenBank
accessions
nuDNA_UCEs
Citations
Ubrunneus_EY978 Urocitellus brunneus brunneus Idaho Adams USNM Uncataloged EY 978 AF157884 KX278603,
KX290211,
KX278647,
KX290256
KFKK00000000 Harrison etal.
(2003) | McLean
etal. (2016) |
McLean etal.
(2022)
Ubrunneus_EY980 Urocitellus brunneus brunneus Idaho Adams EY 980 AF157952 Harrison etal.
(2003)
Ubrunneus_
CS-A0102-Ubb27
Urocitellus brunneus brunneus Idaho Adams CS-A0102-
Ubb27
JQ679203 Hoisington-Lopez
etal. (2012)
Ubrunneus_
ChS-0946-Ubb38
Urocitellus brunneus brunneus Idaho Adams ChS-0946-
Ubb38
JQ679271 Hoisington-Lopez
etal. (2012)
Ubrunneus_
RV-175-Ubb40
Urocitellus brunneus brunneus Idaho Valley RV-175-Ubb40 JQ679274 Hoisington-Lopez
etal. (2012)
Ubrunneus_EY974 Urocitellus brunneus endemicus Idaho Payette USNM Uncataloged EY 974 AF157886 KX278601,
KX290209,
KX278645,
KX290254
KFKM00000000 Harrison etal.
(2003) | McLean
etal. (2016) |
McLean etal.
(2022)
Ubrunneus_EY975 Urocitellus brunneus endemicus Idaho Payette USNM Uncataloged EY 975 AF157883 KX278602,
KX290210,
KX278646,
KX290255
KFKL00000000 Harrison etal.
(2003) | McLean
etal. (2016) |
McLean etal.
(2022)
Ubrunneus_
CP-D0402-Ube11
Urocitellus brunneus endemicus Idaho Payette CP-D0402-
Ube11
JQ679146 Hoisington-Lopez
etal. (2012)
Ubrunneus_
MC-MC005-Ube13
Urocitellus brunneus endemicus Idaho Washington MC-MC005-
Ube13
JQ679154 Hoisington-Lopez
etal. (2012)
Ubrunneus_
SB-D0378-Ube21
Urocitellus brunneus endemicus Idaho Gem SB-D0378-
Ube21
JQ679177 Hoisington-Lopez
etal. (2012)
Ucanus_MSB110676 Urocitellus canus canus Nevada Humboldt MSB 110676 KX278559 KFKJ00000000 McLean etal. (2016)
| McLean etal.
(2022)
Ucanus_MSB110677 Urocitellus canus canus Nevada Humboldt MSB 110677 KX278558 McLean etal. (2016)
Ucanus_MSB110678 Urocitellus canus canus Nevada Humboldt MSB 110678 KX278557 McLean etal. (2016)
Ucanus_EY963 Urocitellus canus vigilis Idaho Owyhee USNM Uncataloged EY 963 KX278526 KX278599, KX290212, KX278643,
KX290252
McLean etal. (2016)
Ucanus_EY964 Urocitellus canus vigilis Idaho Owyhee USNM Uncataloged EY 964 KX278527 KX278600,
KX290208,
KX278644,
KX290253
KFKI00000000 McLean etal. (2016)
| McLean etal.
(2022)
Ucanus_EY966 Urocitellus canus vigilis Idaho Owyhee USNM Uncataloged EY 966 OR813776 KFKH00000000 McLean etal. (2022)
Ucanus_EY965 Urocitellus canus vigilis Idaho Owyhee EY 965 AF157888 Harrison etal.
(2003)
Downloaded from https://academic.oup.com/jmammal/advance-article/doi/10.1093/jmammal/gyae135/7922595 by guest on 30 December 2024
18 | McLean et al.
sample Code Genus specic
Epithet
subspecic
epithet
state
Province
County institution
Code
catalog
Number
tissue
Identier
tissue
Number
GenBank
Accessions
mtDNA
GenBank
Accessions
nuDNA_5gene
GenBank
accessions
nuDNA_UCEs
Citations
Ucanus_EY968 Urocitellus canus vigilis Idaho Owyhee EY 968 AF157889 Harrison etal.
(2003)
Uidahoensis_
MSB152485
Urocitellus idahoensis artemesiae Idaho Butte MSB 152485 NK 145662 KX278528 KX278604,
KX290213,
KX278648,
KX290258
KFJB00000000 McLean etal. (2016)
| McLean etal.
(2022)
Uidahoensis_
MSB152846
Urocitellus idahoensis artemesiae Idaho Butte MSB 152846 NK 145739 KX278579 McLean etal. (2016)
Uidahoensis_
MSB152352
Urocitellus idahoensis artemesiae Idaho Butte MSB 152352 NK 147596 KX278529 KX278605, KX290214, KX278649,
KX290259
McLean etal. (2016)
Uidahoensis_
MSB71991
Urocitellus idahoensis idahoensis Idaho Ada MSB 71991 NK 30724 KX278569 KFJA00000000 McLean etal. (2016)
| McLean etal.
(2022)
Uidahoensis_
MSB89149
Urocitellus idahoensis idahoensis Idaho Ada MSB 89149 NK 5929 KX278552 KX278634,
KX290243,
KX278678,
KX290257
KFIZ00000000 McLean etal. (2016)
| McLean etal.
(2022)
Uidahoensis_
EY1068
Urocitellus idahoensis idahoensis Idaho Ada EY 1068 AF157880 Harrison etal.
(2003)
Uidahoensis_
EY1067
Urocitellus idahoensis idahoensis Idaho Ada EY 1067 AF157949 Harrison etal.
(2003)
Umollis_EY1129a Urocitellus mollis mollis Idaho Owyhee USNM Uncataloged EY 1129a AF157920 KX278597,
KX290206,
KX278641,
KX290250
KFJY00000000 Harrison etal.
(2003) | McLean
etal. (2016) |
McLean etal.
(2022)
Umollis_EY1130a Urocitellus mollis mollis Idaho Owyhee USNM Uncataloged EY 1130a AF157938 KX278598,
KX290207,
KX278642,
KX290251
KFJX00000000 Harrison etal.
(2003) | McLean
etal. (2016)
Umollis_
MVZ224858
Urocitellus mollis mollis California Mono MVZ 224858 KX278535 KX278616, KX290225, KX278660,
KX290270
McLean etal. (2016)
Umollis_MSB47928 Urocitellus mollis mollis Nevada White Pine MSB 47928 KFKA00000000 McLean etal. (2022)
Utownsendii_
EY1160a
Urocitellus townsendii nancyae Washington Kittitas USNM Uncataloged EY 1160a AF157933 KX278596,
KX290205,
KX278640,
KX290249
KFJL00000000 Harrison etal.
(2003) | McLean
etal. (2016) |
McLean etal.
(2022)
Utownsendii_
EY1159
Urocitellus townsendii nancyae Washington Kittitas EY 1159 AF157932 Harrison etal.
(2003)
Utownsendii_
EY1162
Urocitellus townsendii townsendii Washington Yakima EY 1162 AF157934 Harrison etal.
(2003)
Utownsendii_
EY1164
Urocitellus townsendii townsendii Washington Yakima EY 1164 AF157935 Harrison etal.
(2003)
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Journal of Mammalogy, 2024, Vol, XX, Issue XX | 19
sample Code Genus specic
Epithet
subspecic
epithet
state
Province
County institution
Code
catalog
Number
tissue
Identier
tissue
Number
GenBank
Accessions
mtDNA
GenBank
Accessions
nuDNA_5gene
GenBank
accessions
nuDNA_UCEs
Citations
Utownsendii_
UWBM78329
Urocitellus townsendii townsendii Washington Yakima UWBM 78329 JEB 814 KX278537 KX278618,
KX290227,
KX278662,
KX290272
KFJI00000000 McLean etal. (2016)
| McLean etal.
(2022)
Utownsendii_
UWBM78316
Urocitellus townsendii townsendii Washington Yakima UWBM 78316 JEB 801 KX278538 KX278619, KX290228, KX278663,
KX290273
McLean etal. (2016)
Utownsendii_
EY1163a
Urocitellus townsendii Washington Yakima USNM Uncataloged EY 1163a KX278565 KFJK00000000 McLean etal. (2016)
| McLean etal.
(2022)
Utownsendii_
UWBM32803
Urocitellus townsendii Washington Yakima UWBM 32803 KFJJ00000000 McLean etal. (2022)
Uwashingtoni_
EY1157
Urocitellus washingtoni Washington Grant EY 1157 AF157937 Harrison etal.
(2003)
Uwashingtoni_
EY1158
Urocitellus washingtoni Washington Grant USNM Uncataloged EY 1158 AF157936 KX278639, KX290248, KX278683,
KX290292
Harrison etal.
(2003) | McLean
etal. (2016)
Uwashingtoni_
EY1155a
Urocitellus washingtoni Washington USNM Uncataloged EY 1155a KX278576 KFJE00000000 McLean etal. (2016)
| McLean etal.
(2022)
Uwashingtoni_
EY1156a
Urocitellus washingtoni Washington USNM Uncataloged EY 1156a KX278587 KFJD00000000 McLean etal. (2016)
| McLean etal.
(2022)
Uwashingtoni_
UWBM82235
Urocitellus washingtoni Washington Douglas UWBM 82235 TNL 454 KX278542 KX278623,
KX290232,
KX278667,
KX290277
KFJC00000000 McLean etal. (2016)
| McLean etal.
(2022)
Uwashingtoni_
UWBM82234
Urocitellus washingtoni Washington Douglas UWBM 82234 AKW 154 KX278562 McLean etal. (2016)
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20 | McLean et al.
Appendix II
Specimens examined for craniometric analysis.
sampleCode Genus specic
Epithet
subspecic
Epithet
state
Province
County institution
Code
catalog
Number
Sex age Class Inclusive data set
UrbrbrKUM45922 Urocitellus brunneus brunneus Idaho Adams KU 45922 Female Adult Geometric morphometric
UrbrbrKUM45923 Urocitellus brunneus brunneus Idaho Adams KU 45923 Female Adult Geometric morphometric
UrbrbrKUM45925 Urocitellus brunneus brunneus Idaho Adams KU 45925 Female Adult Geometric morphometric
UrbrbrKUM45926 Urocitellus brunneus brunneus Idaho Adams KU 45926 Female Adult Geometric morphometric
UrbrbrKUM45929 Urocitellus brunneus brunneus Idaho Adams KU 45929 Male Adult Geometric morphometric
UrbrbrKUM45930 Urocitellus brunneus brunneus Idaho Adams KU 45930 Female Adult Geometric morphometric
UrbrbrKUM45932 Urocitellus brunneus brunneus Idaho Adams KU 45932 Female Adult Geometric morphometric
UrbrbrKUM45936 Urocitellus brunneus brunneus Idaho Adams KU 45936 Female Adult Geometric morphometric
UrbrbrKUM45937 Urocitellus brunneus brunneus Idaho Adams KU 45937 Male Adult Geometric morphometric
UrbrbrKUM45938 Urocitellus brunneus brunneus Idaho Adams KU 45938 Female Adult Geometric morphometric
UrbrbrKUM130612 Urocitellus brunneus brunneus Idaho Adams KU 130612 Female Adult Geometric morphometric
UrbrbrUSNM202410 Urocitellus brunneus brunneus Idaho Valley USNM 202410 Female Adult Geometric morphometric
UrbrbrUSNM265911 Urocitellus brunneus brunneus Idaho Valley USNM 265911 Male Adult Geometric morphometric
UrbrbrUSNM265913 Urocitellus brunneus brunneus Idaho Valley USNM 265913 Male Adult Geometric morphometric
UrbrenKUM45940 Urocitellus brunneus endemicus Idaho Washington KU 45940 Male Adult Geometric morphometric
UrbrenKUM45942 Urocitellus brunneus endemicus Idaho Washington KU 45942 Female Adult Geometric morphometric
UrbrenKUM45943 Urocitellus brunneus endemicus Idaho Washington KU 45943 Female Adult Geometric morphometric
UrbrenUSNM201726 Urocitellus brunneus endemicus Idaho [Washington?] USNM 201726 Male Adult Geometric morphometric
UrbrenUSNM201727 Urocitellus brunneus endemicus Idaho [Washington?] USNM 201727 Male Adult Geometric morphometric
UrbrenUSNM201728 Urocitellus brunneus endemicus Idaho [Washington?] USNM 201728 Male Adult Geometric morphometric
UrbrenUSNM201730 Urocitellus brunneus endemicus Idaho [Washington?] USNM 201730 Male Adult Geometric morphometric
UrcacaKUM133131 Urocitellus canus canus Nevada Washoe KU 133131 Female Adult Geometric morphometric
UrcacaUSNM80283 Urocitellus canus canus Oregon [Crook?] USNM 80283 Female Adult Geometric morphometric
UrcacaUSNM80284 Urocitellus canus canus Oregon [Crook?] USNM 80284 Female Adult Geometric morphometric
UrcacaUSNM80285 Urocitellus canus canus Oregon [Crook?] USNM 80285 Female Adult Geometric morphometric
UrcacaUSNM80286 Urocitellus canus canus Oregon [Crook?] USNM 80286 Female Adult Geometric morphometric
UrcacaUSNM89183 Urocitellus canus canus Oregon [Crook?] USNM 89183 Male Adult Geometric morphometric
UrcacaUSNM89184 Urocitellus canus canus Oregon [Crook?] USNM 89184 Female Adult Geometric morphometric
UrcacaUSNM204832 Urocitellus canus canus Oregon [Deschutes?] USNM 204832 Male Adult Geometric morphometric
UrcacaUSNM204834 Urocitellus canus canus Oregon [Deschutes?] USNM 204834 Male Adult Geometric morphometric
UrcacaUSNM204835 Urocitellus canus canus Oregon [Deschutes?] USNM 204835 Female Adult Geometric morphometric
UrcacaUSNM204837 Urocitellus canus canus Oregon [Deschutes?] USNM 204837 Male Adult Geometric morphometric
UrcacaUSNM206850 Urocitellus canus canus Oregon [Jefferson?] USNM 206850 Female Adult Geometric morphometric
UrcacaUSNM207175 Urocitellus canus canus Oregon [Jefferson?] USNM 207175 Male Adult Geometric morphometric
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Journal of Mammalogy, 2024, Vol, XX, Issue XX | 21
sampleCode Genus specic
Epithet
subspecic
Epithet
state
Province
County institution
Code
catalog
Number
Sex age Class Inclusive data set
UrcacaUSNM207176 Urocitellus canus canus Oregon [Jefferson?] USNM 207176 Female Adult Geometric morphometric
UrcacaUSNM207177 Urocitellus canus canus Oregon [Jefferson?] USNM 207177 Male Adult Geometric morphometric
UrcacaUSNM207182 Urocitellus canus canus Oregon [Jefferson?] USNM 207182 Male Adult Geometric morphometric
UrcacaUSNM207173 Urocitellus canus canus Oregon [Jefferson?] USNM 207173 Male Adult Geometric morphometric
UrcacaUSNM207178 Urocitellus canus canus Oregon [Jefferson?] USNM 207178 Male Adult Geometric morphometric
UrcacaUSNM207180 Urocitellus canus canus Oregon [Jefferson?] USNM 207180 Female Adult Geometric morphometric
UrcaviKUM131473 Urocitellus canus vigilis Oregon Malheur KU 131473 Female Adult Geometric morphometric
UrcaviKUM131476 Urocitellus canus vigilis Oregon Malheur KU 131476 Male Adult Geometric morphometric
UrcaviKUM131478 Urocitellus canus vigilis Oregon Malheur KU 131478 Female Adult Geometric morphometric
UrcaviKUM131480 Urocitellus canus vigilis Oregon Malheur KU 131480 Female Adult Geometric morphometric
UrcaviKUM131486 Urocitellus canus vigilis Oregon Malheur KU 131486 Female Adult Geometric morphometric
UrcaviKUM131487 Urocitellus canus vigilis Oregon Malheur KU 131487 Male Adult Geometric morphometric
UrcaviKUM131490 Urocitellus canus vigilis Oregon Malheur KU 131490 Male Adult Geometric morphometric
UrcaviKUM131492 Urocitellus canus vigilis Oregon Malheur KU 131492 Male Adult Geometric morphometric
UrcaviKUM131498 Urocitellus canus vigilis Oregon Malheur KU 131498 Male Adult Geometric morphometric
UrcaviKUM131499 Urocitellus canus vigilis Oregon Malheur KU 131499 Female Adult Geometric morphometric
UrcaviKUM131501 Urocitellus canus vigilis Oregon Malheur KU 131501 Male Adult Geometric morphometric
UrcaviKUM131504 Urocitellus canus vigilis Oregon Malheur KU 131504 Female Adult Geometric morphometric
UrcaviKUM131507 Urocitellus canus vigilis Oregon Malheur KU 131507 Female Adult Geometric morphometric
UrcaviUSNM168363 Urocitellus canus vigilis Oregon [Malheur?] USNM 168363 Female Adult Geometric morphometric
UrcaviUSNM168364 Urocitellus canus vigilis Oregon [Malheur?] USNM 168364 Female Adult Geometric morphometric
UrcaviUSNM168484 Urocitellus canus vigilis Oregon [Malheur?] USNM 168484 Male Adult Geometric morphometric
UrcaviUSNM168485 Urocitellus canus vigilis Oregon [Malheur?] USNM 168485 Male Adult Geometric morphometric
UrmoarUSNM23926 Urocitellus idahoensis artemesiae Idaho USNM 23926 Female Adult Geometric morphometric
UrmoarUSNM23927 Urocitellus idahoensis artemesiae Idaho USNM 23927 Male Adult Geometric morphometric
UrmoarUSNM23929 Urocitellus idahoensis artemesiae Idaho USNM 23929 Male Adult Geometric morphometric
UrmoarUSNM23931 Urocitellus idahoensis artemesiae Idaho USNM 23931 Male Adult Geometric morphometric
UrmoarUSNM23932 Urocitellus idahoensis artemesiae Idaho USNM 23932 Male Adult Geometric morphometric
UrmoarUSNM23933 Urocitellus idahoensis artemesiae Idaho USNM 23933 Male Adult Geometric morphometric
UrmoarUSNM243551 Urocitellus idahoensis artemesiae Idaho USNM 243551 Male Adult Geometric morphometric
UrmoarUSNM266540 Urocitellus idahoensis artemesiae Idaho [Clark?] USNM 266540 Female Adult Geometric morphometric
UrmoarUSNM23333 Urocitellus idahoensis artemesiae Idaho USNM 23333 Male Adult Geometric morphometric
UrmoarUSNM23490 Urocitellus idahoensis artemesiae Idaho USNM 23490 Male Adult Geometric morphometric
UrmoarUSNM23930 Urocitellus idahoensis artemesiae Idaho USNM 23930 Male Adult Geometric morphometric
UrmoidMSB70152 Urocitellus idahoensis idahoensis Idaho MSB 70152 Male Adult Geometric morphometric
UrmoidMSB70158 Urocitellus idahoensis idahoensis Idaho MSB 70158 Female Adult Geometric morphometric
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22 | McLean et al.
sampleCode Genus specic
Epithet
subspecic
Epithet
state
Province
County institution
Code
catalog
Number
Sex age Class Inclusive data set
UrmoidMSB70162 Urocitellus idahoensis idahoensis Idaho MSB 70162 Female Adult Geometric morphometric
UrmoidMSB70167 Urocitellus idahoensis idahoensis Idaho MSB 70167 Female Adult Geometric morphometric
UrmoidUSNM168287 Urocitellus idahoensis idahoensis Idaho [Payette?] USNM 168287 Female Adult Geometric morphometric
UrmoidUSNM168288 Urocitellus idahoensis idahoensis Idaho [Payette?] USNM 168288 Female Adult Geometric morphometric
UrmoidUSNM168357 Urocitellus idahoensis idahoensis Idaho [Payette?] USNM 168357 Male Adult Geometric morphometric
UrmoidUSNM168359 Urocitellus idahoensis idahoensis Idaho [Payette?] USNM 168359 Female Adult Geometric morphometric
UrmoidUSNM179649 Urocitellus idahoensis idahoensis Idaho [Canyon?] USNM 179649 Female Adult Geometric morphometric
UrmoidUSNM201733 Urocitellus idahoensis idahoensis Idaho [Washington?] USNM 201733 Male Adult Geometric morphometric
UrmoidUSNM201734 Urocitellus idahoensis idahoensis Idaho [Washington?] USNM 201734 Female Adult Geometric morphometric
UrmoidUSNM398289 Urocitellus idahoensis idahoensis Idaho Ada USNM 398289 Female Adult Geometric morphometric
UrmoidUSNM168510 Urocitellus idahoensis idahoensis Idaho [Canyon?] USNM 168510 Female Adult Geometric morphometric
UrmoidUSNM168511 Urocitellus idahoensis idahoensis Idaho [Canyon?] USNM 168511 Male Adult Geometric morphometric
UrmoidUSNM169582 Urocitellus idahoensis idahoensis Idaho [Elmore?] USNM 169582 Male Adult Geometric morphometric
UrmoidUSNM169581 Urocitellus idahoensis idahoensis Idaho [Elmore?] USNM 169581 Male Adult Geometric morphometric
UrmomoKUM6072 Urocitellus mollis mollis Nevada Esmerelda KU 6072 Male Adult Geometric morphometric
UrmomoKUM6712 Urocitellus mollis mollis Idaho Bannock KU 6712 Female Adult Geometric morphometric
UrmomoKUM46060 Urocitellus mollis mollis Nevada Elko KU 46060 Female Adult Geometric morphometric
UrmomoKUM46061 Urocitellus mollis mollis Nevada Elko KU 46061 Female Adult Geometric morphometric
UrmomoKUM46062 Urocitellus mollis mollis Nevada Elko KU 46062 Female Adult Geometric morphometric
UrmomoKUM46063 Urocitellus mollis mollis Nevada Elko KU 46063 Female Adult Geometric morphometric
UrmomoKUM77590 Urocitellus mollis mollis Nevada Churchill KU 77590 Male Adult Geometric morphometric
UrmomoKUM131469 Urocitellus mollis mollis Idaho Cassia KU 131469 Female Adult Geometric morphometric
UrmomoKUM131470 Urocitellus mollis mollis Idaho Cassia KU 131470 Male Adult Geometric morphometric
UrmomoKUM131471 Urocitellus mollis mollis Idaho Cassia KU 131471 Female Adult Geometric morphometric
UrmomoKUM131529 Urocitellus mollis mollis Idaho Cassia KU 131529 Male Adult Geometric morphometric
UrmomoKUM131537 Urocitellus mollis mollis Idaho Cassia KU 131537 Male Adult Geometric morphometric
UrmomoUSNM22584 Urocitellus mollis mollis Utah [Utah?] USNM 22584 Female Adult Geometric morphometric
UrmomoUSNM29366 Urocitellus mollis mollis Nevada USNM 29366 Female Adult Geometric morphometric
UrmomoUSNM29361 Urocitellus mollis mollis Nevada USNM 29361 Male Adult Geometric morphometric
UrmomoUSNM66378 Urocitellus mollis mollis California Lassen USNM 66378 Female Adult Geometric morphometric
UrmomoUSNM29370 Urocitellus mollis mollis California USNM 29370 Male Adult Geometric morphometric
UrmomoUSNM29496 Urocitellus mollis mollis California USNM 29496 Male Adult Geometric morphometric
UrmomoUSNM29896 Urocitellus mollis mollis California USNM 29896 Male Adult Geometric morphometric
UrmomoUSNM22585 Urocitellus mollis mollis Utah [Utah?] USNM 22585 Male Adult Geometric morphometric
UrtonaKUM131564 Urocitellus townsendii nancyae Washington Benton KU 131564 Male Adult Geometric morphometric
UrtonaKUM131568 Urocitellus townsendii nancyae Washington Benton KU 131568 Female Adult Geometric morphometric
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Journal of Mammalogy, 2024, Vol, XX, Issue XX | 23
sampleCode Genus specic
Epithet
subspecic
Epithet
state
Province
County institution
Code
catalog
Number
Sex age Class Inclusive data set
UrtonaKUM131569 Urocitellus townsendii nancyae Washington Benton KU 131569 Male Adult Geometric morphometric
UrtonaKUM131578 Urocitellus townsendii nancyae Washington Yakima KU 131578 Female Adult Geometric morphometric
UrtonaKUM131579 Urocitellus townsendii nancyae Washington Yakima KU 131579 Female Adult Geometric morphometric
UrtonaKUM131582 Urocitellus townsendii nancyae Washington Yakima KU 131582 Female Adult Geometric morphometric
UrtonaKUM131583 Urocitellus townsendii nancyae Washington Yakima KU 131583 Male Adult Geometric morphometric
UrtonaKUM131552 Urocitellus townsendii nancyeae Washington Benton KU 131552 Male Adult Geometric morphometric
UrtonaKUM131553 Urocitellus townsendii nancyeae Washington Benton KU 131553 Female Adult Geometric morphometric
UrtonaKUM131556 Urocitellus townsendii nancyeae Washington Benton KU 131556 Male Adult Geometric morphometric
UrtonaKUM131557 Urocitellus townsendii nancyeae Washington Benton KU 131557 Male Adult Geometric morphometric
UrtotoKUM131584 Urocitellus townsendii townsendii Washington Benton KU 131584 Male Adult Geometric morphometric
UrtotoKUM131586 Urocitellus townsendii townsendii Washington Benton KU 131586 Male Adult Geometric morphometric
UrtotoKUM131587 Urocitellus townsendii townsendii Washington Benton KU 131587 Female Adult Geometric morphometric
UrtotoKUM131590 Urocitellus townsendii townsendii Washington Benton KU 131590 Male Adult Geometric morphometric
UrtotoKUM131593 Urocitellus townsendii townsendii Washington Benton KU 131593 Female Adult Geometric morphometric
UrtotoKUM131595 Urocitellus townsendii townsendii Washington Benton KU 131595 Female Adult Geometric morphometric
UrtotoKUM131596 Urocitellus townsendii townsendii Washington Benton KU 131596 Female Adult Geometric morphometric
UrtotoKUM131602 Urocitellus townsendii townsendii Washington Benton KU 131602 Female Adult Geometric morphometric
UrtotoKUM131605 Urocitellus townsendii townsendii Washington Yakima KU 131605 Male Adult Geometric morphometric
UrtotoKUM131608 Urocitellus townsendii townsendii Washington Yakima KU 131608 Female Adult Geometric morphometric
UrtotoKUM131612 Urocitellus townsendii townsendii Washington Yakima KU 131612 Female Adult Geometric morphometric
UrtotoKUM131614 Urocitellus townsendii townsendii Washington Yakima KU 131614 Female Adult Geometric morphometric
UrtotoUSNM235736 Urocitellus townsendii townsendii? Washington Yakima USNM 235736 Female Adult Geometric morphometric
UrtotoUSNM235737 Urocitellus townsendii townsendii? Washington Yakima USNM 235737 Female Adult Geometric morphometric
UrtotoUSNM235735 Urocitellus townsendii townsendii? Washington Yakima USNM 235735 Male Adult Geometric morphometric
UrtotoUSNM89320 Urocitellus townsendii townsendii? Washington Klickitat USNM 89320 Male Adult Geometric morphometric
UrtotoUSNM89319 Urocitellus townsendii townsendii? Washington Klickitat USNM 89319 Male Adult Geometric morphometric
UrwaKUM53130 Urocitellus washingtoni Washington Walla Walla KU 53130 Female Adult Geometric morphometric
UrwaKUM53131 Urocitellus washingtoni Washington Walla Walla KU 53131 Female Adult Geometric morphometric
UrwaKUM131679 Urocitellus washingtoni Washington Franklin KU 131679 Male Adult Geometric morphometric
UrwaKUM131680 Urocitellus washingtoni Washington Franklin KU 131680 Male Adult Geometric morphometric
UrwaKUM131681 Urocitellus washingtoni Washington Franklin KU 131681 Female Adult Geometric morphometric
UrwaKUM131686 Urocitellus washingtoni Washington Franklin KU 131686 Female Adult Geometric morphometric
UrwaKUM131695 Urocitellus washingtoni Washington Franklin KU 131695 Male Adult Geometric morphometric
UrwaKUM131696 Urocitellus washingtoni Washington Franklin KU 131696 Male Adult Geometric morphometric
UrwaKUM131698 Urocitellus washingtoni Washington Franklin KU 131698 Male Adult Geometric morphometric
UrwaKUM131701 Urocitellus washingtoni Washington Franklin KU 131701 Male Adult Geometric morphometric
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24 | McLean et al.
sampleCode Genus specic
Epithet
subspecic
Epithet
state
Province
County institution
Code
catalog
Number
Sex age Class Inclusive data set
UrwaUSNM206743 Urocitellus washingtoni Oregon [Umatilla?] USNM 206743 Male Adult Geometric morphometric
UrwaUSNM78577 Urocitellus washingtoni Oregon [Umatilla?] USNM 78577 Female Adult Geometric morphometric
UrwaUSNM79393 Urocitellus washingtoni Oregon [Morrow?] USNM 79393 Female Adult Geometric morphometric
UrwaUSNM79270 Urocitellus washingtoni Oregon [Morrow?] USNM 79270 Male Adult Geometric morphometric
UrwaUSNM79251 Urocitellus washingtoni Oregon [Morrow?] USNM 79251 Male Adult Geometric morphometric
UrwaUSNM79252 Urocitellus washingtoni Oregon [Morrow?] USNM 79252 Female Adult Geometric morphometric
UrwaUSNM78393 Urocitellus washingtoni Oregon [Umatilla?] USNM 78393 Female Adult Geometric morphometric
UrwaUSNM78576 Urocitellus washingtoni Oregon [Umatilla?] USNM 78576 Male Adult Geometric morphometric
UrwaUSNM78189 Urocitellus washingtoni Oregon [Umatilla?] USNM 78189 Male Adult Geometric morphometric
MVZ:Mamm:67346 Urocitellus idahoensis artemesiae Idaho Bingham MVZ 67346 Female Adult Linear measurement
MVZ:Mamm:67347 Urocitellus idahoensis artemesiae Idaho Bingham MVZ 67347 Male Adult Linear measurement
MVZ:Mamm:67348 Urocitellus idahoensis artemesiae Idaho Bingham MVZ 67348 Female Adult Linear measurement
MVZ:Mamm:67349 Urocitellus idahoensis artemesiae Idaho Bingham MVZ 67349 Female Adult Linear measurement
MVZ:Mamm:67351 Urocitellus idahoensis artemesiae Idaho Bingham MVZ 67351 Female Adult Linear measurement
MVZ:Mamm:67352 Urocitellus idahoensis artemesiae Idaho Bingham MVZ 67352 Male Adult Linear measurement
MVZ:Mamm:67353 Urocitellus idahoensis artemesiae Idaho Bingham MVZ 67353 Male Adult Linear measurement
UMNH:Mamm:8948 Urocitellus idahoensis artemesiae Idaho Jerome UMNH 8948 Female Adult Linear measurement
UMNH:Mamm:28295 Urocitellus idahoensis artemesiae Idaho Bingham UMNH 28295 Female Adult Linear measurement
UMNH:Mamm:28296 Urocitellus idahoensis artemesiae Idaho Bingham UMNH 28296 Female Adult Linear measurement
UMNH:Mamm:28297 Urocitellus idahoensis artemesiae Idaho Bingham UMNH 28297 Female Adult Linear measurement
UMNH:Mamm:28298 Urocitellus idahoensis artemesiae Idaho Bingham UMNH 28298 Female Adult Linear measurement
UMNH:Mamm:28299 Urocitellus idahoensis artemesiae Idaho Bingham UMNH 28299 Female Adult Linear measurement
UMNH:Mamm:28300 Urocitellus idahoensis artemesiae Idaho Bingham UMNH 28300 Male Adult Linear measurement
UMNH:Mamm:28301 Urocitellus idahoensis artemesiae Idaho Bingham UMNH 28301 Male Adult Linear measurement
MVZ:Mamm:67309 Urocitellus idahoensis idahoensis Idaho Payette MVZ 67309 Female Adult Linear measurement
MVZ:Mamm:67310 Urocitellus idahoensis idahoensis Idaho Payette MVZ 67310 Male Adult Linear measurement
MVZ:Mamm:67311 Urocitellus idahoensis idahoensis Idaho Payette MVZ 67311 Female Adult Linear measurement
MVZ:Mamm:67312 Urocitellus idahoensis idahoensis Idaho Payette MVZ 67312 Female Adult Linear measurement
MVZ:Mamm:67280 Urocitellus idahoensis idahoensis Idaho Payette MVZ 67280 Male Adult Linear measurement
MVZ:Mamm:67281 Urocitellus idahoensis idahoensis Idaho Payette MVZ 67281 Male Adult Linear measurement
MVZ:Mamm:67282 Urocitellus idahoensis idahoensis Idaho Payette MVZ 67282 Male Adult Linear measurement
MVZ:Mamm:67283 Urocitellus idahoensis idahoensis Idaho Payette MVZ 67283 Male Adult Linear measurement
MVZ:Mamm:67284 Urocitellus idahoensis idahoensis Idaho Payette MVZ 67284 Male Adult Linear measurement
MVZ:Mamm:67295 Urocitellus idahoensis idahoensis Idaho Payette MVZ 67295 Male Adult Linear measurement
MVZ:Mamm:67296 Urocitellus idahoensis idahoensis Idaho Payette MVZ 67296 Female Adult Linear measurement
UMNH:Mamm:28254 Urocitellus idahoensis idahoensis Idaho Elmore UMNH 28254 Female Adult Linear measurement
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Journal of Mammalogy, 2024, Vol, XX, Issue XX | 25
sampleCode Genus specic
Epithet
subspecic
Epithet
state
Province
County institution
Code
catalog
Number
Sex age Class Inclusive data set
UMNH:Mamm:28302 Urocitellus idahoensis idahoensis Idaho Payette UMNH 28302 Female Adult Linear measurement
UMNH:Mamm:28128 Urocitellus mollis mollis Utah Tooele UMNH 28128 Female Adult(1) Linear measurement
UMNH:Mamm:28129 Urocitellus mollis mollis Utah Tooele UMNH 28129 Female Adult(1) Linear measurement
UMNH:Mamm:28130 Urocitellus mollis mollis Utah Tooele UMNH 28130 Male Adult(1) Linear measurement
UMNH:Mamm:28131 Urocitellus mollis mollis Utah Tooele UMNH 28131 Female Adult(1) Linear measurement
UMNH:Mamm:28172 Urocitellus mollis mollis Utah Tooele UMNH 28172 Male Adult(1) Linear measurement
UMNH:Mamm:28173 Urocitellus mollis mollis Utah Tooele UMNH 28173 Male Adult(1) Linear measurement
UMNH:Mamm:28404 Urocitellus mollis mollis Utah Tooele UMNH 28404 Female Adult(1) Linear measurement
UMNH:Mamm:28408 Urocitellus mollis mollis Utah Tooele UMNH 28408 Female Adult(1) Linear measurement
UMNH:Mamm:28409 Urocitellus mollis mollis Utah Tooele UMNH 28409 Male Adult(1) Linear measurement
UMNH:Mamm:28415 Urocitellus mollis mollis Utah Tooele UMNH 28415 Male Adult(1) Linear measurement
UMNH:Mamm:28126 Urocitellus mollis mollis Utah Tooele UMNH 28126 Female Adult(2) Linear measurement
UMNH:Mamm:28134 Urocitellus mollis mollis Utah Tooele UMNH 28134 Male Adult(2) Linear measurement
UMNH:Mamm:28148 Urocitellus mollis mollis Utah Tooele UMNH 28148 Female Adult(2) Linear measurement
UMNH:Mamm:28162 Urocitellus mollis mollis Utah Tooele UMNH 28162 Female Adult(2) Linear measurement
UMNH:Mamm:28310 Urocitellus mollis mollis Utah Tooele UMNH 28310 Female Adult(2) Linear measurement
UMNH:Mamm:28314 Urocitellus mollis mollis Utah Tooele UMNH 28314 Male Adult(2) Linear measurement
UMNH:Mamm:28319 Urocitellus mollis mollis Utah Tooele UMNH 28319 Female Adult(2) Linear measurement
UMNH:Mamm:28320 Urocitellus mollis mollis Utah Tooele UMNH 28320 Male Adult(2) Linear measurement
UMNH:Mamm:28399 Urocitellus mollis mollis Utah Tooele UMNH 28399 Male Adult(2) Linear measurement
UMNH:Mamm:28452 Urocitellus mollis mollis Utah Tooele UMNH 28452 Female Adult(2) Linear measurement
UMNH:Mamm:28121 Urocitellus mollis mollis Utah Tooele UMNH 28121 Male Adult(3) Linear measurement
UMNH:Mamm:28123 Urocitellus mollis mollis Utah Tooele UMNH 28123 Female Adult(3) Linear measurement
UMNH:Mamm:28149 Urocitellus mollis mollis Utah Tooele UMNH 28149 Female Adult(3) Linear measurement
UMNH:Mamm:28323 Urocitellus mollis mollis Utah Tooele UMNH 28323 Female Adult(3) Linear measurement
UMNH:Mamm:28414 Urocitellus mollis mollis Utah Tooele UMNH 28414 Female Adult(3) Linear measurement
UMNH:Mamm:28456 Urocitellus mollis mollis Utah Tooele UMNH 28456 Female Adult(3) Linear measurement
UMNH:Mamm:28457 Urocitellus mollis mollis Utah Tooele UMNH 28457 Female Adult(3) Linear measurement
UMNH:MAMM:28383 Urocitellus mollis mollis Utah Tooele UMNH 28383 Female Adult(4) Linear measurement
UMNH:Mamm:28412 Urocitellus mollis mollis Utah Tooele UMNH 28412 Female Adult(4) Linear measurement
UMNH:Mamm:28331 Urocitellus mollis mollis Utah Tooele UMNH 28331 Female Adult(5) Linear measurement
UMNH:Mamm:28324 Urocitellus mollis mollis Utah Tooele UMNH 28324 Female Adult(6) Linear measurement
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