References
Ali OA, O’Rourke SM, Amish SJ et al. (2016) RAD capture
(Rapture): flexible and efficient sequence-based genotyping.Genetics , 202 , 389–400.
Andrews KR, De Barba M, Russello MA, Waits LP (2018) Advances in Using
Non-invasive, Archival, and Environmental Samples for Population Genomic
Studies. In: Population Genomics , pp. 1–37. Springer, Cham.
Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA (2016)
Harnessing the power of RADseq for ecological and evolutionary genomics.Nature Reviews Genetics , 17 , 81–92.
Assis J, Castilho Coelho N, Alberto F et al. (2013) High and
distinct range-edge genetic diversity despite local bottlenecks (SJ
Goldstien, Ed,). PLoS ONE , 8 , e68646.
Baird NA, Etter PD, Atwood TS et al. (2008) Rapid SNP discovery
and genetic mapping using sequenced RAD markers. PLoS One ,3 , e3376.
Barrett JS (2005) Population Viability of the Southern Idaho Ground
Squirrel (Spermophilus brunneus endemicus ): Effects of an Altered
Landscape. Boise State University.
Bateman A (2019) UniProt: A worldwide hub of protein knowledge.Nucleic Acids Research , 47 , D506–D515.
Besnier F, Glover KA (2013) ParallelStructure: A R Package to Distribute
Parallel Runs of the Population Genetics Program STRUCTURE on Multi-Core
Computers (M Anisimova, Ed,). PLoS ONE , 8 , e70651.
Bi K, Linderoth T, Singhal S et al. (2019) Temporal genomic
contrasts reveal rapid evolutionary responses in an alpine mammal during
recent climate change. PLoS Genetics , 15 , e1008119.
Burak GS (2011) Status review for northern Idaho ground squirrel
( Spermophilus brunneus brunneus) . Boise, ID.
Busscher KL (2009) Improving Success of Translocating Southern Idaho
Ground Squirrels (Spermophilus endemicus ).
Capblancq T, Luu K, Blum MGB, Bazin E (2018) Evaluation of redundancy
analysis to identify signatures of local adaptation. Molecular
Ecology Resources , 18 , 1223–1233.
Carroll EL, Bruford MW, DeWoody JA et al. (2018) Genetic and
genomic monitoring with minimally invasive sampling methods.Evolutionary Applications , 11 , 1094–1119.
Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks:
an analysis tool set for population genomics. Molecular Ecology ,22 , 3124–3140.
Caye K, Jumentier B, Lepeule J, François O (2019) LFMM 2: Fast and
Accurate Inference of Gene-Environment Associations in Genome-Wide
Studies (J Kelley, Ed,). Molecular Biology and Evolution ,36 , 852–860.
CCAA (2002) Southern Idaho Ground Squirrel Candidate Conservation
Agreement with Assurances for the Soulen Livestock Company, Inc.
CCRS, CCMEO, NRCan et al. (2017) 2010 Land Cover of North America
at 30 meters.
Chang ML, Terrill RL, Bautista MM et al. (2007) Large-scale SNP
genotyping with canine buccal swab DNA. Journal of Heredity ,98 , 428–437.
Chen H, Boutros PC (2011) VennDiagram: a package for the generation of
highly-customizable Venn and Euler diagrams in R. BMC
Bioinformatics , 12 , 35.
Clark JR (2000) Endangered and threatened wildlife and plants;
determination of threatened status for the northern Idaho ground
squirrel. Federal Register , 65 , 17779–17786.
CONSBIO (2015a) STATSGO Derived Soil Particle Size in 11 Western States
in USA (Data Basin Dataset).1:250,000.
CONSBIO (2015b) STATSGO Derived Soil Order in 11 Western States in USA
(Data Basin Dataset).1:250,000.
Dabney A, Storey JD, Warnes GR (2010) qvalue: Q-value estimation for
false discovery rate control. R package version 1.0.
Danecek P, Auton A, Abecasis G et al. (2011) The variant call
format and VCFtools. Bioinformatics , 27 , 2156–2158.
Doebeli M, Dieckmann U (2003) Speciation along environmental gradients.Nature , 421 , 259–264.
Eastman LM, Morelli TL, Rowe KC, Conroy CJ, Moritz C (2012) Size
increase in high elevation ground squirrels over the last century.Global Change Biology , 18 , 1499–1508.
ESRI (2013) Terrais: Slope Map.
ESRI (2015) Land Formation.
ESRI (2016) “World Biomass” [basemap].Scale not given. “World
Biomass 2000 (1km)”. Aug 25, 2016.
ESRI (2019) World Ecological Facets Landform Classes.
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of
individuals using the software STRUCTURE: a simulation study.Molecular Ecology , 14 , 2611–2620.
Evans-Mack D (2003) Northern Idaho ground squirrel population
monitoring 2003 annual report . McCall, ID.
Faherty SL, Villanueva-Cañas JL, Blanco MB, Albà MM, Yoder AD (2018)
Transcriptomics in the wild: hibernation physiology in free-ranging
dwarf lemurs. Molecular Ecology , 27 , 709–722.
Fahrig L, Merriam G (1994) Conservation of fragmented populations.Conservation Biology , 8 , 50–59.
Fick SE, Hijmans RJ (2017) WorldClim 2: new 1-km spatial resolution
climate surfaces for global land areas. International Journal of
Climatology , 37 , 4302–4315.
Fišer C, Robinson CT, Malard F (2018) Cryptic species as a window into
the paradigm shift of the species concept. Molecular Ecology ,27 , 613–635.
Fletcher NK, Acevedo P, Herman JS et al. (2019) Glacial cycles
drive rapid divergence of cryptic field vole species. Ecology and
Evolution , 1–13.
Forester BR, Landguth EL, Hand BK, Balkenhol N (2018) Landscape Genomics
for Wildlife Research. In: Population Genomics , pp. 1–40.
Springer, Cham.
Forester BR, Lasky JR, Wagner HH, Urban DL (2018) Comparing methods for
detecting multilocus adaptation with multivariate genotype-environment
associations. Molecular Ecology , 27 , 2215–2233.
François O, Martins H, Caye K, Schoville SD (2016) Controlling false
discoveries in genome scans for selection. Molecular Ecology ,25 , 454–469.
French AR (1982) Intraspecific differences in the pattern of hibernation
in the ground squirrel Spermophilus beldingi . Journal of
Comparative Physiology , 148 , 83–91.
Funk WC, McKay JK, Hohenlohe PA, Allendorf FW (2012) Harnessing genomics
for delineating conservation units. Trends in Ecology and
Evolution , 27 , 489–496.
Garcia-Elfring A, Barrett RDH, Millien V (2019) Genomic signatures of
selection along a climatic gradient in the northern range margin of the
white-footed mouse (Peromyscus leucopus ). Journal of
Heredity , 110 , 684–695.
Garner A, Rachlow JL, Waits LP (2005) Genetic diversity and population
divergence in fragmented habitats: conservation of Idaho ground
squirrels. Conservation Genetics , 6 , 759–774.
Gavin TA, Sherman PW, Yensen E, May B (1999) Population genetic
structure of the northern Idaho ground squirrel (Spermophilus
brunneus brunneus ). Journal of Mammalogy , 80 , 156–168.
Gavrilets S, Acton R, Gravner J (2000) Dynamics of speciation and
diversification in a metapopulation. Evolution , 54 ,
1493–1501.
Gill AE, Yensen E (1992) Biochemical differentiation in the Idaho ground
squirrel Spermophilus brunneus (Rodentia: Sciuridae). Great
Basin Natura , 52 , 155–159.
Goldberg AR (2018) Diet, disease, and hibernation behavior of northern
Idaho ground squirrels. Uiversity of Idaho.
Goldberg AR, Conway CJ (2021) Hibernation behavior of a
federally-threatened ground squirrel: climate change and habitat
selection implications. Journal of Mammalogy , in press.
Goldberg AR, Conway CJ, Mack DE, Burak G (2020) Winter Versus Summer
Habitat Selection in a Threatened Ground Squirrel. Journal of
Wildlife Management , 84 , 1548–1559.
Goldberg AR, Conway CJ, Tank DC et al. (2020) Diet of a rare
herbivore based on DNA metabarcoding of feces: Selection, seasonality,
and survival. Ecology and Evolution , 10 , 7627–7643.
Gossmann TI, Shanmugasundram A, Börno S et al. (2019) Ice-Age
Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic
Diversity. Current Biology , 29 , 1712-1720.e7.
Goudet J (2005) hierfstat, a package for r to compute and test
hierarchical F-statistics. Molecular Ecology Notes , 5 ,
184–186.
Hafner DJ (1998) North American Rodents: Status Survey and
Conservation Action Plan . IUCN.
Hampton M, Melvin RG, Andrews MT (2013) Transcriptomic analysis of brown
adipose tissue across the physiological extremes of natural hibernation
(K Dahlman-Wright, Ed,). PLoS ONE , 8 , e85157.
Hanski I (1998) Metapopulation dynamics. Nature , 396 ,
41–49.
Hanski I, Gaggiotti OE (2004) Ecology, Genetics, and Evolution of
Metapopulations . Elsevier Academic Press, Burlington, MA, USA.
Harrison S, Taylor AD (1997) Empirical evidence for metapopulation
dynamics. In: Metapopulation Biology: Ecology, Genetics, and
Evolution (eds Hanski I, Gilpin M), pp. 27–42. Academic Press, San
Diego, CA, USA.
Helgen KM, Cole FR, Helgen LE, Wilson DE (2009) Generic revision in the
Holarctic ground squirrel genus Spermophilus. Journal of
Mammalogy , 90 , 270–305.
Helmstetter NA, Conway CJ, Stevens BS, Goldberg AR (2021) Balancing
transferability and complexity of species distribution models for rare
species conservation (Y Fourcade, Ed,). Diversity and
Distributions , 27 , 95–108.
Henry P, Russello MA (2013) Adaptive divergence along environmental
gradients in a climate-change-sensitive mammal. Ecology and
Evolution , 3 , 3906–3917.
Hodgson JA, Moilanen A, Wintle BA, Thomas CD (2011) Habitat area,
quality and connectivity: striking the balance for efficient
conservation. Journal of Applied Ecology , 48 , 148–152.
Hoffmann AA, Sgrò CM, Kristensen TN (2017) Revisiting adaptive
potential, population size, and conservation. Trends in Ecology
and Evolution , 32 , 506–517.
Hoisington-Lopez JL, Waits LP, Sullivan J (2012) Species limits and
integrated taxonomy of the Idaho ground squirrel (Urocitellus
brunneus ): genetic and ecological differentiation. Journal of
Mammalogy , 93 , 589–604.
Hoisington J (2007) Conservation genetics, landscape genetics and
systematics of the two subspecies of the endemic Idaho groud squirrel
(Spermophilus brunneus ). PhD Thesis, University of Idaho.
Holderegger R, Kamm U, Gugerli F (2006) Adaptive vs. neutral genetic
diversity: implications for landscape genetics. Landscape
Ecology , 21 , 797–807.
Hope AG, Malaney JL, Bell KC et al. (2016) Revision of widespread
red squirrels (genus: Tamiasciurus ) highlights the complexity of
speciation within North American forests. Molecular Phylogenetics
and Evolution , 100 , 170–182.
Hope AG, Panter N, Cook JA, Talbot SL, Nagorsen DW (2014) Multilocus
phylogeography and systematic revision of North American water shrews
(genus: Sorex ). Journal of Mammalogy , 95 ,
722–738.
Hope AG, Stephens RB, Mueller SD, Tkach V V, Demboski JR (2020)
Speciation of North American pygmy shrews (Eulipotyphla: Soricidae)
supports spatial but not temporal congruence of diversification among
boreal species. Biological Journal of the Linnean Society ,129 , 41–60.
Hut RA, Beersma DGM (2011) Evolution of time-keeping mechanisms: early
emergence and adaptation to photoperiod. Philosophical
Transactions of the Royal Society B: Biological Sciences , 366 ,
2141–2154.
IUCN SSMSG (2000) Urocitellus brunneus . The IUCN Red List of
Threatened Species .
IUCN SSMSG (2018) Urocitellus endemicus. The IUCN Red List of
Threatened Species .
Jombart T, Ahmed I (2011) adegenet 1.3-1: new tools for the analysis of
genome-wide SNP data. Bioinformatics , 27 , 3070–3071.
Kassambara A (2018) ggpubr:“ggplot2” based publication ready plots. R
package version 0.1.7.
Kawecki TJ, Ebert D (2004) Conceptual issues in local adaptation.Ecology Letters , 7 , 1225–1241.
Landguth EL, Balkenhol N (2012) Relative sensitivity of neutral versus
adaptive genetic data for assessing population differentiation.Conservation Genetics , 13 , 1421–1426.
Lane JE, Kruuk LEB, Charmantier A et al. (2011) A quantitative
genetic analysis of hibernation emergence date in a wild population of
Columbian ground squirrels. Journal of Evolutionary Biology ,24 , 1949–1959.
Levin DA (1995) Metapopulations: an arena for local speciation.Journal of Evolutionary Biology , 8 , 635–644.
Li H (2013) Aligning sequence reads, clone sequences and assembly
contigs with BWA-MEM. arXiv , 1303.3997.
Li H, Handsaker B, Wysoker A et al. (2009) The Sequence
Alignment/Map format and SAMtools. Bioinformatics , 25 ,
2078–2079.
Lohr K, Yensen E, Munger JC, Novak SJ (2013) Relationship between
habitat characteristics and densities of southern Idaho ground
squirrels. The Journal of Wildlife Management , 77 ,
983–993.
Lopes CM, de Freitas TRO (2012) Human impact in naturally patched small
populations: genetic structure and conservation of the burrowing rodent,
tuco-tuco (Ctenomys lami). The Journal of Heredity , 103 ,
672–681.
Lotterhos KE, Whitlock MC (2015) The relative power of genome scans to
detect local adaptation depends on sampling design and statistical
method. Molecular Ecology , 24 , 1031–1046.
Luu K, Bazin E, Blum MGB (2017) pcadapt: an R package to perform genome
scans for selection based on principal component analysis.Molecular Ecology Resources , 17 , 67–77.
Macdonald SL, Llewelyn J, Phillips BL (2018) Using connectivity to
identify climatic drivers of local adaptation. Ecology Letters ,21 , 207–216.
Marchenko S (2011) GIPL1.3 simulated mean annual ground temperature
(MAGT) in Celsius averaged for particular decade for the entire Alaskan
permafrost domain. NAD83, Alaska Albers projection.
Marques DA, Meier JI, Seehausen O (2019) A combinatorial view on
speciation and adaptive radiation. Trends in Ecology &
Evolution .
McLaren W, Gil L, Hunt SE et al. (2016) The Ensembl Variant
Effect Predictor. Genome Biology , 17 , 122.
McMichael GL, Gibson CS, O’Callaghan ME et al. (2009) DNA from
buccal swabs suitable for high-throughput SNP multiplex analysis.Journal of Biomolecular Techniques , 20 , 232–235.
Mitt M, Kals M, Pärn K et al. (2017) Improved imputation accuracy
of rare and low-frequency variants using population-specific
high-coverage WGS-based imputation reference panel. European
Journal of Human Genetics , 25 , 869–876.
Murphy WJ, Pringle TH, Crider TA, Springer MS, Miller W (2007) Using
genomic data to unravel the root of the placental mammal phylogeny.Genome Research , 17 , 413–421.
Nee S, May RM (1992) Dynamics of metapopulations: habitat destruction
and competitive coexistence. Journal of Animal Ecology ,61 , 37–40.
Nei M (1972) Genetic distance between populations. The American
Naturalist , 106 , 283–292.
Nei M (1978) Estimation of average heterozygosity and genetic distance
from a small number of individuals. Genetics , 89 ,
583–590.
Oksanen J, Blanchet FG, Kindt R et al. (2011) vegan: Community
Ecology Package. , R package version 2.0–5.
Orsini L, Vanoverbeke J, Swillen I, Mergeay J, De Meester L (2013)
Drivers of population genetic differentiation in the wild: isolation by
dispersal limitation, isolation by adaptation and isolation by
colonization. Molecular Ecology , 22 , 5983–5999.
Palsbøll PJ, Bé Rubé M, Allendorf FW (2006) Identification of management
units using population genetic data. Trends in Ecology and
Evolution , 22 , 11–16.
Panek KC (2005) Dispersal, Translocation, and Population Connectivity in
Fragmented Populations of Southern Idaho Ground Squirrels. Boise State
University.
Peek RA, Bedwell M, O’Rourke SM et al. (2019) Hybridization
between two parapatric ranid frog species in the northern Sierra Nevada,
California, USA. Molecular Ecology , mec.15236.
Peres-Neto PR, Jackson DA, Somers KM (2003) Giving meaningful
interpretation to ordination axes: Assessing loading significance in
principal component analysis. Ecology , 84 , 2347–2363.
Peterson GB, Carl P, Boudt K et al. (2014) PerformanceAnalytics:
econometric tools for performance and risk analysis. R package
version, 1(3541) , 107.
Pironon S, Papuga G, Villellas J et al. (2017) Geographic
variation in genetic and demographic performance: new insights from an
old biogeographical paradigm. Biological Reviews , 92 ,
1877–1909.
Primmer CR, Papakostas S, Leder EH, Davis MJ, Ragan MA (2013) Annotated
genes and nonannotated genomes: cross-species use of Gene Ontology in
ecology and evolution research. Molecular Ecology , 22 ,
3216–3241.
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population
structure using multilocus genotype data. Genetics , 155 ,
945–959.
R Core Team (2013) R: A language and environment for statistical
computing. , 201.
Rellstab C, Gugerli F, Eckert AJ, Hancock AM, Holderegger R (2015) A
practical guide to environmental association analysis in landscape
genomics. Molecular Ecology , 24 , 4348–4370.
Rousset F, Raymond M (1995) Testing heterozygote excess and deficiency.Genetics , 140 , 1413–1419.
Rubidge EM, Patton JL, Lim M et al. (2012) Climate-induced range
contraction drives genetic erosion in an alpine mammal. Nature
Climate Change , 2 , 285–288.
Rundell RJ, Price TD (2009) Adaptive radiation, nonadaptive radiation,
ecological speciation and nonecological speciation. Trends in
Ecology & Evolution , 24 , 394–399.
Santos MJ, Smith AB, Thorne JH, Moritz C (2017) The relative influence
of change in habitat and climate on elevation range limits in small
mammals in Yosemite National Park, California, U.S.A. Climate
Change Responses , 4 , 7.
Savolainen O, Lascoux M, Merilä J (2013) Ecological genomics of local
adaptation. Nature Reviews Genetics , 14 , 807–820.
Sherman PW, Runge MC (2002) Demography of a population collapse: the
northern Idaho ground squirrel (Spermophilus brunneus brunneus ).Ecology , 83 , 2816–2831.
Slatkin M (1987) Gene flow and the geographic structure of natural
populations. Science , 236 , 787–792.
Smith AB, Beever EA, Kessler AE et al. (2019) Alternatives to
genetic affinity as a context for within-species response to climate.Nature Climate Change , 9 , 787–794.
Steinberg EK, Patton JL, Lacey EA (2000) Genetic structure and the
geography of speciation in subterranean rodents: opportunities and
constraints for evolutionary diversification. In: Life
underground, the biology of subterranean rodents (eds Lacey E, Patton
JL, Cameron GN), pp. 301–331. University of Chicago Press, Chicago, IL,
USA.
Suronen EF, Newingham BA (2013) Restoring habitat for the northern Idaho
ground squirrel (Urocitellus brunneus brunneus ): Effects of
prescribed burning on dwindling habitat. Forest Ecology and
Management , 304 , 224–232.
Szkiba D, Kapun M, von Haeseler A, Gallach M (2014) SNP2GO: functional
analysis of genome-wide association studies. Genetics ,197 , 285–289.
USFWS USF and WS (2000) Endangered and threatened wildlife and
plants; Determination of threatened status for the northern Idaho ground
squirrel .
USFWS (2003) Recovery plan for the Northern Idaho ground squirrel
( Spermophilus brunneus brunneus) . Portland, OR.
USFWS (2015) Federal Register, Vol. 80, No. 120. Rules and
Regulations.
USGS (2012) National Elevation Dataset, 1 arc-second.
Waits LP, Cushman SA, Spear SF (2016) Applications of landscape genetics
to connectivity research in terrestrial animals. In: Landscape
Genetics: Concepts, Methods, Applications (eds Balkenhol N, Cushman SA,
Storfer AT, Waits LP), pp. 199–219. Wiley-Blackwell, Oxford, UK.
Waterhouse MD, Erb LP, Beever EA, Russello MA (2018) Adaptive population
divergence and directional gene flow across steep elevational gradients
in a climate-sensitive mammal. Molecular Ecology , 27 ,
2512–2528.
Weeks AR, Sgrò CM, Young AG et al. (2011) Assessing the benefits
and risks of translocations in changing environments: a genetic
perspective. Evolutionary Applications , 4 , 709–725.
Wei T, Simko V, Levy M (2017) corrplot: Visualization of a correlation
matrix.
Wittmann MJ, Stuis H, Metzler D (2018) Genetic Allee effects and their
interaction with ecological Allee effects. Journal of Animal
Ecology , 87 , 11–23.
Wood JLA, Yates MC, Fraser DJ (2016) Are heritability and selection
related to population size in nature? Meta-analysis and conservation
implications. Evolutionary Applications , 9 , 640–657.
Wright BR, Grueber CE, Belov K, Hogg CJ, McLennan EA (2019) Too much of
a good thing? Finding the most informative genetic dataset to answer
conservation questions. Molecular Ecology Resources , 0–2.
Yates AD, Achuthan P, Akanni W et al. (2020) Ensembl 2020.Nucleic Acids Research , 48 , D682–D688.
Yensen E (1991) Taxonomy and distribution of the Idaho ground squirrel,Spermohpilus brunneus . Journal of Mammalogy , 72 ,
583–600.
Yensen E (1999) Population survey of the southern Idaho ground
squirrel, Spermophilus brunneus endemicus. Caldwell, ID.
Yensen E, Dyni EJ (2020) Why is the northern Idaho ground squirrel rare?Northwest Science , 94 , 1–23.
Yensen E, Sherman PW (1997) Spermophilus brunneus .Mammalian Species , 1–5.
Yensen E, Tarifa T (2012) Can southern Idaho ground squirrels be
translocated successfully? Annual Report, Zoo Boise Conservation
Fund , 1–37.
Yensen E, Tarifa T, Clayton Z (2010) Can southern Idaho ground squirrels
be translocated successfully? Annual Report, Zoo Boise
Conservation Fund , 1–36.
Zero VH, Barocas A, Jochimsen DM et al. (2017) Complementary
network-based approaches for exploring genetic structure and functional
connectivity in two vulnerable, endemic ground squirrels.Frontiers in Genetics , 8 , 1–13.
Zheng X, Levine D, Shen J et al. (2012) A high-performance
computing toolset for relatedness and principal component analysis of
SNP data. Bioinformatics , 28 , 3326–3328.
Zink R, Barrowclough GF (2008) Mitochondrial DNA under siege in avian
phylogeography. Molecular Ecology , 1–15.