Supporting Information
Appendix S1. Sources of genetic samples for snowshoe hares and black-tailed jackrabbits
Appendix S2. Number of alleles, size range, and observed (HO) and expected (HE)
heterozygosity for each microsatellite locus, and average values
Locus
No. Alleles
Allele Size Range (bp)
HO
HE
7L1D3
10
71—90
0.45
0.54
SAT02
42
213—257
0.81
0.86
SAT12
16
99—140
0.60
0.59
SAT13
19
112—160
0.50
0.53
SAT16
14
89—117
0.71
0.73
SOL08
31
95—143
0.82
0.81
SOL30
39
157—217
0.58
0.59
SOL33
15
208—222
0.55
0.63
Average
23.25
0.63
0.66
Appendix S3. DNA extraction and genotyping methods
DNA Extraction
We used Qiagen DNeasy Blood & Tissue Kits, following the manufacturer’s protocol, to
extract DNA from 3 mm tissue samples taken while live-trapping. Larger tissue samples from
other sources (including museums) were digested in a detergent-based cell lysis buffer and
purified by isopropyl alcohol precipitation. We used the QIAamp DNA Stool Mini Kit to extract
pellets.
Microsatellite Genotyping
We genotyped DNA samples at 8 loci originally developed in the European rabbit,
Oryctolagus cuniculus, and successfully used with snowshoe hares (Burton et al. 2002; Schwartz
et al. 2007): 7L1D3 (Korstanje et al. 2003); SAT02, SAT12, SAT13, SAT16 (Mougel et al. 1997);
SOL08, SOL30 (with "GTGTCTT" tail added) (Rico et al. 1994); and SOL33 (Surridge et al. 1997).
PCR amplifications were conducted as two multiplex reactions, each with 10 μL volume. Primer
ratios for Multiplex 1 were 9:12:12 for SAT13 : SOL08 : SOL30. For Multiplex 2, primer ratios
were 11:6:7:3.5:4 for SAT02 : SAT16 : 7L1D3 : SAT12 : SOL33. Each multiplex consisted of 0.2 μL
10X primer mix (forward primer was dye-labeled), 1X QIAmultiplex, and 1.5 ng template DNA.
We used two touchdown PCR profiles to amplify microsatellite loci. The conditions for
Multiplex 1 were 95°C for 15 minutes; 24 cycles of 94°C for 30 seconds, 60-50°C for 3 minutes
(step down 0.5°C/cycle for first 20 cycles), and 72°C for 1 minute; followed by 60°C for 30
minutes. Multiplex 2 used identical conditions but with a 58-48°C step down temperature cycle.
PCR amplifications were run on an ABI 3130xl Genetic Analyzer at the Murdoch DNA
Sequencing Facility (University of MT) and genotypes were scored with GeneMapper v. 3.7
(Applied Biosystems Inc., Foster City, CA).
Microsatellite genotypes were manually checked to confirm allele calls. A genotype was
accepted if confirmed with at least two clear chromatograms, otherwise being coded as missing
data. A homozygote genotype was not accepted for a locus if any amplification yielded a
heterozygote genotype. Irregular mutation was found at some loci with alleles with
intermediate sizes relative to the repeat classes expectations (Appendix S3). These cases and
other unclear genotypes were re-checked by repeating the genotyping up to five times per
locus. All samples in the final data set had genotypes confirmed for at least seven loci.
Mitochondrial DNA Sequencing
We amplified a 468 bp segment of the mitochondrial control region (CR) with primers
LCRSEQ (Melo-Ferreira et al. 2007) and LepD2H (Pierpaoli et al. 1999). PCR reaction cycles were
92°C for 2 minutes; 35 cycles of 92°C for 30 seconds, 52°C for 30 seconds, and 72°C for 30
seconds; followed by 72°C for 2 minutes. The mitochondrial cytochrome-b (Cytb) gene has a
slower mutation rate and lower tendency than CR for homoplasy over long time scales. To
confirm CR groupings of haplotype lineages and to calculate deep divergence times between
lineages, we amplified a 633 bp segment of Cytb for 80 geographically distributed snowshoe
hare genetic samples and seven black-tailed jackrabbit samples. Cytb was amplified with
primers LGCYF (Alves et al. 2003) and LCYTBR (Melo-Ferreira et al. 2005). PCR conditions were
as described for the CR fragment. We sequenced CR and Cytb amplified fragments on either an
ABI 3730 or ABI 3130xl Genetic Analyzer (Applied Biosystems Inc., Foster City, CA), following the
manufacturer’s instructions.
References
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DNA into three other hare species in northern Iberia. Molecular Ecology 14:2459-2464.
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relationships of the Italian hare (Lepus corsicanus) as described by mitochondrial DNA
sequencing. Molecular Ecology 8:1805-1817.
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for the European wild rabbit, Oryctolagus cuniculus. Animal Genetics 25:367.
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for identifying individual snowshoe hares using field-collected pellets. Northwest
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Appendix S4. Results from STRUCTURE hierarchical analysis under a model of admixture and
uncorrelated allele frequencies. For each of the first four rounds of hierarchical analysis, bar
plots show proportion assignment of each individual to genetic clusters, and maps show
spatial distribution of clusters. Cluster patterns were identical for the correlated allele
frequency model.
NB1
QC3
WA4
QC4
OR2
ME1
WV1
ON1
PA1
PA2
NY1
ME2
MT1
WA1
WA3
BC1
IR1
MI1
ON3
MN1
OR1
CA1
CA2
WY1
NWT2
BC4
AB2
AB1
SK1
MB1
MN2
BC2
UT1
NWT1
YK2
CO1
1
0.8
0.6
0.4
0.2
0
AK6
1
0.8
0.6
0.4
0.2
0
AK2
Rounds 1 & 2 cluster map
AK4
Round 1 split of samples into Boreal (1A, yellow) and southwestern clusters [K=2]
WA4
OR2
MT1
WA3
BC1
WA1
OR1
CA1
CA2
WY1
UT1
Round 3 cluster map
1
0.8
0.6
0.4
0.2
0
CO1
Round 2 split of southwestern cluster into Greater Pacific
Northwest (2A, green) and U.S. Rockies (2B, blue) clusters [K=2]
Round 3 split of 2A into 3A (orange) & 3B (green) [K=2]
Round 4 cluster map
Round 4 split of 3A into 4A
(purple) & 4B (orange) [K=2]
WY1
UT1
1
0.8
0.6
0.4
0.2
0
CO1
Round 3 split of 2B into 3C (blue) & 3D (purple) [K=2]
Round 4 split of 3B into 4C
(pink) & 4D (green) [K=2]
Round 4 split of 3C into 4E
(light blue & 4F (dark blue) [K=2]
Appendix S5. Division of Boreal cluster into two sub-clusters in the second round of
STRUCTURE hierarchical analysis (admixture model and uncorrelated allele frequencies). Pie
charts and bar plot, with populations ordered west to east, show proportion assignment to
the two sub-clusters. Inset graph shows significant isolation-by-distance (IBD) pattern for
Boreal cluster. The significance of IBD was assessed with 9999 permutations in Genalex v.6.3.
Appendix S6. Results from the highest mean posterior density across 20 Geneland replicates,
for a model with uncorrelated allele frequencies and null alleles filtered. Different shades of
gray identify five distinct Geneland clusters. In the best supported Geneland model with
uncorrelated allele frequencies and null alleles not filtered, cluster assignments were similar
but BC1 (British Columbia) is an additional cluster. The approximate southernmost latitude of
the LGM is marked with a gray dashed line.
AK4
AK2
AK6
NWT1
YK2
NWT2
AB2
BC2
BC1
BC4
AB1
SK1
QC3
MB1
QC4
WA3
WA1
NB1
WA4
OR1
MN2
WY1
OR2
CA1
CA2
ON3 ON1
MT1
UT1
*
*
MN1
ME1
ME2
IR1
MI1
NY1
PA2
PA1
CO1
WV1
Appendix S7. FST (below diagonal) and Nei's D (above diagonal) for each population pair.
Populations are grouped into three microsatellite genetic clusters identified in the first two
rounds of hierarchical STRUCTURE analysis.
Boreal
AB1
AB1
AB2
0.38
Greater Pacific
Northwest
U.S. Rockies
AK2
0.37
AK4
0.44
AK6
0.39
BC2
0.27
BC4
0.43
IR1
0.49
MB1
0.31
ME1
0.22
MI1
0.37
MN1
0.33
MN2
0.27
NB1
0.25
NY1
0.31
ON1
0.23
ON3
0.29
PA1
0.34
PA2
0.29
QC3
0.40
QC4
0.38
SK1
0.30
VT1
0.35
WV1
0.46
YK2
0.39
CO1
1.41
UT1
1.33
WY1
1.49
BC1
1.02
CA1
0.98
CA2
0.74
MT1
0.74
OR1
0.78
OR2
0.79
WA1
0.75
WA3
0.87
WA4
0.64
AB1
0.18
0.17
0.19
0.14
0.21
0.26
0.20
0.17
0.32
0.08
0.15
0.16
0.15
0.11
0.25
0.18
0.12
0.37
0.20
0.22
0.16
0.16
0.22
0.37
0.16
0.71
0.80
0.78
0.84
1.09
0.98
0.74
0.99
0.93
0.72
1.13
0.69
AB2
0.11
0.12
0.16
0.10
0.15
0.18
0.29
0.40
0.27
0.22
0.25
0.24
0.25
0.52
0.55
0.13
0.18
0.22
0.28
0.22
0.25
0.14
0.23
0.15
0.16
0.29
0.33
0.19
0.26
0.24
0.21
0.40
0.55
0.18
0.24
0.31
0.35
0.33
0.32
0.14
0.21
0.28
0.30
0.43
0.55
0.05
0.11
1.02
0.97
1.32
1.18
1.48
1.19
1.06
0.70
1.14
1.12
1.09
0.97
0.82
0.73
1.20
1.16
0.83
1.10
0.96
0.83
1.47
1.42
0.79
0.68
AK2
AK4
0.14
0.27
0.36
0.24
0.29
0.50
0.19
0.25
0.29
0.17
0.15
0.37
0.26
0.21
0.49
0.26
0.33
0.39
0.20
0.32
0.55
0.12
1.16
1.34
1.49
0.94
0.93
0.92
0.84
1.09
0.94
0.92
1.20
0.83
AK6
0.13
0.25
0.15
0.15
0.36
0.11
0.22
0.16
0.08
0.10
0.26
0.11
0.15
0.27
0.14
0.30
0.30
0.13
0.20
0.30
0.11
1.12
1.26
1.32
0.87
0.82
0.78
0.77
0.89
0.77
0.74
1.17
0.68
BC2
0.44
0.24
0.35
0.28
0.23
0.46
0.46
0.17
0.28
0.23
0.42
0.23
0.30
0.17
0.30
0.21
0.25
0.36
0.39
0.23
0.33
0.21
0.21
0.39
0.51
0.24
0.37
0.32
0.45
0.39
0.31
0.22
0.37
0.29
0.32
0.35
0.46
0.22
0.36
1.23
0.98
1.59
0.84
1.54
0.87
1.17
1.07
1.15
0.91
1.04
0.94
0.93
1.20
1.00
1.41
0.75
1.72
0.86
1.20
1.26
1.97
0.89
1.00
BC4
IR1
0.27
0.34
0.18
0.20
0.29
0.17
0.20
0.34
0.23
0.17
0.42
0.26
0.29
0.34
0.24
0.28
0.46
0.21
1.03
1.02
1.01
0.91
1.03
0.93
0.76
0.89
0.74
0.72
1.11
0.74
MB1
0.31
0.17
0.23
0.08
0.14
0.14
0.16
0.10
0.15
0.26
0.12
0.27
0.17
0.18
0.15
0.27
0.23
1.11
1.14
1.16
1.00
1.00
0.93
0.94
1.11
1.25
0.92
1.21
0.83
ME1
0.33
0.26
0.35
0.30
0.33
0.33
0.36
0.31
0.44
0.43
0.39
0.43
0.42
0.06
0.55
0.48
0.98
1.22
1.13
0.98
1.10
1.17
0.91
0.80
0.97
0.66
0.95
0.79
MI1
0.14
0.16
0.12
0.09
0.26
0.11
0.12
0.26
0.16
0.19
0.17
0.12
0.05
0.34
0.13
0.68
0.89
0.93
0.98
1.29
1.20
0.72
1.21
0.80
0.89
1.29
0.73
MN1
0.26
0.20
0.16
0.24
0.21
0.15
0.43
0.28
0.21
0.29
0.28
0.04
0.47
0.26
0.83
0.93
0.97
1.04
1.11
1.13
0.81
0.92
0.81
0.73
1.05
0.79
MN2
0.14
0.14
0.16
0.13
0.15
0.29
0.11
0.27
0.15
0.15
0.03
0.29
0.22
1.12
1.31
1.32
1.04
1.20
1.09
0.91
1.20
1.09
0.97
1.45
0.88
NB1
0.08
0.27
0.11
0.15
0.23
0.16
0.26
0.26
0.12
0.04
0.30
0.13
1.03
1.19
1.25
1.04
0.96
0.93
0.83
0.99
0.84
0.81
1.14
0.75
NWT1
0.25
0.13
0.12
0.30
0.15
0.29
0.21
0.11
0.05
0.35
0.14
0.77
1.09
1.15
0.86
0.91
0.99
0.81
1.09
0.99
0.79
1.32
0.69
NWT2
0.22
0.22
0.44
0.26
0.25
0.21
0.31
0.04
0.37
0.31
1.22
1.20
1.23
1.12
1.12
1.12
0.95
1.05
1.26
0.91
1.18
0.92
NY1
0.16
0.24
0.38
0.12
0.24
0.24
0.16
0.20
0.22
0.13
0.20
0.03
0.04
0.29
0.45
0.19
0.25
0.90
0.94
1.07
1.01
1.14
0.95
1.17
0.92
1.16
1.01
1.08
0.90
0.84
0.84
1.20
1.03
0.94
0.99
0.98
0.81
1.40
1.16
0.80
0.82
ON1
ON3
0.25
0.51
0.39
0.30
0.10
0.24
0.42
1.51
1.76
1.91
1.46
1.35
1.29
1.12
1.40
1.00
1.23
1.46
1.10
PA1
0.34
0.23
0.25
0.16
0.31
0.05
0.07
0.24
0.55
0.19
0.30
1.17
1.11
1.39
1.03
1.57
1.05
0.93
1.07
1.07
1.51
1.04
1.34
0.85
0.83
1.23
1.17
1.05
0.99
0.96
0.97
1.51
1.06
0.79
0.93
PA2
QC3
0.26
0.04
0.31
0.31
0.84
0.84
0.88
1.14
1.59
1.47
0.92
1.51
1.31
1.15
1.39
0.97
QC4
0.04
0.35
0.11
0.94
1.27
1.34
1.05
1.12
1.04
0.79
1.20
0.91
0.88
1.31
0.75
0.45
0.31
1.08
1.18
1.17
1.06
0.99
0.85
0.96
0.99
1.11
0.83
1.20
0.83
VT1
0.48
1.51
1.64
1.83
1.52
1.42
1.57
1.27
1.62
1.28
1.39
1.61
1.23
WV1
0.94
1.19
1.30
0.96
1.08
1.08
0.80
1.21
0.94
0.93
1.41
0.76
YK2
0.49
0.44
1.47
1.65
1.90
0.97
1.87
1.22
1.19
2.18
0.94
CO1
0.10
1.68
1.51
1.12
1.03
1.69
1.52
1.03
0.96
1.51
1.25
1.54
1.60
1.23
0.95
1.48
1.36
0.93
0.87
UT1
WY1
0.99
0.66
0.33
0.59
0.76
0.37
0.77
0.29
BC1
0.41
0.88
0.35
1.12
0.44
0.75
0.51
CA1
0.53
0.37
0.63
0.42
0.62
0.40
CA2
0.41
0.21
0.25
0.56
0.14
MT1
0.48
0.11
0.25
0.21
OR1
0.44
0.66
0.29
0.37
0.13
OR2
WA1
0.42
WA3
AB2
0.07
AK2
AK4
0.11
0.12
0.06
0.04
0.04
AK6
0.09
0.04
0.03
0.04
BC2
0.07
0.04
0.03
0.05
0.03
BC4
IR1
0.10
0.09
0.04
0.04
0.06
0.12
0.09
0.07
0.08
0.09
0.03
0.06
0.11
MB1
0.06
0.04
0.08
0.07
0.06
0.04
0.06
0.07
ME1
0.03
0.03
0.08
0.07
0.08
0.04
0.07
0.04
0.06
MI1
0.05
0.04
0.14
0.13
0.11
0.08
0.10
0.07
0.06
0.05
MN1
0.07
0.01
0.05
0.05
0.05
0.03
0.04
0.05
0.04
0.04
0.06
MN2
0.03
0.01
0.07
0.07
0.05
0.05
0.05
0.07
0.03
0.04
0.02
0.02
NB1
0.04
0.03
0.08
0.07
0.08
0.04
0.06
0.06
0.07
0.01
0.06
0.04
0.04
NWT1
0.02
0.01
0.04
0.06
0.03
0.00
0.02
0.05
0.02
0.01
0.03
0.01
0.02
0.01
NWT2
NWT1 NWT2
0.23
0.24
0.04
0.01
0.05
0.04
0.03
0.02
0.05
0.04
0.04
0.03
0.06
0.01
0.02
0.02
NY1
0.04
0.04
0.09
0.09
0.09
0.07
0.08
0.06
0.07
0.02
0.04
0.05
0.02
0.02
0.04
0.05
ON1
ON3
0.03
0.05
0.02
0.01
0.06
0.08
0.07
0.06
0.06
0.05
0.02
0.04
0.05
0.05
0.06
0.03
0.04
0.03
0.00
0.03
0.05
0.04
0.01
0.02
0.02
0.01
0.01
0.03
-0.01
-0.01
0.01
0.01
0.02
0.03
0.03
0.02
PA1
0.08
0.09
0.15
0.17
0.15
0.09
0.12
0.13
0.12
0.07
0.10
0.07
0.10
0.08
0.05
0.08
0.10
0.05
0.10
PA2
QC3
0.06
0.07
0.04
0.04
0.06
0.10
0.08
0.10
0.07
0.09
0.04
0.08
0.06
0.08
0.08
0.08
0.07
0.06
0.02
0.05
0.09
0.06
0.04
0.04
0.06
0.03
0.02
0.06
0.02
0.04
0.03
0.06
0.05
0.04
0.01
0.04
0.06
0.02
0.07
0.12
0.08
QC4
0.07
0.02
0.11
0.09
0.10
0.08
0.10
0.05
0.07
0.03
0.07
0.03
0.04
0.02
0.04
0.04
0.03
0.03
0.04
0.10
0.05
0.04
SK1
0.05
0.02
0.04
0.05
0.04
0.02
0.04
0.07
0.05
0.03
0.07
0.01
0.04
0.02
-0.01
0.00
0.05
0.00
0.03
0.07
0.02
0.06
0.04
VT1
0.06
0.04
0.09
0.08
0.08
0.05
0.07
0.06
0.06
0.02
0.39
0.23
0.28
0.19
0.27
0.24
0.25
0.22
0.22
0.37
0.23
0.35
0.25
0.26
WV1
0.12
0.10
0.16
0.18
0.18
0.10
0.12
0.13
0.14
0.08
0.13
0.10
0.12
0.09
0.08
0.10
0.10
0.08
0.13
0.08
0.07
0.14
0.09
0.10
0.13
YK2
0.11
0.05
0.01
0.03
0.03
0.04
0.07
0.10
0.06
0.07
0.12
0.04
0.07
0.07
0.03
0.04
0.08
0.05
0.07
0.14
0.06
0.09
0.09
0.02
0.09
0.16
CO1
0.30
0.21
0.30
0.29
0.31
0.30
0.32
0.26
0.28
0.25
0.25
0.21
0.23
0.27
0.27
0.24
0.27
0.25
0.25
0.34
0.30
0.26
0.24
0.26
0.28
0.34
0.28
UT1
WY1
0.30
0.32
0.23
0.24
0.34
0.36
0.32
0.33
0.34
0.36
0.31
0.33
0.35
0.36
0.26
0.27
0.28
0.29
0.25
0.28
0.28
0.28
0.24
0.27
0.24
0.27
0.29
0.31
0.29
0.31
0.28
0.30
0.27
0.29
0.28
0.30
0.26
0.27
0.36
0.38
0.32
0.35
0.25
0.28
0.24
0.26
0.31
0.33
0.29
0.31
0.36
0.38
0.31
0.33
0.23
0.22
0.06
BC1
0.27
0.23
0.32
0.26
0.30
0.27
0.33
0.29
0.27
0.24
0.26
0.26
0.26
0.27
0.28
0.25
0.27
0.29
0.25
0.36
0.28
0.26
0.27
0.29
0.28
0.37
0.29
0.38
0.41
0.40
CA1
0.22
0.22
0.30
0.28
0.26
0.23
0.28
0.22
0.24
0.21
0.22
0.25
0.22
0.24
0.22
0.22
0.22
0.24
0.22
0.30
0.26
0.25
0.26
0.25
0.23
0.32
0.27
0.36
0.33
0.33
0.33
CA2
0.21
0.24
0.32
0.29
0.29
0.25
0.30
0.26
0.26
0.22
0.26
0.27
0.25
0.26
0.25
0.26
0.25
0.27
0.23
0.33
0.28
0.27
0.28
0.28
0.24
0.36
0.30
0.40
0.41
0.40
0.30
0.18
MT1
0.14
0.15
0.20
0.18
0.19
0.18
0.20
0.19
0.16
0.17
0.15
0.16
0.15
0.17
0.16
0.17
0.16
0.16
0.16
0.22
0.18
0.16
0.17
0.16
0.18
0.24
0.19
0.24
0.25
0.26
0.13
0.21
0.17
OR1
0.17
0.19
0.27
0.25
0.24
0.22
0.23
0.23
0.20
0.20
0.16
0.22
0.17
0.22
0.20
0.22
0.19
0.22
0.20
0.26
0.24
0.21
0.23
0.23
0.20
0.29
0.25
0.34
0.32
0.32
0.21
0.12
0.14
0.12
OR2
WA1
0.20
0.13
0.21
0.13
0.25
0.21
0.28
0.18
0.26
0.19
0.22
0.17
0.22
0.18
0.29
0.18
0.20
0.14
0.23
0.15
0.21
0.10
0.20
0.16
0.19
0.12
0.24
0.16
0.21
0.14
0.23
0.15
0.24
0.14
0.22
0.16
0.22
0.14
0.26
0.21
0.26
0.18
0.22
0.15
0.25
0.17
0.23
0.16
0.25
0.15
0.30
0.23
0.25
0.20
0.33
0.27
0.36
0.27
0.37
0.26
0.29
0.14
0.30
0.13
0.24
0.14
0.07
0.06
0.16
0.03
0.13
WA3
0.18
0.20
0.31
0.29
0.27
0.26
0.27
0.27
0.21
0.18
0.19
0.24
0.22
0.24
0.20
0.21
0.28
0.27
0.20
0.23
0.24
0.23
0.31
0.28
0.37
0.35
0.35
0.27
0.23
0.23
0.14
0.08
0.21
WA4
0.12
0.12
0.20
0.16
0.18
0.16
0.18
0.16
0.15
0.14
0.12
0.14
0.13
0.16
0.13
0.14
0.14
0.14
0.15
0.20
0.16
0.15
0.16
0.14
0.15
0.22
0.18
0.24
0.24
0.25
0.12
0.14
0.14
0.04
0.06
0.12
0.02
0.11
AB1
AB2
AK2
AK4
AK6
BC2
BC4
IR1
MB1
ME1
MI1
MN1
MN2
NB1
NY1
ON1
ON3
PA1
PA2
QC3
QC4
SK1
VT1
WV1
YK2
CO1
UT1
WY1
BC1
CA1
CA2
MT1
OR1
OR2
WA1
WA3
0.23
0.23
NWT1 NWT2
0.24
0.07
SK1
WA4
WA4
Appendix S8. For each sampled population, allelic richness plotted against latitude
(top) and longitude (bottom). The gray vertical bar marks the approximate
southernmost latitude of the LGM.
Appendix S9. Median-joining network based on 468 base pairs of mitochondrial control
region for 1006 snowshoe hare specimens. The three major haplotype lineages (Boreal,
Greater Pacific Northwest, and U.S. Rockies) correspond with microsatellite genetic groups
identified in the first two rounds of hierarchical STRUCTURE analysis. Each small circle
represents a unique haplotype. Branch lengths are approximately proportional to the number
of base pair substitutions separating haplotypes. Within the three major haplotype lineages,
three sub-lineages (CO1, OR2, and WA3) distinguished by at least 10 base pair substitutions
are identified by dashed gray ellipses. A white-tailed jackrabbit (GenBank accession number
AY292729) control region haplotype is included as an outgroup.
Appendix S10. MtDNA control region FST for each population pair. Populations are grouped into three major haplotype lineages
identified by SAMOVA.
Boreal
AB1
AB1
U.S. Rockies
AB2
AK2
AK4
AK6
BC1
BC2
BC4
IR1
MB1
ME1
MI1
MN1
MN2
MT1
NB1
NY1
ON1
ON3
PA1
PA2
QC3
QC4
SK1
VT1
WA4
WV1
YK2
CO1
OR2
UT1
WY1
CA1
CA2
OR1
WA1
WA3
0.09
0.18
0.19
0.22
0.75
0.30
0.25
0.28
0.07
0.31
0.08
0.06
0.10
0.09
0.28
0.08
0.09
0.22
0.14
0.10
0.32
0.21
0.19
0.36
0.14
0.28
0.24
0.27
0.20
0.81
0.89
0.92
0.90
0.97
0.95
0.89
0.90
0.94
AB1
0.22
0.15
0.22
0.47
0.11
0.10
0.05
0.04
0.15
0.12
0.02
0.04
0.05
0.09
0.04
0.03
0.06
0.04
0.00
0.17
0.09
0.06
0.14
0.00
0.10
0.23
0.12
0.21
0.75
0.84
0.82
0.87
0.91
0.89
0.87
0.87
0.89
AB2
0.12
0.08
0.67
0.38
0.33
0.41
0.21
0.38
0.34
0.22
0.30
0.14
0.37
0.12
0.18
0.35
0.31
0.24
0.47
0.36
0.29
0.42
0.29
0.38
0.36
0.39
0.04
0.84
0.89
0.90
0.90
0.96
0.95
0.91
0.91
0.94
AK2
0.14
0.58
0.21
0.16
0.26
0.14
0.30
0.27
0.19
0.22
0.12
0.26
0.07
0.13
0.23
0.24
0.17
0.39
0.26
0.14
0.31
0.19
0.24
0.26
0.30
0.12
0.80
0.88
0.88
0.90
0.95
0.93
0.89
0.90
0.93
AK4
0.76
0.41
0.31
0.40
0.21
0.40
0.34
0.23
0.27
0.17
0.37
0.13
0.18
0.36
0.29
0.22
0.49
0.35
0.28
0.42
0.28
0.37
0.28
0.42
0.07
0.81
0.89
0.92
0.91
0.97
0.95
0.90
0.90
0.94
AK6
0.55
0.62
0.70
0.62
0.58
0.78
0.48
0.60
0.35
0.64
0.61
0.50
0.68
0.58
0.48
0.80
0.65
0.45
0.70
0.63
0.72
0.31
0.72
0.57
0.89
0.92
0.97
0.93
1.00
0.99
0.92
0.92
0.98
BC1
0.06
0.16
0.17
0.24
0.34
0.19
0.22
0.11
0.23
0.17
0.14
0.20
0.23
0.16
0.43
0.24
0.04
0.28
0.18
0.22
0.25
0.27
0.34
0.82
0.87
0.88
0.90
0.95
0.94
0.90
0.90
0.93
BC2
0.10
0.13
0.25
0.29
0.18
0.18
0.12
0.20
0.06
0.08
0.20
0.21
0.14
0.41
0.21
0.11
0.25
0.15
0.20
0.18
0.27
0.28
0.79
0.88
0.90
0.90
0.95
0.92
0.88
0.88
0.92
BC4
0.11
0.16
0.27
0.12
0.09
0.11
0.11
0.08
0.09
0.10
0.13
0.08
0.31
0.12
0.14
0.17
0.05
0.12
0.20
0.19
0.34
0.78
0.87
0.89
0.90
0.95
0.92
0.88
0.88
0.92
IR1
0.21
0.08
0.03
0.00
0.05
0.15
0.01
0.01
0.10
0.09
0.03
0.24
0.11
0.14
0.22
0.02
0.13
0.25
0.16
0.21
0.79
0.87
0.88
0.89
0.95
0.92
0.89
0.89
0.92
MB1
0.32
0.20
0.22
0.16
0.04
0.21
0.19
0.03
0.13
0.14
0.33
0.06
0.17
0.03
0.18
0.01
0.33
0.12
0.35
0.77
0.83
0.81
0.86
0.92
0.91
0.89
0.89
0.91
ME1
0.04
0.05
0.13
0.27
0.16
0.13
0.21
0.12
0.08
0.30
0.17
0.25
0.35
0.13
0.27
0.25
0.28
0.31
0.80
0.89
0.92
0.91
0.97
0.95
0.89
0.90
0.94
MI1
0.00
0.07
0.13
0.08
0.05
0.07
0.05
0.00
0.17
0.07
0.15
0.18
0.00
0.13
0.32
0.12
0.23
0.77
0.83
0.80
0.85
0.91
0.90
0.88
0.89
0.90
MN1
0.10
0.16
0.08
0.07
0.08
0.04
0.02
0.19
0.06
0.18
0.20
0.00
0.13
0.25
0.12
0.27
0.76
0.86
0.85
0.88
0.93
0.90
0.88
0.88
0.90
MN2
0.12
0.03
0.03
0.08
0.11
0.04
0.20
0.11
0.09
0.15
0.02
0.11
0.37
0.14
0.17
0.73
0.75
0.71
0.77
0.88
0.87
0.86
0.87
0.87
MT1
0.14
0.12
0.00
0.11
0.08
0.30
0.05
0.14
0.00
0.11
0.00
0.28
0.11
0.33
0.78
0.85
0.85
0.88
0.94
0.92
0.89
0.89
0.92
NB1
0.00
0.12
0.13
0.06
0.29
0.14
0.11
0.21
0.04
0.14
0.20
0.19
0.13
0.76
0.86
0.87
0.89
0.94
0.91
0.88
0.88
0.91
NWT1
0.10
0.11
0.03
0.22
0.11
0.11
0.18
0.01
0.12
0.25
0.16
0.18
0.76
0.85
0.83
0.87
0.92
0.90
0.88
0.88
0.90
NWT2
0.05
0.04
0.26
0.00
0.13
0.04
0.07
0.00
0.25
0.07
0.30
0.78
0.86
0.88
0.89
0.95
0.93
0.89
0.89
0.93
NY1
0.01
0.14
0.05
0.12
0.14
0.06
0.10
0.24
0.09
0.26
0.74
0.85
0.83
0.87
0.93
0.90
0.88
0.88
0.90
ON1
0.15
0.04
0.11
0.11
0.00
0.08
0.25
0.09
0.21
0.74
0.83
0.81
0.86
0.91
0.89
0.87
0.87
0.89
ON3
0.24
0.32
0.37
0.22
0.34
0.27
0.31
0.39
0.81
0.89
0.91
0.90
0.97
0.95
0.90
0.90
0.94
PA1
0.18
0.08
0.06
0.01
0.26
0.09
0.31
0.77
0.86
0.86
0.89
0.94
0.91
0.88
0.89
0.91
PA2
0.19
0.12
0.14
0.22
0.20
0.25
0.78
0.85
0.84
0.88
0.93
0.91
0.88
0.88
0.91
QC3
0.17
0.02
0.27
0.13
0.35
0.78
0.87
0.87
0.89
0.95
0.93
0.89
0.90
0.93
QC4
0.12
0.21
0.15
0.25
0.77
0.86
0.87
0.89
0.94
0.91
0.88
0.88
0.91
SK1
0.23
0.09
0.32
0.78
0.87
0.89
0.90
0.96
0.93
0.89
0.89
0.93
VT1
0.25
0.34
0.51
0.67
0.52
0.71
0.55
0.50
0.57
0.57
0.56
WA4
0.33
0.79
0.88
0.89
0.90
0.96
0.94
0.89
0.90
0.93
WV1
0.80
0.86
0.85
0.88
0.93
0.92
0.89
0.90
0.92
YK2
0.84
0.84
0.86
0.94
0.92
0.89
0.89
0.92
CO1
0.86
0.87
0.97
0.96
0.94
0.94
0.96
OR2
0.72
0.98
0.98
0.92
0.92
0.97
UT1
0.97
0.96
0.94
0.94
0.96
WY1
0.24
0.42
0.26
0.93
CA1
0.26
0.10
0.87
CA2
0.24
0.73
OR1
0.74
WA1
AB2
AK2
AK4
AK6
BC1
BC2
BC4
IR1
MB1
ME1
MI1
MN1
MN2
MT1
NB1
NWT1
NWT1 NWT2
Greater Pacific
Northwest
NWT2
NY1
ON1
ON3
PA1
PA2
QC3
QC4
SK1
VT1
WA4
WV1
YK2
CO1
OR2
UT1
WY1
CA1
CA2
OR1
WA1
WA3
WA3
AB1
AB2
AK2
AK4
AK6
BC1
BC2
BC4
IR1
MB1
ME1
MI1
MN1
MN2
MT1
NB1
NWT1 NWT2
NY1
ON1
ON3
PA1
PA2
QC3
QC4
SK1
VT1
WA4
WV1
YK2
CO1
OR2
UT1
WY1
CA1
CA2
OR1
WA1
WA3
Appendix S11. Mitochondrial control region diversity statistics for 39 sampled snowshoe hare
populations. Populations are grouped into three major haplotype lineages identified by
SAMOVA. N = number of individuals, Hd = haplotype diversity, and π = nucleotide diversity.
Lineage averages and standard deviations (in parentheses) are italicized.
Population
N
AB1
AB2
AK2
AK4
AK6
BC1
BC2
BC4
IR1
MB1
ME1
MI1
MN1
MN2
MT1
NB1
NWT1
NWT2
NY1
ON1
ON3
PA1
PA2
QC3
QC4
SK1
VT1
WA4
WV1
YK2
9
18
28
15
10
17
25
9
8
13
40
8
35
12
127
20
9
18
13
14
19
10
13
19
17
9
10
29
13
30
BOREAL
Total N= 617
CA1
CA2
OR1
WA1
WA3
12
7
32
30
9
GREATER PACIFIC
NORTHWEST
CO1
OR2
UT1
WY1
U.S. ROCKIES
Total N= 90
64
17
25
80
Total N= 186
No. of
Haplotypes
Hd
π
7
17
13
6
7
2
14
7
4
7
16
6
28
11
31
13
9
14
8
12
18
6
8
10
9
9
9
10
3
20
11.13
(6.63)
0.94
0.99
0.91
0.80
0.91
0.12
0.88
0.94
0.79
0.87
0.93
0.89
0.98
0.98
0.94
0.96
1.00
0.97
0.90
0.97
0.99
0.84
0.88
0.86
0.89
1.00
0.98
0.87
0.62
0.97
0.89
(0.17)
0.009
0.019
0.008
0.013
0.009
0.000
0.010
0.014
0.017
0.014
0.014
0.009
0.016
0.019
0.020
0.013
0.018
0.017
0.013
0.018
0.020
0.009
0.016
0.015
0.012
0.018
0.013
0.068
0.011
0.013
0.016
(0.011)
2
2
15
11
7
0.41
0.47
0.93
0.86
0.91
0.001
0.005
0.016
0.016
0.008
7.40
(5.68)
17
8
6
15
11.50
(5.32)
0.72
(0.25)
0.92
0.90
0.62
0.84
0.82
(0.14)
0.009
(0.007)
0.006
0.015
0.002
0.005
0.007
(0.005)
Appendix S12. For each sampled population, haplotype diversity plotted against latitude (top)
and longitude (bottom). The gray vertical bar marks the approximate southernmost latitude
of the LGM.
Boreal
Greater Pacific Northwest
U.S. Rockies
1.2
1
Hd
0.8
0.6
0.4
0.2
0
35
40
45
50
55
60
65
70
La tude (°N)
Boreal
Greater Pacific Northwest
U.S. Rockies
1.2
1
Hd
0.8
0.6
0.4
0.2
0
-180
-160
-140
-120
-100
Longitude (°W)
-80
-60
-40
Appendix S13. For each sampled population, nucleotide diversity plotted against latitude
(top) and longitude (bottom). The gray vertical bar marks the approximate southernmost
latitude of the LGM. Population WA4 (Washington) was omitted from these figures because
its unusually high nucleotide diversity (Nd = 0.0681) obscured large-scale patterns.
Boreal
Greater Pacific Northwest
U.S. Rockies
0.025
0.02
Nd
0.015
0.01
0.005
0
35
40
45
50
55
60
65
70
La tude (°N)
Boreal
Greater Pacific Northwest
U.S. Rockies
0.025
0.02
Nd
0.015
0.01
0.005
0
-180
-160
-140
-120
-100
Longitude (°W)
-80
-60
-40