Electronic Supplementary Information for Roffler et al. “Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates”.
Table 1. Primer name, tail, and primer sequence for the 15 nuclear microsatellite loci and 3 mitochondrial DNA genes used on Dall’s sheep from Wrangell-St.
Elias National Park and Preserve, Alaska.
Primer name
Locus or
Locus Type1
Gene
Tail2
Primer Sequence (5’ – 3’)
Source
Neutral nuclear loci
MAF36
µsat
Dinucleotide repeat
polymorphism
Direct
F: TATACCTGGGAGGAATGC
R: AGTTGGACACAATTGAGC
Swarbrick et al. 1991
AE16
µsat
Dinucleotide repeat
polymorphism
Direct
F: GAGGAATGGGTGAAGACG
R: ATGGCTCGGTAATATTCC
Penty et al. 1993
HH62
µsat
Dinucleotide repeat
polymorphism
Direct
F: AGAGAAAAGCTGGGGTGC
R: CGAGTCAAACACTACTGAG
Ede et al. 1994
MAF209
µsat
Dinucleotide repeat
polymorphism
Direct
F: GCACTTAAGTATGTAGGATGC
R: AGTTGGATACAACCGTGG
Buchanan and Crawford
1992
MAF33
µsat
Dinucleotide repeat
polymorphism
Direct
F: CAGAGAAAGATACACGTGC
R: CTCACTCTTTCTGTCTCTG
Buchanan and Crawford
1992
MAF48
µsat
Dinucleotide repeat
polymorphism
Direct
F: GACTGAGCAACTAAGTACG
R: AAGCCACTTTTCAGATGC
Buchanan et al. 1991
FCB266
µsat
Dinucleotide repeat
polymorphism
Direct
F: ACCAAACACACAGCCTGC
R: CCACTAGCTTTACATAGG
Buchanan and Crawford
1993
FCB304
µsat
Dinucleotide repeat
polymorphism
Direct
F: TGCTGTCAACTGGGTCAG
R: GGAGCTTTCAATAAAGAATCGG
Buchanan and Crawford
1993
1
Electronic Supplementary Information for Roffler et al. “Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates”.
Table 1, cont. Primer name, tail, and primer sequence for the 15 nuclear microsatellite loci and 3 mitochondrial DNA genes used on Dall’s sheep from WrangellSt. Elias National Park and Preserve, Alaska.
Loci linked to nuclear functional genes3
KERA
µsat
Corneal keratin sulfate
proteoglycan
Direct +
M13F(-29)
F: GTACTGAACCAAATAGTACAGCAG
CCAAT
R: GCATGGCAACCCACTCCAGTAT
Tasheva et al. 1998
KRT2
µsat
Intermediate filament
type II keratin
Direct + SP6
F: GCCTCTAGGCGTGAGGGTTTT
R: AAGGGCCAAGAGTCATTCACAT
Powell et al. 1993
SOMAb
µsat
Grunniens growth
hormone receptor
Direct
F: ATGTTCTAATCTTATCTGGTACCAGG
R:
GTCCTCCCCAAATCAATTACATTTTCTC
Ma et al. 2010
ADCYAP1
µsat
Adenylate cyclaseactivating polypeptide 1
Direct
F: CCAGACGCCGACTTCGCCGAGG
R:
GCCTGAAGTCCACTGAGAAGAAAGGA
Moore et al. 2006
MMP9
µsat
Matrix Metallo
Proteinase 9
Direct
F: CTTGCCTTCTCATGCTGGGACT
R:
GTGAGGATAGCAACTCTTGGTCTGGCT
Adamson et al. 2000
OLADRBps
µsat
DRB = MHC class II B
MHCII(F)SP6
MHCII(R)4
MHCII(R)
F: CTGCCAATGCAGAGACACAAGA
R4: TGTCTTGTCATCTCTACG
R: GTCTGTCTCCTGTCTTGTCATC
Scott et al. 1992
TCRBV62
µsat
T-cell receptor
Direct
F: TGAGTCCTCAGCAAGCAGGT
R: ACTGGGACACTACTCCAGCTCTT
Buitkamp et al.
(unpublished)
2
Electronic Supplementary Information for Roffler et al. “Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates”.
Table 1, cont. Primer name, tail, and primer sequence for the 15 nuclear microsatellite loci and 3 mitochondrial DNA genes used on Dall’s sheep from WrangellSt. Elias National Park and Preserve, Alaska.
Loci in mitochondrial DNA
COX1F
COX1R
mtDNA
sequence
Cytochrome oxidase I
M13F(-29)
M13R
F: CTGTTCTTAGATTTACAGTCTA
R: CTGCCAGATGTAGGGAGAAAAT
This study: designed from
GenBank Accession
EF490456 (O. aries)
CYTB_F
CYTB_R
mtDNA
sequence
Cytochrome b
M13F(-29)
M13R
F: CCCCACAAAACCTATCACAAA
R: AGGGAGGTTGGTTGTTCTCC
Pedrosa et al. 2005
CYTB_IN_F
CYTB_IN_R
mtDNA
sequence
Cytochrome b
M13F(-29)
M13R
F: ACCTCCTTTCAGCAATTCCA
R: CCTGTTTCGTGGAGGAAGAG
Pedrosa et al. 2005
OdaProL
OvisCR4H
OvisCR5H
mtDNA
sequence
Control region
M13F(-29)
M13R
M13R
F: ACTATCAACACCCAAAGC
R: CTAGTGGACAGGATACGC
R: GGATTTGACTTTATGTGC
This study; designed from
GenBank Accession
AY858379, FJ545782 (O.
aries) and DQ249916 (O.
nivicola)
1
µsat = microsatellite locus; mtDNA = mitochondrial DNA
2
forward primer of each microsatellite pair, and both primers for mtDNA sequencing were synthesized with an additional 19-20 nt M13F, M13R, or SP6
universal tail on the 5’ end (M13F [-29]: CACGACGTTGTAAAACGAC; SP6:GATTTAGGTGACACTATAG; M13R: GGATAACAATTTCACACAGG)
3
4
Luikart et al. 2008
Redesigned for this study. The redesign reverse is 10 nt smaller than original
3
Electronic Supplementary Information for Roffler et al. “Lack of sex-biased dispersal promotes fine-scale genetic
structure in alpine ungulates”.
Primer references
Adamson R, Logan M, Kinnaird J, Langsley G, Hall R (2000) Loss of matrix metalloproteinase 9 activity in
Theileria annulata-attenuated cells is at the transcriptional level and is associated with differentially
expressed AP-1 species. Molecular Biochemical Parasitology, 106, 51–61.
Buchanan FC, Swarbrick PA, Crawford AM (1991) Ovine dinucleotide repeat polymorphism repeat polymorphism
at the MAF48 locus. Animal Genetics, 22, 379–380.
Buchanan FC, Crawford AM (1992) Ovine microsatellite polymorphism at the MAF70 locus. Animal Genetics, 23,
185.
Buchanan FC, Crawford AM (1993) Ovine microsatellites at the OarFCB11, OarFCB128, OarFCB193, OarFCB266
and OarFCB304 loci. Animal Genetics, 24, 145.
Buitkamp J, Schwaiger F-W, Epplen J-T. Vb6 T-cell receptor elements in artiodactyls; Conservation and germline
polymorphisms. Unpublished.
Ede AJ, Peirson CA, Henry H, Crawford AM (1994) Ovine microsatellites at the OarAE64, OarHH22, OarHH56,
OarHH62, and OarVH4 loci. Animal Genetics, 25, 51–52.
Luikart G, Pilgrim K, Visty J, Ezenwa VO, Schwartz MK (2008) Candidate gene microsatellite variation is
associated with parasitism in wild bighorn sheep. Biology letters, 4, 228–31.
Ma Z, Xu J, Zhong J, Dou Q, et al. (2010) Structural features of the 5’ flanking region of the Yak (Bos grunniens)
growth hormone receptor (GHR) gene. Archiv Tierzucht, 53, 372–378.
Moore S, Alexander L, Brownstein M, Guan L. et al. (2006) BC Cancer Agency, Canada’s Michael Smith Genome
Sciences Centre, Vancouver, British Columbia, Canada.
Pedrosa S, Uzun M, Arranz J et al. (2005) Evidence of three maternal lineages in near eastern sheep supporting
multiple domestication events. Proceedings Philosophical Transactions of the Royal Society of London.
Series B, Biological Sciences, 272, 2211–2217.
Penty JM, Henry HM, Ede AJ, Crawford A (1993) Ovine micro- satellites at the OarAE16, OarAE54, OarAE57,
OarAE119 and OarAE129 loci. Animal Genetics, 24, 219.
Powell BC, Crocker LA, Rogers GE (1993) Complete sequence of a hair-like intermediate filament type II keratin
gene. Mitochondrial DNA, 3, 401–405.
4
Electronic Supplementary Information for Roffler et al. “Lack of sex-biased dispersal promotes fine-scale genetic
structure in alpine ungulates”.
Scott PC, Maddox JF, Gogolin-Ewens KJ, Brandon MR (1992) The nucleotide sequence and evolution of ovine
MHC class II B genes: DQB and DRB. Immunogenetics, 35, 217.
Swarbrick PA, Buchanan FC, Crawford AM (1991) Ovine dinucleotide repeat polymorphism at the MAF36 locus.
Animal Genetics, 22, 377–378.
Tasheva ES, Funderburgh JL, Corpuz LM, Conrad GW (1998) Cloning, characterization and tissue-specific
expression of the gene encoding bovine keratocan, a corneal keratin sulfate proteoglycan. Gene, 218, 63–
68.
5
Electronic Supplementary Information for Roffler et al. “Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates”.
Table 2. Locus-specific genetic variation at 15 microsatellite markers genotyped on Dall’s sheep including the total number of alleles observed (A), mean
observed (Ho) and expected heterozygosity (He) across the study area, Wrangell-St. Elias National Park and Preserve, Alaska. Bold values are significant at the
0.05 level for deviation from Hardy-Weinberg proportions.
CHIS
ECHU
NUTZ
NWR
STE
SWR
WCHU
A
Ho
He
A
Ho
He
A
Ho
He
A
Ho
He
A
Ho
He
A
Ho
He
A
Ho
He
MAF36
5
0.750
0.667
4
0.750
0.561
4
0.609
0.658
6
0.667
0.717
6
0.531
0.553
5
0.661
0.703
3
0.500
0.390
AE16
3
0.625
0.650
3
0.259
0.230
3
0.652
0.655
3
0.435
0.480
4
0.422
0.536
3
0.471
0.577
3
0.333
0.287
HH62
6
0.720
0.729
4
0.429
0.363
6
0.667
0.756
7
0.688
0.686
7
0.541
0.695
6
0.821
0.764
4
0.750
0.666
MAF209
2
0.240
0.269
4
0.357
0.391
3
0.478
0.481
5
0.440
0.466
6
0.535
0.594
3
0.273
0.301
3
0.563
0.506
MAF33
4
0.636
0.538
3
0.464
0.541
3
0.476
0.373
5
0.500
0.540
3
0.552
0.663
4
0.569
0.546
4
0.733
0.727
FCB266
8
0.667
0.733
4
0.556
0.497
5
0.609
0.641
7
0.735
0.724
5
0.430
0.571
5
0.429
0.439
4
0.533
0.496
KRT2
5
0.577
0.669
3
0.630
0.549
4
0.609
0.710
5
0.490
0.537
5
0.539
0.583
4
0.321
0.310
3
0.267
0.238
KERA
3
0.154
0.144
1
0.000
0.000
1
0.000
0.000
2
0.180
0.164
1
0.000
0.000
2
0.018
0.018
1
0.000
0.000
SOMAb
10
0.750
0.779
7
0.615
0.746
7
0.591
0.764
12
0.744
0.772
9
0.511
0.554
8
0.760
0.767
4
0.688
0.635
ADCYAP1
6
0.731
0.761
3
0.679
0.563
7
0.857
0.786
7
0.680
0.741
5
0.620
0.630
6
0.574
0.502
4
0.667
0.629
MMP9
5
0.680
0.609
5
0.741
0.731
6
0.609
0.741
7
0.727
0.792
8
0.787
0.805
7
0.709
0.766
6
0.800
0.704
MAF48
5
0.500
0.521
4
0.593
0.676
4
0.696
0.589
5
0.720
0.635
5
0.600
0.646
5
0.518
0.598
3
0.625
0.623
FCB304
4
0.538
0.575
2
0.464
0.499
3
0.435
0.506
3
0.540
0.521
5
0.430
0.540
4
0.571
0.560
3
0.875
0.635
OLADRBps
8
0.808
0.818
5
0.333
0.408
8
0.826
0.803
8
0.592
0.750
7
0.394
0.524
5
0.596
0.672
4
0.625
0.602
TCRBV62
3
0.440
0.394
2
0.214
0.245
3
0.318
0.491
4
0.540
0.543
3
0.333
0.430
3
0.482
0.490
3
0.500
0.525
6
Electronic Supplementary Information for Roffler et al. “Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates”.
Figure 1. Autocorrelogram of the spatial coefficient, r, as a function of geographic distance for Dalls’ sheep (males, grey dashed line; females, black dashed line;
and both sexes combined, black solid line), Wrangell-St. Elias National Park and Preserve, Alaska, 2007-2009. Significant spatial genetic autocorrelation can be
assumed when mean r exceeds the permuted 95% confidence intervals (dashed lines) and the bootstrapped 95% confidence error bars for each distance class do
not intercept the X-axis of r = 0.
7