SUPPORTING INFORMATIONS2
Title: Genetic landscape with sharp discontinuities shaped by complex demographic history
in moose (Alces alces)
Authors: Lovisa Wennerström, Nils Ryman, Jean-Luc Tison, Anna Hasslow, Love Dalén,
and Linda Laikre
Affiliation of first and senior authors (LW, NR, LL): Division of Population Genetics,
Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
E-mail adresses: lovisa.wennerstrom@zoologi.su.se, nils.ryman@popgen.su.se,
linda.laikre@popgen.su.se
Journal: Journal of Mammalogy
Microsatellite genotyping and mtDNA sequencing
Genomic DNA was isolated from frozen muscle tissue and 12 microsatellite loci that had
previously been analyzed in moose were scored, including 5 loci used in our own previous
work (Charlier et al. 2008): BM757, BM848, CSSM003, CSSM39, IDGA8, IDGVA29,
MAF46, McM58, McM64, McM130, OarCP21, and RT30 (Swarbrick et al. 1992; Bishop et
al. 1994; Hulme et al. 1994; Moore et al. 1994; Ede et al. 1995; Mezzelani et al. 1995; Wilson
et al. 1997; Slate et al. 1998; Haanes et al. 2011; Kangas et al 2013). Laboratory work was
conducted at the Center of Evolutionary Applications, University of Turku, Finland. DNA
was extracted with a salt extraction method modified from Aljnabi and Martinez (1997).
Samples were genotyped with markers divided into 2 multiplexes (MPs) and one single PCR
(MP1: MAF46, McM58, McM130, CSSM003, RT30, OarCP21, CSSM39, MP2: McM64,
BM848, BM757, IDGVA8, single: IDGVA29).
To improve the microsatellite peak profiles, a GTTT-“PIGtail” was added to the 5’ end of
each non-labelled primer (Brownstein et al. 1996). Amplifications were done in 3 (three) 8-µl
reactions with c. 80 ng of DNA, 0.025 to 0.8 µM of each primer (one of which was
fluorescently labeled) and 1X Qiagen multiplex PCR master mix (Qiagen Inc. Valencia, CA,
USA). The PCR profile used was according to the manufacturer’s protocol with annealing
temperatures of 58 °C, 61 °C, and 58 °C for MP1, MP2 and the single reaction, respectively.
Amplifications were performed on PTC-100 (MJ Research) and AB 2720 (Applied
Biosystems) thermal cyclers. The PCR products were pooled for electrophoresis (1.4 µl of
MP1, 1 µl of MP2 and 1.6 µl of the single PCR) and diluted with 100 µl sterile water. 2 µl of
the pooled and diluted PCR product was combined with GS600LIZ size standard (Applied
Biosystems) and HiDi-formamide (Applied Biosystems). Samples were denatured at 98 °C
for 3 minutes and the size of the fragments was determined by capillary electrophoresis on an
ABI PrismTM 3130xl genetic analysis instrument. The genotypes were scored using
GENEMAPPER v4.0 (Applied Biosystems) and following visual inspection, exported to a
spreadsheet program for downstream analyses.
mtDNA
Genomic DNA was extracted from muscle tissue using Qiagen DNEasy blood and tissue kit.
The 5’ end of the mtDNA with the first hypervariable part of the control region (CR1) was
amplified using primers Alces-PRO1F (5’-CCCCACTATCAACACCCAAA-3’) and AlcesDL1R (5’-GTGGGCGATTTTAGRTGAGA-3´). PCR reactions were performed in 25μl
volumes, containing 1μl DNA extract, 0.4µM of each primer, and an Illustra Hot Start mix
RTG bead (GE Healthcare). The PCR thermal conditions started with 10 minutes denaturation
at 95°C, followed by 3 cycles of denaturation for 30 seconds (sec) at 94°C, 30 sec annealing
at 56°C, 60 sec extension at 72°C. This was followed by 32 cycles of 30 sec denaturation at
94°C, 30 sec annealing at 54°C, 60 sec extension at 72°C. PCR products were sequenced for
both the forward and reverse strands using BigDye Kit v.3.1 (Applied Biosystems) and run on
an ABI3130xl sequencer at the Swedish Museum of Natural History, Stockholm. Sequences
were edited using Geneious (Kearse et al. 2012).
Literature cited (not provided in the paper)
ALJNABI S. M. AND I. MARTINEZ. 1997. Universal and rapid salt-extraction of high quality
genomic DNA for PCR-based techniques. Nucleic Acids Research 25:4629-4693.
BISHOP M. D., S. M. KAPPES, J. W. KEELE, R. T. STONE, S. L. F. SUNDEN, G. A. HAWKINGS, S.
S. TOLODOET AL. 1994. A genetic linkage map for cattle. Genetics 136:619-639.
BROWNSTEIN M. J., J. D. CARPTEN, AND J. R. SMITH. 1996. Modulation of non-templated
nucleotide addition by Taq DNA polymerase: primer modifications that facilitate genotyping.
Biotechniques 20:1004-10010.
EDE A. J., C. A. PIERSON, AND A. M. CRAWFORD. 1995. Ovine microsatellites at the OarCP9,
OarCP20, OarCP21, OarCP23 and OarCP26 loci. Animal Genetics 25:129-130.
HULME, D.J., J. P. SILK, J. M. REDWIN, W. BARENDSE, AND K. J. BEH. 1994. Ten polymorphic
ovine microsatellites. Animal Genetics 25:434-435.
KEARSE, M., R. MOIR, A. WILSON, S. STONES-HAVAS, M. CHEUNG, S. STURROCK, S. BUXTON
ET AL. 2012. Geneious Basic: An integrated and extendable desktop software platform for the
organization and analysis of sequence data. Bioinformatics 28:1647-1649.
MEZZELANI, A., Y. ZHANG, L. REDAELLI, B. CASTIGLIONI, P. LEONE, J. L. WILLIAMS, S. S.
TOLDO ET AL. 1995. Chromosomal localization and molecular characterization of 53 cosmidderived bovine microsatellites. Mammalian Genome 6:629-635.
MOORE, S.S., K. BYRNE, K. T. BERGER, W. BARENDSE, F. MCCARTHY, J. E. WOMACK, AND D.
J. S. HETZEL. 1994. Characterization of 65 bovine microsatellites. Mammalian Genome 5:8490.
SLATE, J., D. W. COLTMAN, S. J. GOODMAN, I. MACLEAN, J. M. PEMBERTON, AND J. L.
WILLIAMS. 1998. Bovine microsatellite loci are highly conserved in red deer (Cervus
elaphus), sika deer (Cervus Nippon) and Soay sheep (Ovis aries). Animal Genetics 29:307315.
SWARBRICK, P. A., A. B. DIETZ, J. E. WOMACK, AND A. M. CRAWFORD. 1992. Ovine and
bovine dinucleotide repeat morphism at the MAF46 locus. Animal Genetics 23:182.
WILSON, G. A., C. STROBECK, L. WU, AND J. W. COFFIN. 1997. Characterization of
microsatellite loci in caribou Rangifer tarandus, and their use in other artiodactyls. Molecular
Ecology 6:697-699.