Supporting Information
1
Table S1 Details of loci and PCR primers used.
Accession No.‡
JX284248 - JX284284
JX284366 - JX284378
JX284379 - JX284389
Y
JX269135, JX269139,
JX269141 - JX269142
SMCY7 637
SMCY7Fc CCCCTGCAGACCKRCAT
AAGGCCAAGTTGATRAARCT TD 65-55
JX284390 - JX284397
SMCY7Rc
Chr 2*
RAG1
1234
S70d
TCCGAGTGGAAATTTAAGMTGTT S73d
GAGGAAGGTRTTGACACGGATG 55
JX284319 - JX284365
Chr11*
BRCA1 1313
BRCA1MF ACAAGGAGCCAACGGAACAGAT BRCA1MR ATGGACCGGTTCCTTGAGGTTT
65
JX284285 - JX284318
*Location based on the position on the mouse genome; †Tn is the annealing temperature used in the PCR (where “TD” represents a touchdown procedure); ‡ GenBank
Accession numbers of the sequences produced in this study per locus;
a
Jaarola M, Searle JB (2002) Phylogeography of field voles (Microtus agrestis) in Eurasia inferred from mitochondrial DNA sequences. Molecular Ecology, 11, 2613–2621.
b
Hellborg L, Ellegren H (2004) Low levels of nucleotide diversity in mammalian Y chromosome. Molecular Biology and Evolution, 21, 158-163.
c
Hellborg L, Ellegren H (2003) Y chromosome conserved anchored tagged sequences (YCATS) for the analysis of mammalian male specific DNA. Molecular Ecology, 12,
283-291.
d
Steppan SJ, Storz BL, Hoffmann RS (2004) Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAG1.
Molecular Phylogenetics and Evolution, 30, 703-719.
mtDNA
X
Locus
Cytb
DBX5
DBX6
DBY7
Size (bp)
1143
287
367
501
Forward primer
L14727-SPa GACAGGAAAAATCATCGTTG
DBX5Fb
CAACAACTGTCCTCCACA
DBX6Fb
AGACTTGATGGCTTGTGC
DBY7Fc
GGTCCAGGAGARGCTTTGAA
Reverse primer
Tn†
H15915-SPa GTCTTGTAAACCAGTAATGAA
55
CATGATAATTTCTCCCATCTC TD 65-55
DBX5Rb
ATGCTGCAGTTTTTCCAGA
TD 65-55
DBX6Rb
DBY7Rc
CAGCCAATTCTCTTGTTGGG
TD 65-55
2
Table S2 Assessment of species delimitation for clocklike loci† and all loci, considering
θp (0.0056) and θma (0.0268) (see text).
AICc
Δi
L(Model|data)
ωi
Lineage composition
θ = 0.0056
Clocklike loci†
P, S, N, Marv, Mcab
P, S_N, Marv, Mcab
P_N, S, Marv, Mcab
P_S, N, Marv, Mcab
P_S_ N, Marv, Mcab
-lnL
k
-4266.975
-4326.658
-4383.610
-4378.537
-4487.254
4
3
3
3
2
8543.432
8660.173
8774.077
8763.931
8978.923
0
116.741
230.254
220.499
435.490
1.000
0.000
0.000
0.000
0.000
1.000
0.000
0.000
0.000
0.000
All loci
P, S, N, Marv, Mcab
P, S_N, Marv, Mcab
P_N, S, Marv, Mcab
P_S, N, Marv, Mcab
P_S_ N, Marv, Mcab
-8160.782
-8278.564
-8362.429
-8364.292
-8573.301
4
3
3
3
2
16331.046
16563.984
16731.715
16735.441
17151.017
0
232.939
400.669
404.395
819.971
1.000
0.000
0.000
0.000
0.000
1.000
0.000
0.000
0.000
0.000
θ = 0.0268
Clocklike loci†
P, S, N, Marv, Mcab
P, S_N, Marv, Mcab
P_N, S, Marv, Mcab
P_S, N, Marv, Mcab
P_S_ N, Marv, Mcab
-1349.555
-1368.282
-1381.729
-1389.382
-1411.981
4
3
3
3
2
2708.591
2743.422
2770.314
2785.622
2828.376
0
34.831
61.724
77.031
119.785
1.000
0.000
0.000
0.000
0.000
1.000
0.000
0.000
0.000
0.000
All loci
P, S, N, Marv, Mcab
-2447.600 4
4905.121
0
1.000
1.000
P, S_S, Marv, Mcab
-2479.967 3
4966.791
61.669
0.000
0.000
P_N, S, Marv, Mcab
-2494.755 3
4996.366
91.245
0.000
0.000
P_S, N, Marv, Mcab
-2503.074 3
5013.005
107.884
0.000
0.000
P_S_N, Marv, Mcab
-2551.600 2
5107.614
202.493
0.000
0.000
P – Portuguese lineage ; S – Southern lineage ; N – Northern lineage ; Marv – Microtus arvalis, Mcab –
Microtus cabrerae, -lnL, log-likelihood of the model given the data; k, number of parameters; AICc, corrected
Akaike Information Criteria; Δi, AICc differences; L, relative likelihood of the model given the data; ωi, model
probability.
†Includes introns 5 and 6 from the DBX gene, intron 7 from the DBY gene, intron 7 from the SMCY gene and
the RAG1 exon.
3
Fig. S1 Consensus species tree inferred with ML in STEM for clocklike loci (a, b, e) and for
all loci (c, d), with θp = 0.0056 (a, c), θma = 0.0268 (b, d) and θa = 0.0118 (e). Grey bars
show 95% highest posterior density intervals of branch lengths in coalescent units (number of
2Ne generations). Bootstrap support (above) and branch lengths (mean and 95%HPD, below)
are shown for each node.
4
(a)
(c)
(b)
(d)
(e)
5
Fig. S1
6