Genes Genet. Syst. (2008) 83, p. 77–88

Mosaic genealogy of the Mus musculus genome revealedby 21 nuclear genes from its three subspecies
Yu-Hua Liu1,4, Aya Takahashi1, Takashi Kitano1,5, Tsuyoshi Koide2,
Toshihiko Shiroishi2, Kazuo Moriwaki3 and Naruya Saitou1*
1

Division of Population Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
2
Mammalian Genetics Laboratory, National Institute of Genetics, Mishima,
411-8540, Japan
3
RIKEN Bioresource Center, RIKEN Tsukuba Institute, Tsukuba, 305-0074, Japan
4
Present address: Department of Pathology, University of Washington,
Seattle, WA 98915-6340, USA
5
Present address: Department of Biomolecular Function Engineering,
Ibaraki University, Hitachi, 316-8511, Japan(Received 26 March 2007, accepted 4 November 2007)

Patterns of genetic variation provide insight into the evolutionary history of a
species. Mouse (Mus musculus) is a good model for this purpose. Here we
present the analysis of genealogies of the 21 nuclear loci and one mitochondrial
DNA region in M. musculus based on our nucleotide sequences of nine inbred
strains from three M. musculus subspecies (musculus, domesticus, and castaneus)and one M. spicilegus strain as an outgroup. The mitochondrial DNA genegenealogy of those strains confirmed the introgression pattern of one musculus
strain. When all the nuclear DNA data were concatenated to produce a phylogenetic tree of nine strains, musculus and domesticus strains formed monophyleticclusters with each other, while the two castaneus strains were paraphyletic.
When each DNA region was treated independently, the phylogenetic networks
revealed an unnegligibly high level of subspecies admixture and the mosaic natureof their genome. Estimation of ancestral and derived population sizes and migration rates suggests the effects of ancestral polymorphism and gene flow on thepattern of genetic variation of the current subspecies. Gene genealogies of Fut4and Dfy loci also suggested existence of the gene flow between M. musculus andM. spicilegus or other distant species.
Key words: mouse, phylogenetic network, introgression, inbred strains
INTRODUCTION
Allele frequency data of many loci are often averaged toobtain genetic distances between closely related populations such as different subspecies of the same species(e.g., Nei, 1987). Admixture may occur among subspecies, but the signature of admixture will eventually disappear by backcrossing of hybrid individuals in the later
generations. Yet the introgression of a small DNA
region from one subspecies to another may remain for a
relatively long evolutionary time. Therefore, comparisonof many gene genealogies of different loci from different
subspecies can tell us a detailed evolutionary history of
their genomic structure.
Edited by Yoko Satta* Corresponding author. E-mail: saitounr@lab.nig.ac.jp
Note: Supplementary materials in this article are at
http://wwwsoc.nii.ac.jp/gsj3/sup/83(1)Liu/

Mouse (Mus musculus) is an appropriate organism todelineate such a detailed history of a genome. The
variation in the genetic background and morphologicalcharacters of wild mice has been well documented (e.g.,
Bonhomme et al., 1984; Moriwaki et al., 1994; Prager etal., 1993; Sage et al., 1993; She et al., 1990). M. musculus
is genetically classified largely into four subspecies, M. m.
domesticus, M. m. musculus, M. m. castaneus, and M. m.
bactrianus (Bonhomme and Guenet, 1989; Sage et al.,
1993; Yonekawa et al. ,1981) with several other minorgroups such as M. m. molossinus and M. m. brevirostrisused in this study. They are found in different
geographic areas of the world. The subspecies M. m.
domesticus is known to be indigenous to west Europe andis also found in America, Australia, and various Atlantic
and Pacific islands (Boursot et al., 1993; Marshall, 1981;
Tichy et al., 1994). M. m. brevirostris is treated as alocal form of M. m. domesticus in this study. M. m.

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Y.-H. LIU et al.

musculus has a native range encompassing east Europe
and east Asia, while M. m. castaneus is found primarily
in southeastern Asia (Bonhomme et al., 1994; Boursot etal., 1993; Prager et al., 1993; Sage et al., 1993). The
subspecies that is currently grouped as M. m. bactrianus
inhabits through Iran to Myanmar harboring heterogeneous forms. M. m. molossinus, known to have originated from the hybrids of M. m. musculus and M. m.
castaneus (Bonhomme et al., 1989; Yonekawa et al.,1988), inhabits Japan (Yonekawa et al., 1981, 1988).
Since this hybrid is mostly musculus origin and a verysmall castaneus counterpart, we treat this group as oneof the local representatives of M. m. musculus in thisstudy. Abe et al. (2004) determined BAC-end sequencesof MSM strain of M. m. molossinus, and found that there
was as high as ca. 1% nucleotide difference between thisstrain and a commonly used laboratory strain, C57BL/6J,
whose genome was derived from mostly M. m. domesticus.
Thus, leaving out M. m. bactrianus, we consider three large
subspecies groups, M. m. domesticus, M. m. musculus, andM. m. castaneus, in this study.
Many genetic markers have been used to investigate
the origin and the radiation of these house mice as
above. There have been studies on chromosomal C-band
patterns (Moriwaki et al., 1990), protein electrophoresis(Bonhomme et al., 1984; Boursot et al., 1989; Miyashita
et al. ,1985), and DNA RFLP (Ferris et al., 1983a, 1983b;
Redi et al., 1990; Suzuki et al., 1986; Yonekawa et al.,1981). Historically, because of the rather conservative
morphology of mice, the definition of subspecies is largely
based on the combinations of allele frequencies at many
nuclear DNA loci (Bonhomme et al., 1984).
The above classification into four subspecies hasreceived good support from the further studies of mtDNA(Boursot et al., 1996; Prager et al., 1998, 1996). However,the studies of Y-chromosome revealed two major Ychromosome lineages whose distributions are apparently
discordant with that of the mtDNA lineages (Bishop etal., 1985; Boissinot and Boursot, 1997). Boissinot andBoursot (1997) suggested that selection has played a rolein the rapid spread of Y-chromosome haplotypes acrosssubspecies. This pattern of shared genetic variants
across subspecies is also observed in several other locisuch as in the class I MHC (Moriwaki et al., 1990) and in
the p53 pseudogene (Ohtsuka et al., 1996), and is
expected to be found in many other nuclear DNA genes.
After the genome sequence of a laboratory inbred strain,
C57BL/6J, was assembled (Mouse Genome Sequencing
Consortium, 2002), there have been number of studies
which indicated complex origin of the laboratory inbred
strain (Wade et al., 2002; Frazer et al., 2004; Zhang et al.,2005). The main focus of these studies has been on themosaic origin of the laboratory inbred mouse and its
relevance to designing QTL mapping and positional
cloning experiments. Recently, Baines and Harr (2007)

have sequenced 6 X-linked and 7 autosomal loci frommultiple population samples of M. musculus. Theirintention was to contrast the diversity pattern of X-linked
and autosomal loci, and they indeed showed that the Xlinked diversity is too large to be explained by a simple
demographic model in some of the populations. Different
from those studies, our purpose is to construct thephylogenies of multiple loci from wild-derived strains andto investigate the clustering pattern for each locus. Also,
we want to obtain a rough idea about the ancestral
population size and migration rates to understand the evolutionary history of this species complex, particularly thefeatures of population subdivision with migration model.
We sequenced about 1 kb regions of 21 nuclear genes
distributed among 16 chromosomes and the control regionof mtDNA from nine mouse strains from three M. musculus
subspecies and one Mus spicilegus strain in the present
study. Takahashi et al. (2004) analyzed these sequencesand detected a positive correlation between the recombination rate and nucleotide diversity within subspecies,
and a negative correlation between that and GST. The
same set of nine strains was also used for the ABO bloodgroup gene studied by Yamamoto et al. (2001). We constructed phylogenetic network for each nuclear DNA
locus, as well as a phylogenetic tree of concatenatedsequences. We also provide rough estimates of theancestral and derived population sizes and migration
rates between M. m. domesticus and M. m. musculus.
Possibility of intersubspecific and interspecific introgressions based on the incongruent gene genealogies isdiscussed.
MATERIALS AND METHODS
Mouse strains The mouse strains used in this study
are listed in Table 1. One old laboratory inbred strain of
M. m. domesticus (C57BL/10J, abbreviated as B10), eightstrains of wild-derived M. musculus (PGN2, BFM/2,
BLG2, NJL, MSM, SWN, CAST/Ei, and HMI), and one
strain of wild-derived Mus spicilegus (ZBN) wereused. The wild-derived strains were captured from different localities over the world (Table 1), and have been
established as inbred strains in the National Institute of
Genetics for more than 20 generations (Koide et al.,2000). All of these strains except C57/10J (B10) arewild-derived and the origin is controlled in contrast to
some “old inbred” lines whose multiple origin is suspected(Bonhomme et al., 1987). Two M. m. musculus strains(BLG2 and NJL) originated near the well-studied hybridzone between M. m. musculus and M. m. domesticus inEurope (reviewed in Sage et al., 1993). The source M. m.
domesticus strains of the DNA sequences from the DDBJ/
EMBL/GenBank International Nucleotide Sequence
Database used in the analyses are listed in Supplementary Table 1.

Mosaic genealogy of mouse genome
Table 1.

Inbred mouse strains used for DNA sequencing in thisstudy

Species and subspecies

Straina

Abbreviation

OriginB10 (C57BL/10J)

D1

Unknown

PGN2

D2

CanadaBFM/2

D3

FranceBLG2

M1

Bulgaria

NJL

M2

Denmark

MSM

M3

Japan

SWN

M4

Korea

CAST/Ei

C1

Thailand

HMI

C2

TaiwanZBN

S

Bulgaria

Mus musculus
domesticus(brevirostris)b
musculus(molossinus)c
castaneus
Mus spicilegus (outgroup)a: All the strains except B10 are wild-derived and maintainedat the National Institute of Genetics, Japan. Details aredescribed in Koide et al. (2000).
b: Treated here as a local form of M. m. domesticus.
c: Originated from hybridization between M. m. musculus
and M. m. castaneus (Bonhomme et al., 1989; Yonekawa
et al., 1988). Treated here as one of the representativesof M. m. musculus.

Table 2.
SymbolGenes sequenced We chose a total of 22 loci for
sequence determination, including 19 autosomal loci, one
X-linked locus, one Y-linked locus, and a part of themitochondrial DNA. We chose autosomal loci fromdifferent chromosomes rather randomly, though some lociare in the same chromosome. The list of the genes
sequenced is shown in Table 2 with the chromosome
location and the accession numbers of the sequences used
to design primers. The sequenced region and the intronexon structure for each gene are shown in Supplementary
Fig. 1.
PCR and sequencing DNA was extracted from theliver tissue of mice by SDS-proteinase-K method(Sambrook et al., 1989). An internal fragment, approximately 1 kb in size, of each of the 21 nuclear genes andthe control region of the mtDNA were sequenced fromnine stains of M. musculus and one strain of M. spicilegus
described above, using the PCR-direct sequencing
method. A hot start-PCR was carried out in 25 μl reaction volume, containing 2.5 μl of 10x Universal Buffer™
(Nippon Gene), 1.5 μl of 25mM MgCl2, 2.5 μl of Gene Amp

The list of the 22 mouse genes analyzed in this study

Name

A. b3GT1
B. b3GT2
C. b3GT3
D. b3GT4
E. BNP
F. CD14
G. Cramp
H. DfyI. FauJ. fisp-12
K. Fut1
L. Fut2
M. Fut4
N. GdX
O. Hox-1.11
P. MECL1
Q. sec1
R. Sox15
S. TNF
T. Tspy
U. Wnt-1β1,3-galatosyltranferase-I
β1,3-galatosyltranferase-II
β1,3-galatosyltranferase-III
GM1/GD1b/GA1 synthase
Brain natriuretic peptide
Monocyte and granulocyte cell surface glycoprotein homolog
Cathelicidin (Cramp) gene
Duffy-like blood group
Cellular homolog of the fox sequence of FBR-MuSV
Growth factor inducible gene
α (1,2)fucosyltransferase
α (1,2)fucosyltransferase
α (1,3)fucosyltransferase
Housekeeping protein DXS254E
Homeobox protein 1.11
Proteasome subunit MECL1
α (1,2)fucosyltransferase
HMG-box transcription factor 15
Tumor necrosis factor
Testis-specific Y-encoded protein
Mammary proto-oncogene

mtDNA

Mitochondrial DNA

a79

Chromosome

Accession

SourceLength (bp)

Location

NumberaStrainb (DB)Sequencedc

2
1
3
17
4
18
9
1
19
10
7
7
9
X
6
8
7
11
17
Y
15

AF029790
AF029791
AF029792
AF082504
D82049
M34510AF035680
AF016697
L33715
M70641
Y09883
AF064792
D63380
J04761
M93148
D85562
Y09882
AB014474
M20155
AJ001379
K02593129/svj
129/svj
129/svj

917
1228
996
1112
1112
1254
987
1509
1241
1156
1134
963
1170
1013
907
652
1107
1340
1201
1284
1044

J01420LA9 or
111-OB3(L-cell lines)–d129/sv
BALB/c129/svj
B6CBA/F1
BALB/c–d
ICR
ICR
129/sv
BALB/cICR
BALB/cICR
129–d
C57BL/6
BALB/c975: Accession numbers of the sequences used to design primers for PCR.
: Source strains of the sequences used to design primers for PCR. Each of these strains are represented as “(DB)” in Figs. 3,4, and 5.
c: Size of the sequenced fragment.
d: Information not provided.
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Y.-H. LIU et al.

dNTP Mix™ (20 mM), 0.5U of AmpliTaq Gold™ (Applied
Biosystems), 12.5 pmol of primer, and 5–20 ng genomic
DNA. Annealing temperature was between 50°C and
65°C, depending on the primers. PCR products were
purified by MicroSpin columns S-300HR™ (Amersham
Pharmacia Biotech). Sequencing reactions were performed using the Big Dye Terminal Cycle Sequencing
Ready Reaction Kit™, and DNA sequence data wereobtained by using ABI PRISM310™ and ABI PRISM
377™ DNA automatic sequencer (Applied Biosystems).
PCR primers used in this study are listed in Supplementary
Table 1.
Sequence alignment and phylogenetic analyses
CLUSTAL W version 1.6 (Thompson et al., 1994) wasused for multiple sequence alignment. The neighborjoining method (Saitou and Nei. 1987) was used for constructing phylogenetic trees. Phylogenetic networks (seeBandelt, 1994) were constructed manually, as done forthe primate ABO blood group gene sequences (Saitou andYamamoto, 1997). Alignment gaps were not used fortree and network construction. The phylogenetic networks have the advantage of showing all the possible
pathways of nucleotide changes between sequences, thus,
visualize more sequence information about the discordantpartition among nucleotide positions compared to the phylogenic trees (Saitou, 1996; Saitou and Yamamoto, 1997).
Estimation of demographic parameters The population genetic parameters (ancestral and derived population sizes, population split time, and migration rates)
included in the “isolation with migration model” was estimated using the method suggested by Hey and Nielsen(2007). The computer program “IMa”, provided by theseauthors were utilized to conduct the Marcov chain Monte
Carlo (MCMC) simulations. First, 10,000 genealogies
were generated from the multilocus sequence data after

the initial burn-in period of 100,000 steps. Then, thejoint parameter estimate was conducted from these saved
genealogies. Convergence by the Markov chain simulations was assessed by monitoring multiple independent
chains at different starting points and by assessing the
autocorrelation of the parameter values over the course of
the runs. Each locus was assigned an inheritance scalar
to adjust for its relative effective population size: 1.0 for
autosomal loci, 0.75 for X-linked and 0.25 for Y-linked loci.
RESULTS
Determined Nucleotide Sequences A total of approximately 243 kb sequences were determined from 22 loci ofnine M. musculus strains and one M. spicilegus strain.
There were no heterozygous sites observed in any of theloci from each inbred strain. DDBJ/EMBL/GenBank
International Nucleotide Sequence Database accession
numbers for those sequences are AB039044-AB039263.
Phylogenetic trees based on mitochondrial andnuclear DNA sequences The 975 bp of the control
region and its flanking tRNA gene of mouse mtDNA (seeSupplementary Fig. 1V) were sequenced. The neighborjoining tree of this locus from sequences of the nine M.
musculus strains and a sequence from the nucleotide
sequence database (designated as “DB”), rooted by an outgroup sequence from M. spicilegus, is shown in Fig. 1.
The strains that belong to the same subspecies cluster
together by branches with high bootstrap values (> 90%)
except for one strain of M. m. musculus (NJL), which clustered more closely with M. m. domesticus strains thanwith themselves (Fig. 1). Comparing the above sequenceswith those in Prager et al. (1993, 1996) as described indetail below, the interpretation of this exception would bethat the sequences of BLG2 (M1), MSM (M3), and SWN(M4) represent the authentic M. m. musculus lineage andFig. 1. The neighbor-joining tree constructed from mtDNA sequences of nine inbred strains fromthree Mus musculus subspecies. One sequence from the database (J01420) designated as “DB”
is also included as a M. m. domesticus sequence. The tree is rooted by Mus spicilegus sequence(ZBN). The numbers on the interior branches are bootstrap probabilities (%) based on 1000
bootstrap resampling (only those higher than 90% are shown). The scale bar indicates thenumber of nucleotide substitutions per site.

Mosaic genealogy of mouse genomethat of NJL (M2) represents an domesticus mtDNA introgressed at the hybrid zone. This mtDNA status of northern Denmark mice has been described earlier (Ferris etal., 1983a; Gyllensten and Wilson, 1987; Vanlerberghe etal., 1988).
Six of the nine mtDNA sequences determined in thisstudy are identical to some known haplotypes determinedby Prager et al. (1993, 1996). The sequences from B10(D1) and PGN2 (D2) are identical to M. m. domesticus
mtDNA type 1 (U47430) and type 2 (U47431), respectively.
MSM and SWN are both identical to M. m. musculus
mtDNA type 34 (U47531). CAST/Ei (C1) was identical to
M. m. castaneus mtDNA type 1 (U47534), and NJL (M2)
was identical to M. m. domesticus mtDNA type 27(U47455). The 75-bp tandem repeat reported to be present
in some strains of M. m. musculus (Prager et al., 1996) was
observed in strain BLG2 (M1) but not in other strains.
We constructed the neighbor-joining tree for the concatenated sequence of all the 21 nuclear loci (Fig. 2). Itsclustering pattern of the three subspecies is somewhat
different from that for mtDNA tree (Fig. 1). All four M.
m. musculus strains (M1–M4) cluster together with highbootstrap values in contrast to the mtDNA pattern, while
two M. m. castaneus strains (C1 and C2) did not form acluster.
Clustering of strains belonging to the same subspecies Figure 3 shows the phylogenetic network of eachnuclear locus. Inconsistent clustering patterns are commonly seen among these networks in Fig. 3. The twostrains of M. m. castaneus (C1 and C2) do not cluster
together in the networks of b3GT3, Dfy, Fau, and TNF(Figs. 3C, 3H, 3I, and 3S), while their sequences wereidentical to each other in six other loci, b3GT1, CD14,

81

fisp-12, Fut4, Hox-1.11, and Tspy (Figs. 3A, 3F, 3J, 3M,
3O, and 3T). One M. m. musculus strain (M2) thatrevealed a musculus to domesticus introgression event in
the mtDNA clustered together with other M. m. musculus
strains in many of the nuclear loci. The same clustering
pattern as that of mtDNA for the M2 strain is observed
only at the Fut1 locus (Fig. 3K). Hox-1.11 sequenceswere identical in all strains except for M2, which is different at one nucleotide site (Fig. 3O). The BNP and sec1loci show complicated networks suggesting past recombination events within and among subspecies (Figs. 3E and
3Q). Hence these networks indicate that the mouse
genome is highly heterogeneous in terms of subspecies
genealogy.
Partial sequences of Tspy, a Y-chromosome gene that has
been determined as a pseudogene in mouse (Mazeyrat andMitchell, 1998), were obtained from all the 10 strains (Fig.
3T). There were four Y-chromosome haplotypes depictedfrom this locus in these strains. The two major Ychromosome lineages in Boissinot and Boursot (1997), one
found in M. m. domesticus and the other found in M. m.
musculus and M. m. castaneus, are not apparent from thepresent study. The haplotype of the ZBN, a M. spicilegus
strain, was identical to one of the four types present in M.
musculus strains. A similar pattern was seen in othermurine species at this locus (Schubert et al., 2000).
Most of the laboratory mice strains are considered tohave originated from domesticus strains. If we include
sequences retrieved from database (designated as DB in
Fig. 3; see Table 1 for specific strain names used) todomesticus subspecies, most of the loci showed clusteringof the strains within this locus, except for two loci. The
DB sequence is one nucleotide different from the threeidentical domesticus sequences (D1–D3) for the Fut2

Fig. 2. The neighbor-joining tree constructed from the concatenated sequence of all the 21
nuclear loci of nine inbred strains from three Mus musculus subspecies, rooted by Mus spicilegus
sequence (ZBN). The sequences retrieved from the database described in Table 2 are also
concatenated as M. m. domesticus sequences. All the notations are the same as in Fig. 1.

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(continued)

Mosaic genealogy of mouse genome

83

Fig. 3. The phylogenetic networks of the 21 nuclear loci in Mus musculus. The full circles denote sequences of each inbred mousestrain from three subspecies. Sequences from one Mus spicilegus strain (S) are also included in the networks. The numbers on theedges show variant nucleotide positions responsible for corresponding splits (see multiple alignment data presented in our website fornucleotide positions). The underlined numbers indicate positions of the non-synonymous nucleotide changes. The numbers indicatedby * in the BNP gene is interpreted as two independent substitution events. “DB” indicates the sequence of unknown M. m. domesticus
strain in the DDBJ/EMBL/GenBank database (see Table 2).

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Y.-H. LIU et al.

locus, and the DB sequence is identical with one ofmusculus strain (M2) for the locus sec1 (Fig. 3Q). This
mosaic nature of the inbred laboratory mouse strainsobserved in this study was also reported by other authors(Wade et al., 2002; Frazer et al., 2004; Zhang et al., 2005).
One strain (S or ZBN; see Table 1) of M. spicilegus wasused as outgroup in the present study. We expect thatthe branch leading to strain S is much longer than thoseconnecting sequences of M. musculus strains. Many lociin fact showed this expected pattern (see Fig. 3). However,some loci showed unexpected patterns between M.
musculus and M. spicilegus. The b3GT3 and Fut1 hadvery short branches leading to strain S (Figs. 3C and 3K),
while sequences of strain S falled within the variation of
M. musculus sequences in b3GT1 and Tspy (Figs. 3A and
3T). The sequence of strain S of Hox-1.11 falls within
the variation of M. musculus sequences (Fig. 3O), though
the pattern may be due to very low evolutionary rate ofthis locus.
Strain M1 (BLG of M. m. musculus) exhibits a clear
anomaly at the Fut4 locus, i.e. considerably larger number (35) of nucleotide changes accumulated than that (4)in the outgroup sequence S (Fig. 3M). The remaining
three strains (M2–M4) of the musculus subspecies are
similar with each other, and 5 other strains of M.
musculus also cluster with these musculus subspecies
strains. Various mechanisms that can explain this pattern will be discussed in Discussion.
We observed yet another unusual pattern in the Dfy
locus (Fig. 3H). The phylogenetic network of this locus
shows a large divergence within M. musculus. Seventeen
nucleotide differences divide the ten strains into two clusters, one of which contains sequences of C2, D1, M1, M2,
M3, and M4, while the other contains those of C1, D2, D3
and DB. Possible mechanisms that can explain this pattern will be discussed in Discussion.

tion genetic parameters (ancestral and derived population
sizes, population split time, and migration rates) includedin the “isolation with migration model” (Hey and Nielsen,
2007). This model captures demographic phenomenathat occur when one ancestral population splits into twodescendant populations. The three populations could
differ in size, but the model does not implement population size change. Gene exchanges are allowed during thetime since population split.
We used 4 strains each from two subspecies, M. m.
musculus and M. m. domesticus, for the analyses. A
total of concatenated introns from 9 sequenced genes(Cramp, Fau, fisp12, Gdx, Hox-1.11, MECL1, Sox15,Tspy, Wnt-1) were subjected to the multilocus analyses of
the joint parameter estimates using MCMC simulations.
Note that since Hey and Nielsen (2007)’s model assumes
no recombination within loci, we had excluded introns
that showed reticulations in their phylogenetic networks.
Repeated runs of the IMa computer program revealed
unambiguous marginal posterior probability distributionsof the parameters except for the population split time, t(Supplemental Fig. 2). The peak and the range of theparameters are summarized in Table 3. The output ofthe program gives estimated parameters scaled by per
locus mutation rate. We used the mutation rate u = 3.94
× 10–7 per locus per generation calculated from the average divergence between M. musculus and M. spicilegus of
the nine loci used in the analyses.
The 90% Highest Posterior Density (HPD) intervals of
the parameter estimates are large due to complex lineage
sorting and limited data (Table 3). However, the locations of peaks in the marginal posterior probability distributions in Table 3 suggest that the ancestral population
size (NA) of M. m. domesticus and M. m. musculus maybe~3–8 fold larger than the population sizes of the current
subspecies (N1 and N2). The range of population migration rates (4N1m1 and 4N2m2) could not be obtained fromthe analyses, however, 90% HPDs of per generation
migration rates (m1 and m2) exclude zero.

Parameter estimation In order to obtain quantitative
measures of the level of admixture, we estimated popula-

Table 3

Estimates of the demographic parameters obtained by the method proposed by Hey and Nielsen (2007)

Parametersa

N1

N2

NA

4N1m1

4N2m2

td

7.8 × 104

3.6 × 104

3.1 × 105

0.017

0.119

–

Lower 90% HPDc

1.9 × 104

7.6 × 103

5.1 × 103–c

4.6 × 10

1.7 × 10

3.1 × 10–

Peakb

Upper 90% HPD
a

5

5

6

: N1, N2, and NA are effective population sizes of current M. m. domesticus, M. m. musculus, and their ancestral
population, respectively. 4N1m1 and 4N2m2 are the population migration rates of M. m. domesticus and M.
m. musculus, respectively.
b: Locations of peaks in the marginal posterior probability distributions (Supplementary Fig. 2).
c: Highest Posterior Density (HPD) intervals are the shortest spans that contain 90% of the posterior probability.
d: Unambiguous marginal posterior probability distribution could not be obtained for the population split time, t(Supplemental Fig. 2).

Mosaic genealogy of mouse genome
DISCUSSION
A High level of mice subspecies admixture The mosaic genealogy of genes among subspecies in the nuclear
DNA could have occurred via either or both of the two factors besides the possibility of any selective force
involved. First is the large ancestral population sizethat harbored many variable sites. A major proportionof the genome admixture could have happened in theancestral population before the divergence of thesubspecies. A large ancestral population and a shortdivergence time could produce such incomplete lineage
sorting, i.e. mosaic genealogy.
The second possible factor is the vague reproductive
barrier among the current subspecies. In mice, despite
capable hybridization in captivity, the reproductive barrier among subspecies is documented well in the hybridzone studies (reviewed in Sage et al., 1993), which may be
attributed to the potential fitness reduction of the hybrids
such as the increased loads of intestinal parasites (Moulia
et al.. 1993; Sage et al., 1986). However, the informationis scarce in other regions of the world. It is of our interest to know to what extent this barrier has affected thegenetic structure of the current M. musculus species
genome.
Phylogenic networks obtained from 21 nuclear DNA
regions of the M. musculus genome (Fig. 3) suggest thatthe genetic exchange at the subspecies level is fairly common in this species. Our data confirms the existence ofimperfect separation of the peripheral subspecies according to their nuclear genes and the mosaicism in this species complex implicated earlier (Bonhomme et al., 1994;
Wade et al., 2002; Frazer et al., 2004; Zhang et al.,2005). Those networks of the loci showed that thestrains of the same subspecies, especially those of M. m.
castaneus and M. m. domesticus, do not cluster together
closely in some genes (Fig. 3, see also Result).
Estimated parameters of population size andmigration In addition to the observation of the clustering pattern in the phylogenetic networks (Fig. 3), we
obtained a rough estimates of the demographic parameters by the method proposed by Hey and Nielsen(2007). The method is useful for analyzing a pair ofclosely related populations or species such as subspecies
in our study. The estimated parameters in Table 3 indicate large ancestral population size with frequent migration, although the ranges of estimates are large.
Recently, Ideraabdullah et al. (2004) showed that theextent of ancient polymorphism is substantial among thewild-derived inbred strains of M. musculus. Thus, themosaic nature of the M. musculus genome is likely to be
due to both ancestral polymorphism and migration amongsubspecies.
Eyre-Walker et al. (2002) has estimated the effective

85

population size (Ne) of M. m. domesticus to be 1.6 × 105 or
2.9 × 105 depending on different divergence time estimates between M. m. domesticus and M. caroli. Bainesand Harr (2007) estimated Ne of Iranian population of M.
m. domesticus to be 4.4 × 105 – 7.9 × 105. Those Ne estimates are not directly comparable to our estimates of N1
and N2 based on the “isolation with migration model”(Hey and Nielsen, 2007), because in this model, implementation of ancestral polymorphism and migration
allows N1 and N2 to take lower values. Nevertheless, ourpopulation size estimates maybe slightly under estimatedbecause we intentionally chose loci that had no reticulation in the phylogenetic network to avoid recombination
within loci. This may have caused the sampled genealogies to coalesce faster than other average genomic regions(Hey and Nielsen, 2004). Indeed the loci we chose had
lower average nucleotide diversity compared to the average silent π of the 19 autosomal loci used in this study(Takahashi et al., 2004). Nucleotide diversity, divergence between M. musculus and M. spicilegus, and population divergence (GST) of those 19 loci are listed in
Takahashi et al. (2004). It should also be noted that thecurrent estimate of NA using only two subspecies maybe
smaller than the ancestral population size of the whole M.
musculus subspecies. In any case, these population size
estimates need to be treated with caution because of thesmall sample size.
Unique position of the BLG2 strain in the Fut4
locus We observed that the BLG2 (M1) strain of the M.
m. musculus was very different from other strains in the
Fut4 locus (Fig. 3M). There may be four possible explanations for the unique position of this strain. First is theacceleration of the evolutionary rate due to directional
natural selection or loss of function. The second possibility is the gene conversion from other paralogous
genes. The third is introgression of a distant species, farapart from M. speciligus, used in this study as an outgroup species. The fourth one is long-term coexistence of
two distinct lineages through balancing selection.
We predict a high ratio of non-synonymous to synonymous substitutions in the BLG2 lineage under the firstpossibility. The MK test (McDonald and Kreitman,
1991) was performed to investigate whether there had
been particularly strong positive selection or relaxation of
selection on the M1 lineage. In this study, the test wasapplied to the intraspecific data. Instead of comparing asequence from another species versus multiple sequencesfrom one species in the ordinary MK test, we compared
the M1 sequence versus the remaining conspecificsequences of the Fut4 locus. There are 26 non-synonymous and 14 synonymous substitutions that are notshared between M1 and any of the other M. musculus
strains, whereas there are 12 non-synonymous and foursynonymous sites that are variable within other M.

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Y.-H. LIU et al.

musculus strains. Application of the MK test showedthat there is no particular acceleration in amino acidsubstitutions over synonymous substitutions in the M1
lineage compared to the rate within other lineages(Fisher’s exact test; p > 0.10).
To examine the second possibility, we conducted a
BLAST search (Altschul et al., 1990) of the latest DDBJ/
EMBL/GenBank International Nucleotide Sequence
Database using the M1 Fut4 sequence as the query.
However, we found only the mouse Fut4 gene itself, andno other regions of the completely sequenced mouse
genome (Mouse Genome Sequencing Consortium, 2002)
can be aligned with the M1 Fut4. Therefore, there seems
to exist no gene paralogous to the Fut4 gene.
Therefore, we are left with the last two possibilities:
introgression or balancing selection. Unfortunately,
however, there is no way to test these hypotheses at thismoment. The nucleotide sequence of the donor species of
introgression should be investigated in the future. Whenbalancing selection operates, two allelic lineages are
expected to coexist, as observed for the Dfy locus (see Fig.
3H), as we discuss below. Therefore, we are inclined tochoose the introgression hypothesis for this locus, because
only one strain (M1) showed anomaly in the Fut4 locus.
Existence of the two divergent lineages in the Dfy
locus The mouse Dfy gene, homolog of human FY (genefor Duffy blood group), is a member of the superfamily of
chemokine receptors (Luo et al., 1997). Two distinct alleles exist among the 10 mice strains, and both variants arepresent in at least two of the three subspecies. (Fig.
3H). We can consider three nonexclusive possibilities
responsible for this peculiar pattern of Dfy sequences; (1)they have been maintained by some kind of a balancing
selection through the divergence of the subspecies, (2)introgression of alleles from one subspecies to other, and(3) the ancestral polymorphism is kept to present-day
populations. If balancing selection is quite strong, bothlineages may coexist in many local populations of all thesubspecies. This can be examined in future. Possibilities(2) and (3) are not easy to be distinguish, for they are notexclusive.
Introgression between M. musculus and other species Our data suggest that even the reproductive barrier between M. musculus and other species is incomplete.
A rough estimation of the divergence time between M.
musculus and M. spicilegus without considering the complicated lineage sorting becomes about 2.4 Myr, using themutation rate λ = 4.8 × 10–9 per site per year in intronsof rodent lineages (Li et al., 1996). The divergence time(T) is obtained under the assumption of rate constancy,
where the evolutionary distance d = 2λT. The average
number of synonymous substitutions per site (ds; Ina,
1995) between most distant pairs of strains in the two

species was used as d. The divergence time estimate
between M1 (BLG2) and M3 (MSM) in Fut4 is about 5.7
Myr, which is more than two times larger than the estimated musculus – spicilegus divergence time.
Difference in genetic distances between M. musculus
and M. spicilegus also indicates the recent introgression
from an outgroup species. Two loci show very shortbranches leading to an outgroup S (Figs. 3C and 3K), andthe sequence from S falls within the variation of M.
musculus sequences in three loci (Figs. 3A, 3O, and
3T). The divergence time between M. musculus and M.
spicilegus is estimated to be about 1.1Myr (She et al.,1990) or larger (Moriwaki et al., 1994; see also our estimate above). From these estimates, although we needagain to consider the effect of ancestral polymorphism,
the observation that about 25% of the loci (five out of 21)
show the above pattern seems substantial, and indicatesthat the reproductive barrier between even different species of genus Mus is lower than one might have imagined.
In conclusion, an unnegligibly high level of subspecies
admixture and the mosaic pattern of the genome were
found from M. musculus by comparing 21 nuclear genegenealogies. This pattern is likely to be formed by ancestral polymorphism and frequent migration. Uniquegenealogy patterns of some loci could be resulted fromintrogression from other species and/or balancing
selection. The nucleotide sequences of multiple loci sampled from many genomic regions in this study provide
informative genealogical data for obtaining complicatedpicture of the evolutionary history of this species.
Credits. This study was planned by N. Saitou. All themouse samples were provided by T. Koide, T. Shiroishi,
and K. Moriwaki. Sequencing was done by Y.-H. Liu for
18 loci and by T. Kitano for 4 loci. Initial sequence
analyses were conducted by Y.-H. Liu and later extended
by A. Takahashi. Manuscripts were written by Y.-H. Liu,
A. Takahashi, and N. Saitou.
This study was partially supported by grants-in-aid for scientific studies from the Ministry of Education, Science, Sport, andCulture, Japan, to N.S., the COE foreign visiting researcher fellowship to Y.H.L, and JSPS Postdoctoral Fellowship to A.T. We
appreciate Ms. H. Kobayakawa for her help in the laboratory, andDrs. R. Noda and K. Kryukov for their help on the data analyses.

REFERENCES
Abe, K., Noguchi, H., Tagawa, K., Yuzuriha, M., Toyoda, A.,
Kojima, T., Ezawa, K., Saitou, N., Hattori, M., Sakaki, Y.,
Moriwaki, K., and Shiroishi, T. (2004) Contribution of Asianmouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC end
sequence-SNP analysis. Genome Res. 14, 2239–2247.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman,
D. J. (1990) Basic local alignment search tool. J. Mol. Biol.
215, 403–410.

Mosaic genealogy of mouse genome
Baines, J. F., and Harr, B. (2007) Reduced X-linked diversity inderived populations of house mice. Genetics 175, 1911–
1921.
Bandelt, H. J. (1994) Phylogenetic networks. Verh.
Naturewiss. Ver. Hamburg. (NF). 34, 51–71.
Bishop, C. E., Boursot, P., Baron, B., Bonhomme, F., and Hatat,
D. (1985) Most classical Mus musculus domesticus laboratory mouse strains carry a Mus musculus musculus Y
chromosome. Nature 315, 70–72.
Boissinot, S., and Boursot, P. (1997) Discordant phylogeographic
patterns between the Y chromosome and mitochondrial
DNA in the house mouse: selection on the Y chromosome?
Genetics 146, 1019–1034.
Bonhomme, F., Anand, R., Darviche, D., Din, W., and Boursot,
P. (1994) The house mouse as a ring species? In: Genetics in
Wild Mice (eds.: K. Moriwaki, T. Shiroishi, and H.
Yonekawa) pp. 13–23. Japan Sci. Soc. Press, Tokyo/S
Karger, Basel.
Bonhomme, F., Catalan, J., Britton-Davidian, J., Chapman, V.
M., Moriwaki, K., Nevo, E., and Thaler, L. (1984) Biochemical
diversity and evolution in the genus Mus. Biochem. Genet.
22, 275–303.
Bonhomme, F., and Guenet, J.-L. (1989) The wild house mouseand its relatives. In: Genetic Variants and Strains of theLaboratory Mouse (eds.: M. F. Lyon, and A. G. Searle), pp.
649–662. Gustav Fischer Verlag, Stuttgart.
Bonhomme, F., Guenet, J.-L., Dod, B., Moriwaki, K., andBulfield, G. (1987) The polyphyletic origin of laboratory
inbred mice and their rate of evolution. Biol. J. Linnean
Soc. 30, 51–58.
Bonhomme, F., Miyashita, N., Boursot, P., Catalan, J., andMoriwaki, K. (1989) Genetical variation and polyphyletic
origin in Japanese Mus musculus. Heredity 63, 299–308.
Boursot, P., Auffray, J.-C., Britton-Davidian, J., and Bonhomme,
F. (1993) The Evolution of house mice. Annu. Rev. Ecol.
Syst. 24, 119–152.
Boursot, P., Bonhomme, F., Catalan, J., and Moriwaki, K. (1989)
Variations of a Y chromosome repeated sequence across subspecies of Mus musculus. Heredity 63, 289–297.
Boursot, P., Din, W., Anand, R., Darviche, D., Dod, B., Von
Deimling, F., Tawlar, G. P., and Bonhomme, F. (1996) Origin
and radiation of the house mouse: mitochondrial DNA
phylogeny. J. Evol. Biol. 9, 391–415.
Eyre-Walker, A., Keightley, P. D., Smith, N. G. C., and Gaffney,D. (2002) Quantifying the slightly deleterious mutation
model of molecular evolution. Mol. Biol. Evol. 19, 2142–
2149.
Ferris, S. D., Sage, R. D., Huang, C. M., Nielsen, J. T., Ritte, U.,
and Wilson, A. C. (1983a) Flow of mitochondrial DNA
accross a species boundary. Proc. Natl. Acad. Sci. USA 80,
2290–2294.
Ferris, S. D., Sage, R. D., Prager, E. M., Ritte, U., and Wilson,
A. C. (1983b) Mitochondrial DNA evolution in mice.
Genetics 105, 681–721.
Frazer, K. A., Wade, C. M., Hinds, D. A., Patil, N., Cox, D. R.
and Daly, M. J. (2004) Segmental phylogenetic relationships
of inbred mouse strains revealed by fine-scale analysis ofsequence variation across 4.6Mb of mouse genome. Genome
Res. 14, 1493–1500.
Gyllensten, U., and Wilson, A. C. (1987) Interspecific DNA
transfer and the colonization of Scandinavia by mice. Gen.
Res. 49, 25–29.
Hey, J., and Nielsen, R. (2004) Multilocus methods for
estimating population sizes, migration rates and divergencetime, with applications to the divergence of Drosophila

87

pseudoobscura and D. persimilis. Genetics 167, 747–760.
Hey, J., and Nielsen, R. (2007) Integration within Felsensteinequation for improved Markov chain Monte Carlo methodsin population genetics. Proc. Natl. Acad. Sci. USA 104,
2785–2790.
Ideraabdullah, F. Y., de la Casa-Esperon, E., Bell, T. A.,
Detwiler, D. A., Magnuson, T., Sapienza, C., and de Villena,
F. P.-M. (2004) Genetic and haplotype diversity among wildderived mouse inbred strains. Genome Res. 14, 1880–
1887.
Ina, Y. (1995) New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J. Mol. Evol.
40, 190–226.
Koide, T., Moriwaki, K., Ikeda, K., Niki, H., and Shiroishi, T.
(2000) Multi-phenotype behavioral characterization of
inbred strains derived from wild stocks of Mus musculus.
Mamm. Genome 11, 664–670.
Li, W. H., Ellsworth, D. L., Krushkal, J., Chang, B. H., andHewett-Emmett, D. (1996) Rates of nucleotide substitution
in primates and rodents and the generation-time effecthypothesis. Mol. Phylogenet. Evol. 5, 182–187.
Luo, H., Chaudhuri, A., Johnson, K. R., Neote, K., Zbrzezna, V.,
He, Y., and Pogo, A. O. (1997) Cloning, characterization, andmapping of a murine promiscuous chemokine receptor gene:
homolog of the human Duffy gene. Genome Res. 7, 932–941.
Marshall, J. T. (1981) Taxonomy. In: The Mouse in Biomedical
Research (eds.: H. L. Forter, H. J. D. Small, and J. G. Fox),
pp. 17–26. Academic Press, New York.
Mazeyrat, S., and Mitchell, M. J. (1998) Rodent Y chromosome
TSPY gene is functional in rat and non-functional in mouse.
Hum. Mol. Genet. 7, 557–562.
McDonald, J. H., and Kreitman, M. (1991) Adaptive protein
evolution at the Adh locus in Drosophila. Nature 354, 114–
116.
Miyashita, N., Moriwaki, K., Minezawa, M., Yonekawa, H.,
Bonhomme, F., Migita, S., Yu, Z. C., Lu, D. Y., Cho, W. S.,
and Thohari, M. (1985) Allelic constitution of the hemoglobin
beta chain in wild populations of the house mouse Mus
musculus. Biochem. Genet. 23, 975–986.
Moriwaki, K., Shiroishi, T., and Yonekawa, H. (1994) Genetics in
Wild Mice. Jpn. Sci. Soc. Press, Tokyo/S Karger, Basel.
Moriwaki, K., Sagai, T., Shiroishi, T., Bonhomme, F., Chenghuai,W., Xinquao, H., Meilei, J., and Zhengan, W. (1990) Mouse
subspecies differentiation and H-2 polymorphism. Biol. J.
Linnean Soc. 41, 125–139
Moulia, C., le Brun, N., Dallas, J., Orth, A., and Renaud, F.
(1993) Experimental evidence of genetic determinism inhigh susceptibility to intestinal pinworm infection in mice: ahybrid zone model. Parasitol. 106, 387–393.
Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature
420, 520–562.
Nei, M. (1987) Molecular Evolutionary Genetics. Columbia
University Press, New York.
Ohtsuka, H., Oyanagi, M., Mafune, Y., Miyashita, N., Shiroishi, T.,
Moriwaki, K., Kominami, R., and Saitou, N. (1996) The
presence/absence polymorphism and evolution of the p53
pseudogene in the genus Mus. Mol. Phylogenet. Evol. 5, 548–
556.
Prager, E. M., Orrego, C., and Sage, R. D. (1998) Genetic variation and phylogeography of central Asian and other house
mice, including a major new mitochondrial lineage in
Yemen. Genetics 150, 835–861.
Prager, E. M., Sage, R. D., Gyllensten, U., Kelley, T., W., Hübner,
R., Jones, C. S., Noble, L., Searle, J. B., and Wilson, A. C.

88

Y.-H. LIU et al.

(1993) Mitochondrial DNA sequence diversity and the colonization of Scandinavia by house mice from East Holstein.
Biol. J. Linnean Soc. 50, 85–122.
Prager, E. M., Tichy, H., and Sage, R. D. (1996) Mitochondrial
DNA sequence variation in the eastern house mouse Mus
musculus: comparison with other house mice and report of a
75-bp tandem repeat. Genetics 143, 427–446.
Redi, C. A., Garagna, S., Della, Valle, G., Bottiroli, G., Dell’Orto,
P., Viale, G., Peverali, F. A., Raimondi, E., and Forejt, J.
(1990) Differences in the organization and chromosomal
allocation of satellite DNA between the European long tailed
house mice Mus domesticus and Mus musculus. Chromosoma.
99, 11–17.
Sage, R. D., Atchley, W. R., and Ernesto, C. (1993) House miceas models in systematic biology. Syst. Biol. 42, 523–561.
Sage, R. D., Whitney, J. B. R., and Wilson, A. C. (1986) Genetic
analysis of a hybrid zone between domesticus and musculus
mice (Mus musculus complex): hemoglobin polymorphisms.
Curr. Top. Microbiol. Immunol. 127, 75–85.
Saitou, N. (1996) Reconstruction of gene trees from sequence
data. Methods Enzymol. 266, 427–449.
Saitou, N., and Nei, M. (1987) The neighbor-joining method: a
new method for reconstructing phylogenetic trees. Mol. Biol.
Evol. 4, 406–425.
Saitou, N., and Yamam oto, F. (1997) Evolution of primate ABO
blood group genes and their homologous genes. Mol. Biol.
Evol. 14, 399–411.
Sambrook, J., Fritisch, E. F., and Maniatis, T. (1989) Molecular
Cloning: a Laboratory Manual. Cold Spring Habor Laboratory
Press, Cold Spring Harbor, NY.
Schubert, S., Dechend, F., Skawran, B., Krawczak, M., andSchmidtke, J. (2000) Molecular evolution of the murine tspy
genes. Cytogenet. Cell Genet. 91, 239–242.
She, J. X., Bonhomme, F., Boursot, P., Thaler, L., and Catzeflis, F.
(1990) Molecular phylogenies in the genus Mus: Comparative
analysis of electrophoretic, scnDNA hybridization, and
mtDNA RFLP data. Biol. J. Linnean Soc. 41, 83–103.
Suzuki, H., Miyashita, N., Moriwaki, K., Kominami, R.,
Muramatsu, M., Kanehisa, T., Bonhomme, F., Petras, M. L.,
Yu, Z. C., and Lu, D. Y. (1986) Evolutionary implication ofheterogeneity of the nontranscribed spacer region of riboso-

mal DNA repeating units in various subspecies of Mus
musculus. Mol. Biol. Evol. 3, 126–137.
Takahashi, A., Liu, Y.-H., and Saitou, N. (2004) Genetic variation versus recombination rate in a structured population of
mice. Mol. Biol. Evol. 21, 404–409.
Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994)
CLUSTAL W: improving the sensitivity of progressive
multiple sequence alignment through sequence weighting,position-specific gap penalties and weight matrix choice.
Nucleic Acids Res. 22, 4673–4680.
Tichy, H., Zaleska-Rutczynska, Z., O’Huigin, C., Figueroa, F.,
and Klein, J. (1994) Origin of the North American house
mouse. Foli. Biola. (Praha) 40, 483–496.
Vanlerberghe, F., Boursot, P., Nielsen, J. T., and Bonhomme, F.
(1988) A steep cline for mitochondrial DNA in Danish mice.
Gen. Res. 52, 185–193.
Wade, C. M., Kulbokas, III E. J., Kirby, A. W., Zody, M. C.,
Mullikin, J. C., Lander, E. S., Lindblad-Toh, K., and Daly,
M. J. (2002) The mosaic structure of variation in the laboratory mouse genome. Nature 420, 574–578.
Yamamoto, M., Lin, X.-H., Kominato, Y., Hata, Y., Noda, R.,
Saitou, N., and Yamamoto, F. (2001) Murine equivalent of
the human histo-blood group ABO gene is a cis-AB gene andencodes a glycosyltransferase with both A and B transferase
activity. J. Biol. Chem. 276, 13701–13708.
Yonekawa, H., Moriwaki, K., Gotoh, O., Hayashi, J. I.,
Watanabe, J., Miyashita, N., Petras, M. L., and Tagashira,Y. (1981) Evolutionary relationships among five subspeciesof Mus musculus based on restriction enzyme cleavage patterns of mitochondrial DNA. Genetics 98, 1–16.
Yonekawa, H., Moriwaki, K., Gotoh, O., Miyashita, N.,
Matsushima, Y., Shi, L. M., Cho, W. S., Zhen, X. L., andTagashira, Y. (1988) Hybrid origin of Japanese mice “Musmusculus molossinus”: evidence from restriction analysis of
mitochondrial DNA. Mol. Biol. Evol. 5, 63–78.
Zhang, J., Hunter, K. W., Gandolph, M., Rowe, W. L., Finney, R.
P., Kelley, J. M., Edmonson, M., and Buetow, K. H. (2005) A
high-resolution multistrain haplotype analysis of laboratory
mouse genome reveals three distinctive genetic variation
patterns. Genome Res. 15, 241–249.