Y Chromosome Intron Data

We examined 39 pygmy shrews for 2,939 bp (including indels) of concatenated Y introns (DBY1: 1098 bp, DBY3: 596 bp, DBY7: 441 bp, UTY11: 804 bp), which resulted in 23 unique haplotypes (see Table 1 and Fig. 2). Sixty polymorphic sites

Table 2 Nucleotide diversity (p ± SD) of and number of individuals (n) in each mtDNA and concatenated Y chromosomal intron lineage

Lineage n mtDNA

Y chromosome introns n p ± SD

Northern 30

Western 14

Italian 9

Balkan 7

Spanish 3

0.00033 ± 0.00009 0.00084 ± 0.00017 0.00136 ± 0.00048

Total

Table 3 Estimates of percentage divergence (Da ± 95% CI) between control region lineages (upper diagonal) and estimates of divergence times [ky BP (± 95% CI)] (lower diagonal) using an evolutionary rate of 23% My-1

ky/Da ± SE% Northern Western Italian Balkan Spanish

Northern

Western

Italian

Balkan

Spanish

263 (171-356) 221(136-307) 240 (144-337) 237 (144-330)

5.45 ± 2.14% 3.62 ± 1.74% 3.03 ± 1.73% 6.49 ± 2.26%

Northern

Western

Italian

Balkan

Spanish

263 (171-356) 221(136-307) 240 (144-337) 237 (144-330)

Table 4 Estimates of SSD, FS, t and time since expansion (TSE)

in y BP for each lineage

mtDNA lineage

SSD

FS t (95% CI)

TSE (95% CI)

Northern

0.00375

-15.945* 4.088 (2.801-5.260)

72,844 (49,911-93,728)

Western

0.07546

0.680 4.578 (0.420-8.410)

87,300 (8,009-160,374)

Italian

0.00367

-2.661 3.363 (1.408-6.920)

64,698 (27,087-133,128)

Balkan

0.03880

0.083 3.234 (0.025-6.068)

54,499 (421-102,258)

*Indicates significance (p < 0.05)

*Indicates significance (p < 0.05)

(including indels) were found in the concatenated Y chromosome dataset. Twenty-two (36.7%) polymorphic sites were found in DBY1; 8 (13.3%) in DBY3; 8 (13.3%) in DBY7, and 22 (36.7%) in UTY11. A 4 bp indel separated the Northern lineage from all other samples in DBY1 and the Northern lineage also possessed an extra repeat motif (CAAA) in the UTY11 intron.

Four major lineages were identified from the concatenated dataset by the median-joining network (Fig. 2). The Western Y lineage consisted of individuals from the Western and Spanish mtDNA lineages plus individuals from the Northern mtDNA lineage found in Northern France (Fig. 2). The Northern Y lineage included all individuals found in the Northern mtDNA lineage with the exception of those from Northern France and also included individuals from Austria and Slovakia, which belonged to the Balkan mtDNA lineage. The Italian Y lineage contained the same individuals as the Italian mtDNA lineage. Bootstrap support was high for

Fig. 2 Median-joining network of 23 concatenated Y chromosomal intron haplotypes (2,939 bp). Numbers on branches indicate more than one mutation. Inferred haplotypes are represented by black dots. Bootstrap support for the Northern Y lineage is 100% and support for the Western Y lineage is 96% using both NJ and MP methods, respectively. See Table 1 for haplotype designations

Fig. 2 Median-joining network of 23 concatenated Y chromosomal intron haplotypes (2,939 bp). Numbers on branches indicate more than one mutation. Inferred haplotypes are represented by black dots. Bootstrap support for the Northern Y lineage is 100% and support for the Western Y lineage is 96% using both NJ and MP methods, respectively. See Table 1 for haplotype designations

Western (NJ/MP: 96/96%) and Northern (NJ/MP: 100/100%) Y lineages, with weak support for the Italian Y lineage. Only one individual belonged to the Balkan Y lineage. These lineages were also identified from each Y intron individually, with the exception of DBY3 which failed to separate the Western and Italian lineages (data not shown). The nucleotide diversity (p) of each lineage is given in Table 2.

Eleven haplotypes were found in 23 individuals in the Northern Y lineage (see Table 1 and Fig. 2), with Y haplotype North1 found in 10 localities spread from Norway to Siberia. The Y haplotype Aut1 had several large indels. Seven haplo-types were found in the Western Y lineage and four in the Italian Y lineage. However, the Y haplotype Ita2 was quite different from other Italian individuals (Fig. 2). This was also the case for this individual in the control region analysis (haplotype Ita7; Fig. 1).

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