Introduction 1 2 3 http://www.yhrd.org/index.html 4 5 4 4 5 6 7 Materials and methods 5 5 8 in silico 9 1 2 Taq 1 Products were analysed by mixing 1 μl of PCR product with 15 μl Hi–Di formamide and 0.2 μl size marker (CXR 60–400 bases, Promega UK, Southampton, UK) and running on 36 cm × 50 μm capillaries containing POP-4 polymer (Applied Biosystems) on an ABI Prism 3100 Genetic Analyzer (Applied Biosystems, Warrington, UK). Electrophoresis was carried out at 3 kV for 3 s followed by 15 kV for 45 min with a run temperature of 60°C. Allele sizes were measured using GeneMapper v3.0 (Applied Biosystems). Most loci were sequenced because of the lack of previous sequence data, to confirm previous results or to investigate the structure of intermediate-sized sizes. Such alleles were amplified using unlabelled primers and sequenced by the Wellcome Trust Sanger Institute small-scale sequencing facility using standard methods. Results 2 3 10 1 Table 1 Loci showing multiple peaks, missing peaks or intermediate alleles Locus a Comments DYF386S1  Two peaks in many individuals, excluded from analysis DYF390S1  Two peaks in many individuals, excluded from analysis DYS448  Two peaks in two individuals DYS522 10 (U2Ains) 10 A 10 DYS525  No product in one individual, two peaks in one individual DYS531 11 (D6Tins) Intermediate-sized allele DYS549  Two peaks in one individual DYS556  No product in two individuals DYS567  Two peaks in two individuals DYS576  Two peaks in two individuals DYS589  No product in one individual DYS636  No product in one individual U D ins a 1 5 7 1 1 2 10 2 10 4 Table 2 Variation of 50 new Y-STR loci in the YCC panel Locus Mean repeat count Number of alleles Diversity Variance DYS481 23.3 11 0.90 7.87 DYS570 17.6 11 0.86 3.89 DYS576 17.3 7 0.82 2.16 DYS643 11.1 9 0.82 2.33 DYS485 15.9 7 0.78 1.92 DYF406S1 10.6 7 0.75 1.26 DYS522 11.2 6 0.74 1.03 DYS589 12.3 6 0.73 1.07 DYS533 11.2 6 0.72 1.03 DYS549 12.1 5 0.72 0.92 DYS505 12.1 6 0.71 1.00 DYS508 11.4 8 0.71 1.44 DYS525 9.9 7 0.71 0.95 DYS531 11.0 4 0.69 0.39 DYS556 11.7 6 0.67 1.03 DYS572 10.3 5 0.64 0.61 DYS565 11.5 6 0.64 0.71 DYS594 9.5 7 0.63 0.87 DYS540 11.4 4 0.62 0.52 DYS487 13.2 6 0.62 1.38 DYS511 10.9 5 0.62 0.73 DYS573 9.9 4 0.62 0.73 DYS617 12.4 5 0.62 1.06 DYS495 15.3 5 0.61 0.76 DYS567 10.4 6 0.61 0.72 DYS497 14.2 4 0.60 0.51 DYS488 13.4 6 0.58 0.91 DYS492 11.6 5 0.56 0.45 DYS490 12.9 7 0.56 2.43 DYS568 11.1 7 0.56 0.92 DYS636 11.3 5 0.56 0.49 DYS537 10.9 4 0.53 0.43 DYS618 11.8 4 0.51 0.37 DYS638 10.9 4 0.49 0.34 DYS491 12.1 5 0.46 0.40 DYS578 8.1 4 0.41 0.40 DYS640 11.2 3 0.39 0.39 DYS476 11.2 4 0.36 0.29 DYS494 9.0 4 0.35 0.28 DYS641 9.6 4 0.33 0.93 DYS554 9.0 5 0.31 0.36 DYS575 10.0 4 0.25 0.22 DYS583 8.0 3 0.22 0.12 DYS590 7.9 3 0.22 0.23 DYS480 7.9 3 0.22 0.16 DYS569 11.0 3 0.18 0.11 DYS530 9.1 2 0.17 0.09 DYS580 9.1 4 0.11 0.19 DYS472 8.0 2 0.08 0.04 DYS579 9.0 2 0.05 0.89 Loci are ordered according to their diversity. Discussion 5 R 2 R 2 R 2 5 2 3 Electronic supplementary material Below is the link to the electronic supplementary material. 
 Table S1 Multiplex organization and primer concentrations (DOC 102 kb) Table S2 PCR product size range and allele range (DOC 92 kb) Table S3 Haplotypes of the YCC DNAs (XLS 58 kb) (Note: this table is provided as an Excel file and is the table mentioned in CE7. We transformed it into text because some journals insist on this, but the text version is difficult to interpret as CE5 highlights. The loci are ordered according to their positions in multiplexes 1–16 in  Table S1  and  Table S2 , and it seems most consistent to keep the same order for  Table S3 ). 
 Table S4 Subdivision of minimal haplotypes by new Y-STRs (DOC 87 kb)