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REPORTS
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Low-Pass DNA Sequencing of 1200 mutation, reversion, and recurrence rates, can
be particularly informative for these evolution-
ary analyses (3, 4). Recently, high-coverage Y
Sardinians Reconstructs European chromosome sequencing data from 36 males from
different worldwide populations (5) assessed
Y-Chromosome Phylogeny 6662 phylogenetically informative variants and
estimated the timing of past events, including a
putative coalescence time for modern humans of
Paolo Francalacci,1* Laura Morelli,1 Andrea Angius,2,3 Riccardo Berutti,3,4 Frederic Reinier,3 ~101,000 to 115,000 years ago.
Rossano Atzeni,3 Rosella Pilu,2 Fabio Busonero,2,5 Andrea Maschio,2,5 Ilenia Zara,3 MSY sequencing data reported to date still
Daria Sanna,1 Antonella Useli,1 Maria Francesca Urru,3 Marco Marcelli,3 Roberto Cusano,3 represent a relatively small number of individuals
Manuela Oppo,3 Magdalena Zoledziewska,2,4 Maristella Pitzalis,2,4 Francesca Deidda,2,4 from a few populations. Furthermore, dating esti-
Eleonora Porcu,2,4,5 Fausto Poddie,4 Hyun Min Kang,5 Robert Lyons,6 Brendan Tarrier,6 mates are also affected by the calibration of the
Jennifer Bragg Gresham,6 Bingshan Li,7 Sergio Tofanelli,8 Santos Alonso,9 Mariano Dei,2
Sandra Lai,2 Antonella Mulas,2 Michael B. Whalen,2 Sergio Uzzau,4,10 Chris Jones,3 1
Dipartimento di Scienze della Natura e del Territorio, Uni-
David Schlessinger,11 Gonalo R. Abecasis,5 Serena Sanna,2 Carlo Sidore,2,4,5 Francesco Cucca2,4*
versit di Sassari, 07100 Sassari, Italy. 2Istituto di Ricerca Genetica
e Biomedica (IRGB), CNR, Monserrato, Italy. 3Center for Ad-
Genetic variation within the male-specific portion of the Y chromosome (MSY) can clarify the vanced Studies, Research and Development in Sardinia (CRS4),
origins of contemporary populations, but previous studies were hampered by partial genetic Pula, Italy. 4Dipartimento di Scienze Biomediche, Universit di
Sassari, 07100 Sassari, Italy. 5Center for Statistical Genetics,
information. Population sequencing of 1204 Sardinian males identified 11,763 MSY single-nucleotide Department of Biostatistics, University of Michigan, Ann Arbor,
polymorphisms, 6751 of which have not previously been observed. We constructed a MSY MI 48109, USA. 6DNA Sequencing Core, University of Michigan,
phylogenetic tree containing all main haplogroups found in Europe, along with many Ann Arbor, MI 48109, USA. 7Center for Human Genetics Re-
Sardinian-specific lineage clusters within each haplogroup. The tree was calibrated with search, Department of Molecular Physiology and Biophysics,
Vanderbilt University, Nashville, TN 37235, USA. 8Dipartimento
archaeological data from the initial expansion of the Sardinian population ~7700 years ago.
di Biologia, Universitdi Pisa, 56126 Pisa, Italy. 9Departamento
The ages of nodes highlight different genetic strata in Sardinia and reveal the presumptive de Gentica, Antropologa Fsica y Fisiologa Animal, Universi-
timing of coalescence with other human populations. We calculate a putative age for coalescence dad del Pas Vasco/Euskal Herriko Unibertsitatea, 48080 Bilbao,
of ~180,000 to 200,000 years ago, which is consistent with previous mitochondrial DNAbased Spain. 10Porto Conte Ricerche, Localit Tramariglio, Alghero,
estimates. 07041 Sassari, Italy. 11Laboratory of Genetics, National Institute
on Aging, Baltimore, MD 21224, USA.
*Corresponding author. E-mail: pfrancalacci@uniss.it (P.F.);
ew sequencing technologies have pro- more accurately (1). Sequencing data from the
0
(AB)T
466
500 CT
DE
146 868
145
7 1
20
38
19
119
750
102 124
153
257 231
7 237 285
24
0.0
43
210 66 tzi
38 98 148 Tuscan
Corsican 3
30 152
11.9
209 24 46 57
51 38
83
7.0
92
79.3
1000
123.7
101.3
120.3
75.7
13.8
109.5
125.1
91.9
8.5
112.7
37.2
114.9
96.1
87.4
Fig. 1. Phylogenetic tree of the 1209 (1204 Sardinians and 5 non- menclature. The left axis indicates the number of SNPs from the root. The
Sardinians) Y-chromosome sequences. The bifurcations AT, BT, CT, and DE asterisk indicates the calibration point. The colored dots indicate private
have been inferred because of the absence of individuals belonging to Sardinian clusters with an average number of SNPs in the range of 35 to 40 in
haplogroups B, C, and D in our sample. Colored branches represent different red, 25 to 30 in green, and 7 to 12 in blue. The black dots indicate clusters
Y-chromosome haplotypes. The number of polymorphisms for the main with an average number of SNPs in the range of 70 to 120. The arrow indicates
branches is shown in black; the average number of SNPs of sub-haplogroups is the position on the tree of the tzi, Tuscan, and Corsican samples. The gray
given in blue. The sub-haplogroups are named according to ISOGG no- box is enlarged in Fig. 2.
124
41
177
2
42 17
88
43
67
0.0
46
N. Italian Basque
10
24
72.2
0.0
1
38.1
19
36.0
39.1
34.1
37.3
I2a1a1
I2a1a
I2a1a1
I1a3a2
I2a1a
I2a1b
I2a2a
I2c
Fig. 2. Phylogenetic tree of the 492 (490 Sardinians and 2 non-Sardinians) ISOGG nomenclature. The red dots indicate Sardinian private clades, labeled in Greek
Y-chromosome sequences belonging to haplogroup I. The number of poly- letters as in Table 1. The black dots indicate clusters with an average number of SNPs
morphisms for the main branches is shown in black; the average number of SNPs of in the range of 70 to 120. The arrows indicate the position of the northern Italian and
sub-haplogroups is shown in blue. The sub-haplogroups are named according to Basque samples on the tree. The asterisk indicates the calibration point.