Molecular biology and evolution 31:975-983

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Direct Estimates of Natural Selection in Iberia Indicate Calcium
Absorption Was Not the Only Driver of Lactase Persistence
in Europe
´ sk Sverrisdo´ttir,*,1 Adrian Timpson,2,3 Jamie Toombs,4 Cecile Lecoeur,5,6 Philippe Froguel,5,6,7
Oddny´ O
Jose Miguel Carretero,8 Juan Luis Arsuaga Ferreras,9 Anders Go¨therstro¨m,1,10 and Mark G. Thomas2
1
Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
3
Institue of Archaeology, University College London, London, United Kingdom
4
Department of Molecular Neuroscience, Institute of Neurology, University College London, London, United Kingdom
5
European Genomic Institute for Diabetes (EGID), FR3508, Lille, France
6
CNRS UMR8199, Biology Institute of Lille 1, Lille, France
7
Department of Genomics of Common Disease, School Of Public Health, Imperial College London, London, United Kingdom
8
Laboratorio de Evolucio´n Humana, Edificio I+D+i, Universidad de Burgos, Burgos, Spain
9
Paleontology Department, Universidad Complutense de Madrid, Madrid, Spain
10
Archaeological Research Laboratory, Stockholm University, Stockholm, Sweden
*Corresponding author: E-mail: [email protected]
Associate editor: Beth Shapiro
2
Key words: lactase persistence, Iberia, Neolithic, forward simulation, ancient DNA, natural selection.
Introduction
The intestinal enzyme lactase (lactase-phlorizin hydrolase) is
required for digestion of lactose, the main carbohydrate in
milk, into the readily absorbable monosaccharides glucose
and galactose (Swallow and Harvey 1993). While lactase is
present in infants, its production is usually downregulated
following weaning and it is near absent in about 68% of
adults worldwide (Itan et al. 2010). Continued production
of lactase into adulthood—lactase persistence (LP)—is a
genetically determined, Mendelian dominant trait that
shows a highly structured global geographic distribution. It
is common in Europe, particularly northwestern Europe, parts
of the Indian subcontinent, as well as in many African
and Middle Eastern pastoralist groups (Itan et al. 2010;
Gallego Romero et al. 2012). It is associated with different
allelic variants in different regions (Enattah et al. 2002;
Ingram et al. 2007; Tishkoff et al. 2007; Enattah et al. 2008;
Ingram et al. 2009) indicating convergent evolution. In Europe
(Itan et al. 2009; Itan et al. 2010), the Indian subcontinent
(Gallego Romero et al. 2012), and some African peoples
(Mulcare et al. 2004), a C to T transition 13,910 bp upstream
of the lactase gene (LCT), called -13,910*T (Enattah et al.
2002), predominates, whereas in the Middle East and most
parts of Africa three other variants are commonly found in LP
individuals (13,915*G, 13,907*G, and 14,010*C) (Ingram et al.
ß The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please
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Mol. Biol. Evol. 31(4):975–983 doi:10.1093/molbev/msu049 Advance Access publication January 21, 2014
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Article
Lactase persistence (LP) is a genetically determined trait whereby the enzyme lactase is expressed throughout adult life.
Lactase is necessary for the digestion of lactose—the main carbohydrate in milk—and its production is downregulated
after the weaning period in most humans and all other mammals studied. Several sources of evidence indicate that LP has
evolved independently, in different parts of the world over the last 10,000 years, and has been subject to strong natural
selection in dairying populations. In Europeans, LP is strongly associated with, and probably caused by, a single C to T
mutation 13,910 bp upstream of the lactase (LCT) gene (-13,910*T). Despite a considerable body of research, the reasons
why LP should provide such a strong selective advantage remain poorly understood. In this study, we examine one of the
most widely cited hypotheses for selection on LP—that fresh milk consumption supplemented the poor vitamin D and
calcium status of northern Europe’s early farmers (the calcium assimilation hypothesis). We do this by testing for natural
selection on -13,910*T using ancient DNA data from the skeletal remains of eight late Neolithic Iberian individuals, whom
we would not expect to have poor vitamin D and calcium status because of relatively high incident UVB light levels. None
of the eight samples successfully typed in the study had the derived T-allele. In addition, we reanalyze published data
from French Neolithic remains to both test for population continuity and further examine the evolution of LP in the
region. Using simulations that accommodate genetic drift, natural selection, uncertainty in calibrated radiocarbon dates,
and sampling error, we find that natural selection is still required to explain the observed increase in allele frequency. We
conclude that the calcium assimilation hypothesis is insufficient to explain the spread of LP in Europe.
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Abstract
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Sverrisdo´ttir et al. . doi:10.1093/molbev/msu049
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these frequencies are also the result of natural selection after
the establishment of the Neolithic, then the Calcium
Assimilation Hypothesis should not be invoked for this
region of Europe.
Although a number of statistical methods that use contemporary data have been developed for detecting natural
selection acting on novel alleles (Sabeti et al. 2006), all of these
indirect approaches have poor sensitivity and temporal resolution, most are confounded by past demographic processes,
and many are insensitive to selection acting on standing variation (Peter et al. 2012). In principle, none should be as powerful as direct comparison allele frequencies at different times
in a continuous population. Given such data and conditions,
any test for natural selection needs only discount genetic drift
as the null explanation for allele frequency change.
Furthermore, such an approach should permit temporal resolution of episodic selection given sufficient ancient DNA
data. However, in central Europe and in Scandinavia, population continuity between Early Neolithic farming and
modern (Bramanti et al. 2009) and between Late Neolithic
hunter-gatherer and modern (Malmstro¨m et al. 2009) populations, respectively, has been rejected using ancient DNA
data. While rejection of population continuity does not constitute evidence of complete population replacement, it
clearly indicates that a degree of inward gene flow has
taken place (Skoglund et al. 2012).
In this study, we report -13,910 C/T allele frequencies from
Late Neolithic and Early Bronze Age northeastern Iberia. Using
previously published mitochondrial data from Neolithic farmers from the same region (Sampietro et al. 2007; Lacan, Keyser,
Ricaut, Brucato, Tarrus et al. 2011), as well as modern northeast Iberian sequences (Crespillo et al. 2000), we show by
coalescent simulation that population continuity in the intervening period cannot be rejected. We then apply a novel
forward simulation approach that accommodates genetic
drift, natural selection, uncertainty in calibrated radiocarbon
dates, and ancient and modern sampling errors to test
whether natural selection is still required to explain that
rise in Iberian -13,910*T allele frequencies over the last 7,000
years. Additionally, we perform the same analyses on previously published mtDNA and -13,910*T allele frequency data
from southern France (Lacan, Keyser, Ricaut, Brucato,
Duranthon et al. 2011).
Results
PCR and Sequencing
Of the 18 individual skeletal remains examined from the
Iberian site of El Portalo´n, eight yielded reproducible sequences (see table 1). In total, we pyrosequenced these
eight samples 60 times; each sample was sequenced between
five and ten times (sequences are available from authors upon
request). Out of these 60 genotypings, 53 indicated homozygozity for the LCT -13,910*C allele, and 7 indicated heterozygozity (in five of the eight samples). However, for all eight
samples, the majority of genotypings consistently indicated
homozygozity for the -13,910*C allele (the worst case was
ATP6, where 25% of the genotypings indicated heterozygozity
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2007; Tishkoff et al. 2007). In addition, the presence of several
additional alleles in Ethiopian LP pastoralists suggests the
possibility of a recent soft selective sweep (Ingram et al. 2009).
In addition to evidence for the convergent evolution of LP,
a low frequency or absence of -13,910*T in Early Neolithic
central European farmers (Burger et al. 2007), Middle
Neolithic Scandinavian hunter-gatherers (Malmstrom et al.
2010), Early Neolithic farmers from northeast Iberia (Lacan,
Keyser, Ricaut, Brucato, Tarrus et al. 2011), and Late Neolithic
farmers from southern France (Lacan, Keyser, Ricaut, Brucato,
Duranthon et al. 2011), as well as long haplotypes surrounding LCT (Bersaglieri et al. 2004; Voight et al. 2006; Sabeti et al.
2007; Tishkoff et al. 2007; Gallego Romero et al. 2012;
Schlebusch et al. 2013), low variation in closely linked microsatellites (Coelho et al. 2005), and demic (Gerbault et al. 2009)
and spatially-explicit (Itan et al. 2009) simulations, all indicate
a recent origin for, and strong natural selection acting on, LPassociated alleles.
There is a clear association between the presence of LP and
a history of pastoralism in living populations (Holden and
Mace 1997), and estimates of the ages of major LP-associated
alleles—specifically -13,910*T in Europe and -14,010*C in
Africa—bracket dates for the domestication of milkable animals (Peters et al. 1999; Vigne et al. 2001; Helmer et al. 2005;
Peters et al. 2005; Bollongino et al. 2012) and evidence of
dairying (Craig et al. 2005; Vigne 2006; Evershed et al. 2008)
based in archaeological data.
The reasons why LP should provide such a strong selective
advantage have been the subject of considerable speculation
(Gerbault et al. 2011). The calcium assimilation hypothesis
(Flatz and Rotthauwe 1973) focuses on key nutritional components in milk, specifically vitamin D and calcium. Vitamin
D is essential for calcium absorption in the gut and can be
obtained from a few dietary sources (e.g., fish and eggs) or by
the action UVB light on the skin, which photoconverts 7dehydrocholesterol into cholecalciferol (vitamin D3). At
high latitudes, incident UVB levels are often too low for adequate vitamin D production (Jablonski and Chaplin 2010),
so, in the absence of sufficient dietary sources of vitamin D,
early northern European farmers may have been calcium deficient and in danger of developing rickets. Milk is a modest
source of vitamin D but an excellent source of calcium, and
the Calcium Assimilation Hypothesis (Flatz and Rotthauwe
1973) proposes that LP was selectively favorable in northern
Europe as a means of avoiding poor calcium and vitamin D
status.
While the Calcium Assimilation Hypothesis (Flatz and
Rotthauwe 1973) may explain the high frequencies of LP observed in northern Europe, UVB levels in southern Europe, the
Middle East, the Indian subcontinent, and Africa should be
sufficient to avoid vitamin D deficiency (Jablonski and
Chaplin 2010). Despite this, available estimates of selection
coefficients for high-UVB non-European regions are also typically high (Bersaglieri et al. 2004; Tishkoff et al. 2007; Gallego
Romero et al. 2012; Schlebusch et al. 2013). In modern
Iberians, the -13,910*T allele is found at a frequency of
around 37% (Rasinpera et al. 2005), consistent with an estimated LP frequency of 66% (Leis et al. 1997; Itan et al. 2010). If
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Lactase Persistence Evolution in Europe . doi:10.1093/molbev/msu049
and 75% homozygozity for the -13,910*C allele). Previous
studies on ancient cattle single-nucleotide polymorphisms
using the pyrosequencing approach have demonstrated the
presence of damaged bases (Svensson et al. 2007), and after
numerous repeat sequencing of our samples we concluded
that most of the few apparent heterozygote genotypes are
due to postmortem cytosine deamination or type-two
damage (Gilbert et al. 2003). Further support for this can be
seen from the molecular behavior of considerably older cave
bear (Ursus deningeri) (Dabney, Knapp et al. 2013) and hominin (Meyer et al. 2014) sequences recovered from the Sima de
los Huesos cave, which is part of the Atapuerca cave system to
which El Portalo´n forms the entrance. In both sets of bone
material, nucleotide misincorporation rates in sequencing
reads generated on Illumina’s HiSeq 2500 platform were elevated at the 30 and 50 ends, indicating authentic ancient DNA
(Malmstrom et al. 2007; Dabney, Meyer et al. 2013). Negative
controls used in batches showed no or negligible evidence of
contamination. However, it should be noted that despite
stringent anti-contamination measures, modern contamination can never be completely discounted (Gilbert et al. 2005;
Malmstrom et al. 2005; Malmstrom et al. 2007; Malmstro¨m
et al. 2009).
Population Continuity
Table 1. The Number of Times Each Genotype at Position -13910 in
the Lactase Gene Was Successfully Obtained in the Iberian Sample.
C/C
5
6
6
7
8
8
8
5
C/T
1
2
2
1
Selection on LCT -13,910*T
In all three comparisons of LCT -13,910*T allele frequency
between ancient and modern samples, neutrality was rejected
B
5
1
0.4
4
4
A
T/T
5
Sample
ATP 3
ATP 4
ATP 6
ATP 7
ATP 8a
ATP 8b
ATP 9
ATP 11
NUP x103
2
3
NUP x103
2
3
0.3
0.2
1
1
0.1
0.0
1
20
40
60
NN x10
3
80
100
1
20
40
60
NN x10
80
100
3
FIG. 1. Probabilities of obtaining simulated molecular FSTs greater than those observed between Neolithic and modern samples. (A) Comparison of 118
modern mtDNA hypervariable region I (HVR1) sequences from northeastern Iberia (Crespillo et al. 2000) and a combined sample of 11 homologous
sequences from Neolithic remains from Granollers (Catalonia, northeast Spain) dated to 5,500 years BP (Sampietro, et al. 2007) and 7 sequences from
Neolithic remains excavated from a Spanish funeral cave dating to around 7,000 years BP (Lacan, Keyser, Ricaut, Brucato, Tarrus, et al. 2011)
(FST = 0.0101; P = 0.154). (B) Comparison of a combined modern sample of 37 mtDNA hypervariable region I sequences from the department of
Var in the region Provence-Alpes-Coˆte d’Azur in Provence and 69 sequences from the region of Pe´rigord Limousin, straddling three western-central
departments (northern Dordogne, western Corre`ze, and southern Haute-Vienne) (Dubut, et al. 2004), and 29 sequences from a Late Neolithic
necropolis in Treilles (Lacan, Keyser, Ricaut, Brucato, Duranthon, et al. 2011) (FST = 0.00553; P = 0.201). Two phases of exponential growth were modeled,
the first after the initial colonization of Europe 45,000 years ago, of assumed effective female population size NUP (y axis), and ending with the Neolithic
transition in Iberia 7,500 years ago (Lo´pez de Pablo and Go´mez Puche 2009), of assumed effective female population size NN (x axis), and the second
leading up to the present, with an assumed a female effective population size of 369,715. P values greater than 0.05 are shaded on a gray scale.
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Coalescence simulations were unable to reject population
continuity in northeastern Iberia from the Neolithic to the
present (see fig. 1a) using 18 ancient HVR1 mtDNA sequences (Sampietro et al. 2007; Lacan, Keyser, Ricaut,
Brucato, Tarrus et al. 2011) and 118 modern sequences
(Crespillo et al. 2000). Likewise, we were unable to reject population continuity in southeastern France between the Late
Neolithic and today (see fig. 1b) using 29 ancient HVR1
mtDNA sequences (Lacan, Keyser, Ricaut, Brucato,
Duranthon et al. 2011) and 109 modern sequences (Dubut
et al. 2004).
Because our test for population continuity in northeastern
Iberia from the Neolithic to the present involved using ancient mtDNA data from two independent studies (Sampietro
et al. 2007; Lacan, Keyser, Ricaut, Brucato, Tarrus et al. 2011),
raising the possibility of local structuring, we also performed
coalescent simulations to test for continuity using those two
samples independently (see supplementary fig. S2a and b,
Supplementary Material online). As can be seen, for both
samples we are still unable to reject population continuity
over the vast majority of combinations of the NUP and NN
parameters.
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Sverrisdo´ttir et al. . doi:10.1093/molbev/msu049
A
B
8
Selection (%)
4
6
Selection (%)
8
6
4
2
2
0
0
20
40
60
Initial Ne (x103)
80
100
20
40
60
80
Initial Ne (x103) 7,000 B.P.
1.0
C
8
0.8
6
0.6
4
0.4
2
0.2
Two−tailed empirical
p−values for obtaining
the observed allele
frequency increase.
(values less than 0.01
are shaded grey).
0
20
40
60
80
Initial Ne (x103) 5,000 B.P.
100
FIG. 2. Two-tailed empirical P values for the similarity between the observed modern LCT -13,910*T frequency and the distribution of simulated
frequencies, given the demographic and natural selection model parameters modeled between Neolithic and modern populations. Allele frequencies
were compared between (A) the ancient northeastern Iberian population sampled here and modern northeastern Iberians (Rasinpera, et al. 2005), (B)
the ancient northeastern Iberian population (sampled by Lacan, Keyser, Ricaut, Brucato, Tarrus, et al. 2011) and the same modern northeastern Iberians
as above (Rasinpera et al. 2005), and (C) a population from the Late Neolithic necropolis in Treilles, southern France (Lacan, Keyser, Ricaut, Brucato,
Duranthon, et al. 2011) and modern French from the same region (Balkau 1996). P values less than 0.01 are shaded gray.
for all simulated values of ancestral population size (see fig. 2).
We performed two separate analyses of LCT -13,910*T allele
frequency change in northeastern Iberia, the first between the
ancient sample presented here and a modern data set
(Rasinpera et al. 2005) and the second between the ancient
LCT data presented by Lacan et al (2011) and the same
modern Iberian data set. It is notable that the selection
values giving the highest P values for the observed allele frequency increase are greater for the ancient LCT data presented here (1.8%) than the data presented by Lacan et al.
(2011) (1.2%). This is almost certainly because the LCT data
presented here comes from individuals living more recently
(mean cal. BP = 3,735 years) than those analyzed by Lacan
et al. (2011) (7,000 years BP), and because the LCT 13,910*T allele was not observed in either ancient Iberian
sample, the rise in frequency over a shorter period requires
greater selection pressures. The selection value (2.4%) giving
the highest P values for the observed allele frequency increase
in southern France (Balkau 1996; Lacan, Keyser, Ricaut,
Brucato, Duranthon et al. 2011) is somewhat higher than
that for the Iberian data presented here (1.8%).
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Discussion
We have formally tested for population discontinuity between a combined Early (Lacan, Keyser, Ricaut, Brucato,
Tarrus et al. 2011) and Middle Neolithic (Sampietro et al.
2007) sample and a modern sample (Crespillo et al. 2000)
from northeast Iberia. For virtually all combinations of NUP
and NN, a significant proportion of simulated FST values were
equal to or greater than that observed (fig. 1), and so we were
unable to reject population continuity. These results are reminiscent of those presented by Gamba et al. (2012) except that
we used a combined ancient sample. If the two ancient northeast Iberian samples considered were from a relatively unstructured population, then combining them should
increase scope for rejecting continuity, thus making our test
more conservative. However, to allow for the possibility that
those samples were from differentiated populations, we also
performed coalescent simulations with each ancient sample
independently (see supplementary fig. S2a and b,
Supplementary Material online) and were still unable to
reject population continuity over the majority of combinations of the NUP and NN parameters. We were likewise unable
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Selection (%)
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Hervella et al. 2012; Pinhasi et al. 2012) indicate little population turnover in Iberia since at least the Middle Neolithic, it is
difficult to account for the observed change in LCT -13,910*T
allele frequency by gene flow from neighboring regions, unless
mediated primarily by males, further supporting the strong
selection coefficients estimated here.
If the selection coefficients estimated for southeastern
France and northwestern Iberia are correct, or underestimates, it is unlikely that they are explained by the Calcium
Assimilation Hypothesis (Flatz and Rotthauwe 1973) as incident UVB levels in both regions permit adequate vitamin D
production (Jablonski and Chaplin 2010). It is not currently
possible to compare the selection coefficients estimated here
with those for northern Europe using the same selection detection approach because, although LCT -13,910*T allele frequency data are available for ancient samples from northern
Europe and Scandinavia (Burger et al. 2007; Malmstrom et al.
2010), in both regions population continuity between
Neolithic and modern populations has been rejected
(Bramanti et al. 2009; Malmstro¨m et al. 2009; Skoglund
et al. 2012). However, the selection coefficients estimated
here are remarkably similar to those presented in a recent
study (Peter et al. 2012) for the LCT -13,910*T allele (2.5%; 95%
CI 0.4–20%) using a Finnish sample and approximate Bayesian
computation (Beaumont et al. 2002), which also concluded
that LCT selection acted on de novo, rather than standing
variation. The selection coefficient estimate mode reported
by Itan et al. (2009) was 9.53%, but this was assumed to apply
to less than half of the population of Europe (dairying farmers) and to be spatiotemporally constant. To a first order of
approximation, this could be interpreted as indicating a
Europe-wide selection coefficient of 4% or 5%, which is
about twice the levels we estimate here for southwestern
Europe. Thus, it is conceivable that additional factors, possibly
including calcium assimilation, led to different selection coefficients in Northern Europe. Alternatively, as suggested by
Itan et al. (2009), higher frequencies of LCT -13,910*T in northwestern Europe may be the result of a combination of strong
selection and allele surfing (Edmonds et al. 2004; Klopfstein
et al. 2006) on a wave of advance of farmers spreading across
the continent.
A temporal dimension to estimates of selection coefficients on LCT -13,910*T is still lacking, but it is certainly possible that selection on this allele was episodic (Itan et al. 2009),
possibly in response to oscillations in food supply (Gerbault
et al. 2011). While the data that we present is insufficient
to detect episodic selection, the method we present here
should be adequate for this purpose given sufficient serial
sampled data.
Despite overwhelming evidence for strong selection on LP
alleles, including that presented here, the reasons for that
selection remain elusive (Gerbault et al. 2011). In addition
to the calcium assimilation hypothesis (Flatz and Rotthauwe
1973) various other hypotheses have been proposed. Apart
from the obvious nutrient value of milk in terms of protein,
fat, calories, and various vitamin and mineral micronutrients,
milk production may have offered significant economic advantages (Benecke 1994) and a good source of relatively
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to reject population continuity between Late Neolithic and
modern populations in southeastern France, using a larger
ancient DNA sample (Lacan, Keyser, Ricaut, Brucato,
Duranthon et al. 2011). To examine the sensitivity of our
continuity tests to the modern population size parameter,
we performed identical coalescent simulations to those described earlier except that we set the modern effective population sizes to 0.1 times and 10 times the values assumed
from census data (see supplementary fig. S1a–d,
Supplementary Material online). Varying this parameter by
an order of magnitude each way made little difference to our
results and were still unable to reject population continuity
across all combinations of the NUP and NN parameters.
Since continuity is the null hypothesis, failure to reject it
does not constitute a demonstration of it. However, we note
that population continuity has been rejected between
Neolithic farmers and modern populations from central
Europe (Bramanti et al. 2009) and between Late Neolithic
hunter-gatherers and modern populations from Scandinavia
(Malmstro¨m et al. 2009) using smaller ancient sample sizes. It
thus seems likely that population turnover since or shortly
after the Neolithic transition has been less severe in southwestern Europe than in central or northern Europe (Pinhasi
et al. 2012).
Our test for neutrality of the LCT -13,910*T allele is contingent on population continuity and accounts for genetic
drift, ancient and modern sampling errors, and calibrated
radiocarbon date uncertainty. We believe that our accommodation of the latter is a first in evolutionary inference using
serial DNA samples. An important caveat to the selection
coefficients estimates presented here is the assumption that
selection is constant and starts at the time of the ancient
sample used. This is illustrated by the differences between the
point estimate of S = 1.2% using the Early Neolithic data of
Lacan et al. (2011) and the point estimate of S = 1.8% using
the Late Neolithic/Early Bronze Age LCT data presented here;
higher selection coefficients are required to increase allele
frequency by the same amount but over a shorter period of
time, because they start with zero observed -13,910*T alleles.
Thus, our estimates of S should be considered conservative—
the true values may be higher.
The LCT data presented here comes from an archaeological site where faunal remains from the same layers have a
mean age of 3,735 years cal. BP. Although the sample is relatively small, using the classical formula p = 1 (1/n), where
is the probability of no occurrences of an allele in n observations (Burger et al. 2007), we estimate that the maximum
frequency, p, of the LCT -13,910*T allele in this population
should be no more than 0.17 with 95% confidence and no
more than 0.25 with 99% confidence and could have been
zero. If frequencies were very low then this is intriguing given
the relatively recent date range and suggests a late introduction but rapid rise in frequency of LCT -13,910*T in Iberia. This,
in turn, suggests that LCT -13,910*T was not introduced—or
was only introduced at very low frequencies—with arrival of
the Neolithic in Iberia. As the mtDNA analyses presented here
and elsewhere (Izagirre and de la Rua 1999; Lacan, Keyser,
Ricaut, Brucato, Tarrus et al. 2011; Gamba et al. 2012;
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Material and Methods
Samples
We attempted to extract DNA from 18 human mixed skeletal
remains, out of which 8 yielded usable DNA. The remains
were excavated from the Holocene site of El Portalo´n, the present day entrance to the Cueva Mayor Karst complex, in the
Sierra de Atapuerca, 15 km east of Burgos, Spain (Carretero
et al. 2008). There are no direct radiocarbon dates for these
samples, but 13 radiocarbon dates are available from horse
and cattle remains from the same layers (Lira et al. 2010).
DNA Extraction
Samples were handled in a clean laboratory under positive air
pressure, UV irradiated daily, and isolated from post-polymerase chain reaction (PCR) work. Personnel wore disposable
facemasks, zip suits, and sterile latex gloves at all times and
do not enter the facility if they have worked in a post-PCR
environment the same day. Equipment, nonorganic buffers,
and reagents were UV irradiated.
Bone samples were individually irradiated in a crosslinker
(Ultra-Violet Products Ltd., Cambridge, UK) with 6.0 J/cm2.
From each bone, a millimeter of approximately 1 cm surface
area was removed by drilling. Two 0.10 g samples of bone
powder were taken from each bone using a drill hood
which was UV radiated between sample batches. DNA was
then extracted from the bone powder using a modification
(Malmstrom et al. 2005) of the silica spin method (Yang et al.
1998). One in every four samples included an extraction control (milli-Q water).
Genotyping
A 53 bp fragment containing the -13,910 C/T polymorphism
was amplified using primers “GCTGGCAATACAGATA
AGATAATG” and “GAGGAGAGTTCCTTTGAGGC” (Tag
Copenhagen). The forward primer was biotinylated
(Malmstrom et al. 2005). Amplification was performed
using 5 ml of DNA extract, 300 nM primers, and two units
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of Smart Taq Hot Start (Naxo). One in every three PCRs
was a negative control containing only milli-Q water. PCR
amplification conditions were 15 min at 95 C, followed by
50 cycles of 94 C for 30 s, 55 C for 30 s, and 72 C for 30 s.
The -13,910* alleles were identified through pyrosequencing
using primer “CCTTTGAGGCCAGGG”, as previously described (Anderung et al. 2005). Dispensation order for the
Pyrosequencer was CATCAGT/CGATG.
Data Analysis
To test for population continuity in northeastern Iberia from
the Neolithic until present, we first calculated the molecular
FST (Excoffier et al. 1992) between 118 modern mtDNA hypervariable region I (HVR1) sequences from northeastern
Iberia (Crespillo et al. 2000) and a combined sample of 18
homologous sequences from Neolithic remains from comprising 11 sequences from Granollers (Catalonia, northeast
Spain) dated to 5,500 years BP (Sampietro et al. 2007) and
7 sequences from remains excavated from a Spanish funeral
cave dating to around 7,000 years BP (Lacan, Keyser, Ricaut,
Brucato, Tarrus et al. 2011). The region of overlap for these
three HVR1 samples was 310 bp (from 16,053 to 16,362 on the
Cambridge reference sequence [Anderson et al. 1981]). The
FST between the ancient and modern sequence samples
(0.0101; P = 0.154) was calculated using the amova() function
in the “R” (R Core Team 2012) library ade4 (Dray and Dufour
2007). P values for these FST estimates were calculated by
permuting the data 100,000 times. We then examined
whether this observed FST was greater than expected under
a model of population continuity for a range of combinations
of female effective population sizes at the Upper Palaeolithic
transition in Europe (NUP) 45,000 years ago (Powell et al.
2009), and the Neolithic transition in Iberia (NN) 7,500 years
ago (Lo´pez de Pablo and Go´mez Puche 2009), as described
previously (Bramanti et al. 2009; Malmstro¨m et al. 2009), assuming exponential growth between 45,000 years ago and
7,500 years ago, and between 7,500 years ago and the present,
and a generation time of 25 years. We assumed a modern
female effective population size of 369,715 (one-tenth of the
modern female population size of Catalonia and Aragon combined [census estimates for 1999, source: http://www.google.
co.uk/publicdata/, last accessed February 4, 2014] for the
region from which the modern sequences were sampled
[Crespillo et al. 2000]). Ten thousand coalescent simulations
were performed for each of all 10,000 combinations of 100
equally spaced values of NUP, ranging from 10 to 5,000, and
100 equally spaced values of NN, ranging from 1,000 to
100,000, using Fastsimcoal (Excoffier and Foll 2011).
Simulated FST values were calculated using the same
amova() function as used to calculate the observed FST
values, and the proportion of simulated FST values equal to
or greater than the observed FST were plotted for each combination of NUP and NN.
The above analysis was repeated for southeastern France
using a combined modern sample of 106 mtDNA hypervariable region I sequences comprising 37 sequences from the
department of Var in the region Provence-Alpes-Coˆte d’Azur
Downloaded from http://mbe.oxfordjournals.org/ at University College London on April 11, 2014
uncontaminated fluid, particularly in arid environments
(Cook and al-Torki 1975), although this may be less relevant
in Europe (Gerbault et al. 2011). Others have suggested that a
milk-rich diet may offer some protection against malaria
(Anderson and Vullo 1994; Cordain et al. 2012) or that LP
spread as prestige class behavior (Durham 1991).
Alternatively, dairy-based economies are likely to have been
more buffered against food supply fluctuations than cerealbased economies, both because of the boom-and-bust of
growing seasons and the possibility of crop failure (Gerbault
et al. 2011). In mixed economies when crops have failed, fermented milk products are an alternative source of nutrients
to LP and non-LP individuals alike. However, as lower lactose
content milk products are consumed, so high lactose content
products (milk and yoghurt) would be left. In famine conditions, the consequences of high lactose food consumption in
non-LP individuals (particularly diarrhea) would be more
severe than in well-nourished non-LP individuals, perhaps
leading to high but episodic selection differentials.
MBE
Lactase Persistence Evolution in Europe . doi:10.1093/molbev/msu049
the formula 1 2 j 0.5 P j , where P is the proportion of
simulated modern allele frequencies that are greater than that
observed. This yields a two-tailed empirical P value for the
similarity between the observed modern allele frequency and
the distribution of simulated allele frequencies, given the demographic and natural selection model parameters modeled
(Voight et al. 2005).
The above analysis was repeated for published ancient LCT
13,910*T allele frequency data from seven Neolithic remains
excavated from a Spanish funeral cave dating to around 7,000
years BP (Lacan, Keyser, Ricaut, Brucato, Tarrus et al. 2011),
using the same northeast Iberian modern -13,910*T allele
frequency data (Rasinpera et al. 2005), and from 26 human
samples from a Late Neolithic necropolis in Treilles, southern
France (Lacan, Keyser, Ricaut, Brucato, Duranthon et al. 2011)
using a combined modern French -13,910*T allele frequency
data set of 270 chromosomes from individuals unrelated at
the second cousin level (Balkau 1996).
The Sequences obtained from the eight individuals from
this study are available from the authors upon request.
Supplementary Material
Supplementary figures S1 and S2 are available at Molecular
Biology and Evolution online (http://www.mbe.oxfordjournals.
org/).
Acknowledgments
O.O.S. is funded by an EU Marie Curie FP7 Framework
Programme grant (LeCHE, grant ref. 215362-2) awarded to
A.G., M.G.T., and others not involved in this study. The authors acknowledge the use of the UCL Legion High
Performance Computing Facility ([email protected]), and associated support services, in the completion of this work.
Atapuerca project is funded by Spanish Government project
CGL2012-38434-C03-01 and field work at the Atapuerca sites
by the Junta de Castilla y Leo´n. The authors thank David
Balding and Douglas Speed for their helpful advice and all
the participants of the D.E.S.I.R study—genotyping for the
modern French LCT data was supported by the Conseil
Re´gional Nord-Pas-de-Calais Fonds Europe´en de
De´veloppement Economique et Regional CPER axe
Cartdiodiabe`te 2010–2011 grant to Nabila Bouatia-Naji.
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