Hunting for the LCT-13910*T allele between the Middle Neolithic and the Middle Ages suggests its absence in dairying LBK people entering the Kuyavia region in the 8th millennium BP

Abstract

Populations from two medieval sites in Central Poland, Stary Brześć Kujawski-4 (SBK-4) and Gruczno, represented high level of lactase persistence (LP) as followed by the LCT-13910*T allele's presence (0.86 and 0.82, respectively). It was twice as high as in contemporaneous Cedynia (0.4) and Śródka (0.43), both located outside the region, higher than in modern inhabitants of Poland (0.51) and almost as high as in modern Swedish population (0.9). In an attempt to explain the observed differences its frequency changes in time were followed between the Middle Neolithic and the Late Middle Ages in successive dairying populations on a relatively small area (radius ∼60km) containing the two sites. The introduction of the T allele to Kuyavia 7.4 Ka BP by dairying LBK people is not likely, as suggested by the obtained data. It has not been found in any of Neolithic samples dated between 6.3 and 4.5 Ka BP. The identified frequency profile indicates that both the introduction and the beginning of selection could have taken place approx. 4 millennia after first LBK people arrived in the region, shifting the value of LP frequency from 0 to more than 0.8 during less than 130 generations. We hypothesize that the selection process of the T allele was rather rapid, starting just after its introduction into already milking populations and operated via high rates of fertility and mortality on children after weaning through life-threatening conditions, favoring lactose-tolerant individuals. Facing the lack of the T allele in people living on two great European Neolithization routes, the Danubian and Mediterranean ones, and based on its high frequency in northern Iberia, its presence in Scandinavia and estimated occurrence in Central Poland, we propose an alternative Northern Route of its spreading as very likely. None of the successfully identified nuclear alleles turned out to be deltaF508 CFTR.

Fig 1. Location of the explored Polish archaeological sites.

Fig 2. Each 3D plot together with its 2D projection presents probability of a scenario with given selection coefficient and the T allele introduction time, assuming variable population size (see S1 Fig. for the shape of the size curve).

The height/color of each bar represents the percentage of Wright-Fisher curves (number per 1000) falling into appropriate confidence intervals shown in Table 2: A—the T allele, B—LP, C—the T allele and LP jointly.

Fig 3. Mean allele frequency calculated for two chosen scenarios from Fig. 2A (only curves falling into confidence intervals were taken into account) along with their probabilities marked on the interpolated version of 2D part of Fig. 2A (curve 1—probability 0.027, curve 2—probability 0.297).

Fig 4. Median joining phylogenetic network of 131 ancient inhabitants of Polish lands based on HVR-I sequences (nt 16115–16340, motifs in red).

80 samples are from archaeological sites located on a relatively small area belonging to Kuyavia and the Chełmno land and represent people living between 6.5–6.1 Ka BP and 0.8–0.6 Ka BP, i.e. 9 individuals dated to Polish Neolithic (3—Lengyel culture, 6—Globular Amphora culture), 8 from Polish Late Bronze Age/Early Iron Age (Hallstatt culture), 34 from Polish Roman Period (Wielbark culture; Linowo—13, Rogowo—21) and 29 from Polish Middle Ages (Gruczno—15, SBK-4–14). Additional 51 medieval samples collected outside Kuyavia and the Chełmno land (Cedynia—35, Sródka—16) constituted the reference group. Origin of the sample is marked with different colors. The size of the node is proportional to the number of individuals.

Fig 5. Suggested Northern Route of LCT-13910*T spreading.

Contrasted is time-dependent occurrence of the T allele along west-east gradient from Iberia (0.27; >5 Ka BP [66]), through Scandinavia (0.05; >4 Ka BP [67]), up to Kuyavia and the Chełmno land (<4 Ka BP as predicted by us), with its simultaneous absence along the Danubian and Mediterranean Routes.