Patterns of genetic connectedness between modern and medieval Estonian genomes reveal the origins of a major ancestry component of the Finnish population

The Finnish population is a unique example of a genetic isolate affected by a recent founder event. Previous studies have suggested that the ancestors of Finnic-speaking Finns and Estonians reached the circum-Baltic region by the 1^st millennium BC. However, high linguistic similarity points to a more recent split of their languages. To study genetic connectedness between Finns and Estonians directly, we first assessed the efficacy of imputation of low-coverage ancient genomes by sequencing a medieval Estonian genome to high depth (23×) and evaluated the performance of its down-sampled replicas. We find that ancient genomes imputed from >0.1× coverage can be reliably used in principal-component analyses without projection. By searching for long shared allele intervals (LSAIs; similar to identity-by-descent segments) in unphased data for >143,000 present-day Estonians, 99 Finns, and 14 imputed ancient genomes from Estonia, we find unexpectedly high levels of individual connectedness between Estonians and Finns for the last eight centuries in contrast to their clear differentiation by allele frequencies. High levels of sharing of these segments between Estonians and Finns predate the demographic expansion and late settlement process of Finland. One plausible source of this extensive sharing is the 8^th-10^th centuries AD migration event from North Estonia to Finland that has been proposed to explain uniquely shared linguistic features between the Finnish language and the northern dialect of Estonian and shared Christianity-related loanwords from Slavic. These results suggest that LSAI detection provides a computationally tractable way to detect fine-scale structure in large cohorts.

Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe

Syphilis is a globally re-emerging disease, which has marked European history with a devastating epidemic at the end of the 15^th century. Together with non-venereal treponemal diseases, like bejel and yaws, which are found today in subtropical and tropical regions, it currently poses a substantial health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis' potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a high diversity of Treponema pallidum in early modern Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws-causing T. pallidum subspecies were already present in Northern Europe in the early modern period. We also discovered a previously unknown T. pallidum lineage recovered as a sister group to yaws- and bejel-causing lineages. These findings imply a more complex pattern of geographical distribution and etiology of early treponemal epidemics than previously understood.

The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East

In this study, we compare the genetic ancestry of individuals from two as yet genetically unstudied cultural traditions in Estonia in the context of available modern and ancient datasets: 15 from the Late Bronze Age stone-cist graves (1200-400 BC) (EstBA) and 6 from the Pre-Roman Iron Age tarand cemeteries (800/500 BC-50 AD) (EstIA). We also included 5 Pre-Roman to Roman Iron Age Ingrian (500 BC-450 AD) (IngIA) and 7 Middle Age Estonian (1200-1600 AD) (EstMA) individuals to build a dataset for studying the demographic history of the northern parts of the Eastern Baltic from the earliest layer of Mesolithic to modern times. Our findings are consistent with EstBA receiving gene flow from regions with strong Western hunter-gatherer (WHG) affinities and EstIA from populations related to modern Siberians. The latter inference is in accordance with Y chromosome (chrY) distributions in present day populations of the Eastern Baltic, as well as patterns of autosomal variation in the majority of the westernmost Uralic speakers [1-5]. This ancestry reached the coasts of the Baltic Sea no later than the mid-first millennium BC; i.e., in the same time window as the diversification of west Uralic (Finnic) languages [6]. Furthermore, phenotypic traits often associated with modern Northern Europeans, like light eyes, hair, and skin, as well as lactose tolerance, can be traced back to the Bronze Age in the Eastern Baltic. VIDEO ABSTRACT.

Three Thousand Years of Continuity in the Maternal Lineages of Ancient Sheep (Ovis aries) in Estonia

Although sheep (Ovis aries) have been one of the most exploited domestic animals in Estonia since the Late Bronze Age, relatively little is known about their genetic history. Here, we explore temporal changes in Estonian sheep populations and their mitochondrial genetic diversity over the last 3000 years. We target a 558 base pair fragment of the mitochondrial hypervariable region in 115 ancient sheep from 71 sites in Estonia (c. 1200 BC–AD 1900s), 19 ancient samples from Latvia, Russia, Poland and Greece (6800 BC–AD 1700), as well as 44 samples of modern Kihnu native sheep breed. Our analyses revealed: (1) 49 mitochondrial haplotypes, associated with sheep haplogroups A and B; (2) high haplotype diversity in Estonian ancient sheep; (3) continuity in mtDNA haplotypes through time; (4) possible population expansion during the first centuries of the Middle Ages (associated with the establishment of the new power regime related to 13^th century crusades); (5) significant difference in genetic diversity between ancient populations and modern native sheep, in agreement with the beginning of large-scale breeding in the 19^th century and population decline in local sheep. Overall, our results suggest that in spite of the observed fluctuations in ancient sheep populations, and changes in the natural and historical conditions, the utilisation of local sheep has been constant in the territory of Estonia, displaying matrilineal continuity from the Middle Bronze Age through the Modern Period, and into modern native sheep.

Thermally induced suppression of friction at the atomic scale

Atomic-scale friction, as accessed in tip-based experiments, is investigated theoretically in the full range of surface corrugations, temperatures, and velocities. Emphasis is given to the regime of thermal drift, when the regular stick-slip behavior is completely ruined by thermal effects. The possibility of nearly vanishing friction ("thermolubricity") is predicted even for strong (overcritical) surface corrugations, when traditional models would predict significant friction. The manifestation of this effect in recently published experimental data is demonstrated.

Influence of phosphorus intake on excretion and blood plasma and saliva concentrations of phosphorus in dairy cows

Phosphorus (P) balance, and blood plasma P and saliva P concentrations were measured in multiparous dairy cows through two lactations and two dry periods. The cows were fed three amounts of P at either 100, 80 or 67% of the Dutch P recommendation, actually resulting in dietary P concentrations of 3.2 to 3.9, 2.6 to 2.9 and 2.2 to 2.6 g P/kg dry matter during lactation for the three treatments, respectively. On the basis of plasma P values as low as 0.9 mmol/l and saliva P values as low as 5.1 mmol/l during the second lactation period within the experiment, the 67% group was considered to be deficient in P. By decreasing milk production, and thus lowering P losses with milk, P retention in the 67% group remained near zero. The P supply with the 80% ration was considered to be just sufficient. At high milk yield and marginal dietary P concentrations, plasma P and saliva P concentrations were decreased. The higher P intake in high-compared with low-producing cows resulted in a constant absolute fecal P excretion, due to the fact that the apparent P digestibility was raised with increasing milk yield. There was a direct relationship between milk P output and the percentage of apparent P digestibility for individual animals.

Influence of long-term feeding of limited amounts of phosphorus on dry matter intake, milk production, and body weight of dairy cows

For almost two lactations, 24 high-yielding, multiparous dairy cows were fed a basal diet and concentrate mixtures with three different P concentrations. The basal diet consisted of grass (silage or artificially dried), corn silage, wet beet pulp, straw, and concentrates. The concentrate mixtures differed only in P content by varying the amount of monosodium phosphate. The number of cows and the amount of dietary P, expressed as a percentage of current recommendations in the Netherlands were: 6 cows, 100% (P100); 9 cows, 80% (P80); and 9 cows, 67% (P67). This resulted in dietary P concentrations of 3.3, 2.8, and 2.4 g/kg of dietary DM for the P100, P80, and P67 treatments, respectively. The trial lasted for 21 mo, including two lactations and two dry periods. Feed intake of the P67 group was reduced significantly during the first dry period. Dry matter intake, milk yield, and body weight were all reduced with the low P treatment during the second lactation. Phosphorus had no effect on reproductive performance. Between P100 and P80, no effect on any of the variables in this trial was observed. Results suggests that the diet with 2.8 g of P/kg of dietary DM proved to be sufficient to meet the P requirement of dairy cows producing approximately 9000 kg of milk per lactation.

Intake and excretion of sodium, potassium, and nitrogen and the effects on urine production by lactating dairy cows

The present study was designed to describe the relationship between mineral metabolism and urine production by lactating dairy cows. Regression studies were performed to predict urine volume from either observed concentrations of K, Na, and N in urine or observed intakes of K, Na, and N. In addition, empirical equations were derived to assist in the estimation of urinary excretion of K, Na, and N in practical situations. Data used to derive the relationships (n = 67 observations) and to evaluate them (n = 62 observations) were obtained from a wide range of feeding conditions in 10 independent balance trials with lactating cows. Linear relationships of K, Na, and N that were excreted in urine or consumed were fitted against the observed urine production, which explained 89.8% (SE = 4.2 kg of urine/d) and 84.8% (SE = 5.2 kg of urine/d) of the variance. In evaluating these relationships, the observed variation in urine production was predicted with acceptable accuracy. Mean prediction errors were 4.5 and 5.6 kg of urine/d. Urine production could be predicted based on relationships between intakes of digestible Na, K, and N and their excretion in milk and urine. Reliable predictions of urine production are important as attention on the effect of manure production by dairy cows on nutrient management at the farm level increases.

Nutrient fluxes in splanchnic tissue of dairy cows: influence of grass quality

A crossover design was used to investigate the effects of high (450 kg of N/ha) or low (150 kg of N/ha) N fertilization of ryegrass on fermentation and nutrient fluxes in splanchnic tissue of dairy cows fed those grasses. Grass that was fertilized with the high amount of N contained more N and less sugar than did grass that was fertilized with less N. In rumen fluid, the concentration of NH3 N was lower for ryegrass that was fertilized with the low amount of N. The NH3 release by portal-drained viscera and urea synthesis in the liver were higher for cows fed ryegrass that was fertilized with the high amount of N. The concentration of NH3 N in rumen fluid, NH3 N release in portal-drained viscera, urea synthesis in the liver, urea release from the liver, and urea concentrations in milk were highly correlated. The release of acetate and propionate in portal-drained viscera was similar for both grasses and was well correlated with the proportion of volatile fatty acids in rumen fluid. The proportion of butyrate in rumen fluid was closely correlated with the release of butyrate and beta-hydroxybutyrate in portal-drained viscera. Glucose synthesis in the liver indicated gluconeogenesis from amino acids, which corresponded well with urea synthesis in the liver. For the grass fertilized with more N, availability of energy sources for rumen microbes was low, and, therefore, cows did not use the N in that grass efficiently.

Effects of partial replacement of ryegrass by low protein feeds on rumen fermentation and nitrogen loss by dairy cows

Three rumen fermentation studies in combination with three feeding trials were carried out to investigate the effect of partial replacement of heavily fertilized perennial ryegrass by low protein feedstuffs on pH and concentrations of VFA and NH3 N in the rumen and on N excretion in milk, urine, and feces by dairy cows. Feedstuffs tested were high fiber concentrate mixtures based on sugar beet pulp and soybean hulls and high starch concentrate mixtures based on corn (Experiments 1 and 2), corn silage (Experiment 1), dried and ensiled pressed sugar beet pulp and high moisture ear corn silages with or without husks (Experiment 3). In the fermentation studies, N intake ranged between .43 and .57 kg/d. Partial replacement often increased DMI (maximal by 2.6 kg), resulting in minor effects on N intake. Urinary N excretion ranged between 30 and 58% of N intake and decreased by 30 to 40% when grass was partially replaced. Fecal N output was between 25 and 30% of N intake and tended to increase with the low protein feed. The reduction in urinary N excretion corresponded to a decrease of rumen NH3 N. Replacement by concentrate mixtures based on corn reduced milk fat content; for mixtures based on beet pulp, milk fat content was not changed.

Effect of fibrous and starchy carbohydrates in concentrates as supplements in a herbage-based diet for high-yielding dairy cows

The effects of 2 concentrates composed of different carbohydrate sources (beet pulp vs. maize) on intake, digestibility, yield and composition of milk from high-yielding dairy cows given fresh herbage indoors was investigated. In 1988 two diets and in 1989 three diets were used with 9 cows/diet. In 1989 concentrates were supplied on an equal amount of DM and in 1989 on an equal amount of energy. The animals received the concentrates after milking time. In 1988 the experimental period lasted 8 wk and in 1989 10 wk. In 1988 intake of herbage DM tended to be higher on the maize-enriched diet, resulting in a significantly (P