Dairying, diseases and the evolution of lactase persistence in Europe.

In European and many African, Middle Eastern and southern Asian populations, lactase persistence (LP) is the most strongly selected monogenic trait to have evolved over the past 10,000 years1. Although the selection of LP and the consumption of prehistoric milk must be linked, considerable uncertainty remains concerning their spatiotemporal configuration and specific interactions2,3. Here we provide detailed distributions of milk exploitation across Europe over the past 9,000 years using around 7,000 pottery fat residues from more than 550 archaeological sites. European milk use was widespread from the Neolithic period onwards but varied spatially and temporally in intensity. Notably, LP selection varying with levels of prehistoric milk exploitation is no better at explaining LP allele frequency trajectories than uniform selection since the Neolithic period. In the UK Biobank4,5 cohort of 500,000 contemporary Europeans, LP genotype was only weakly associated with milk consumption and did not show consistent associations with improved fitness or health indicators. This suggests that other reasons for the beneficial effects of LP should be considered for its rapid frequency increase. We propose that lactase non-persistent individuals consumed milk when it became available but, under conditions of famine and/or increased pathogen exposure, this was disadvantageous, driving LP selection in prehistoric Europe. Comparison of model likelihoods indicates that population fluctuations, settlement density and wild animal exploitation-proxies for these drivers-provide better explanations of LP selection than the extent of milk exploitation. These findings offer new perspectives on prehistoric milk exploitation and LP evolution.

A minimally destructive protocol for DNA extraction from ancient teeth.

Ancient DNA sampling methods-although optimized for efficient DNA extraction-are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.

Human auditory ossicles as an alternative optimal source of ancient DNA.

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

Parallel palaeogenomic transects reveal complex genetic history of early European farmers.

Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000-2900 bc, n = 100), Germany (5500-3000 bc, n = 42) and Spain (5500-2200 bc, n = 38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions.

The evolution of dual meat and milk cattle husbandry in Linearbandkeramik societies.

Cattle dominate archaeozoological assemblages from the north-central Europe between the sixth and fifth millennium BC and are frequently considered as exclusively used for their meat. Dairy products may have played a greater role than previously believed. Selective pressure on the lactase persistence mutation has been modelled to have begun between 6000 and 4000 years ago in central Europe. The discovery of milk lipids in late sixth millennium ceramic sieves in Poland may reflect an isolated regional peculiarity for cheese making or may signify more generalized milk exploitation in north-central Europe during the Early Neolithic. To investigate these issues, we analysed the mortality profiles based on age-at-death analysis of cattle tooth eruption, wear and replacement from 19 archaeological sites of the Linearbandkeramik (LBK) culture (sixth to fifth millennium BC). The results indicate that cattle husbandry was similar across time and space in the LBK culture with a degree of specialization for meat exploitation in some areas. Statistical comparison with reference age-at-death profiles indicate that mixed husbandry (milk and meat) was practised, with mature animals being kept. The analysis provides a unique insight into LBK cattle husbandry and how it evolved in later cultures in central and western Europe. It also opens a new perspective on how and why the Neolithic way of life developed through continental Europe and how dairy products became a part of the human diet.

Quantification of spinal ataxia in dogs with thoracolumbar spinal cord injury.

The clinical sign of ataxia is related to several neurological diseases and is seen in conjunction with paresis in dogs with spinal cord injury (SCI). Endeavours to objectify canine spinal ataxia in SCI remain limited. The aim of this clinical study was to determine and quantify differences between gait characteristics of ataxic dogs with thoracolumbar myelopathy and healthy control dogs using a computer-and treadmill-based gait analysis system. Five dogs with spinal ataxia and six healthy dogs underwent video-and computer-assisted gait analysis while walking on a four-ground reaction force plate treadmill system (maximum speed of 0.7 m/s). Spatio-temporal and kinetic gait characteristics regarding the dogs' locomotion were analysed with a focus on the individual coefficient of variation (CV), as a potential measure for quantification of the level of ataxia. Ataxic dogs with thoracolumbar SCI showed no effect on symmetry indices but higher variability in spatio-temporal and kinetic gait parameters mainly in the pelvic, but also in the thoracic limbs. Double support phase of the individual limb was prolonged in SCI dogs at the cost of the single support and swing phase. Reduced peaks of ground reaction forces (GRF) could potentially be explained by reduction of muscle strength, as a strategy of avoiding falling by taking enthusiastic steps, or by alteration of the rhythmogenic spinal circuits between the pelvic and thoracic limb pattern generators.

Quantification of phenobarbital-induced ataxia in dogs with idiopathic epilepsy.

Ataxia is a clinical sign seen in several neurological diseases and has been reported as an adverse effect of anti-seizure medication such as phenobarbital (PB). Efforts to objectify canine ataxia in order to provide appropriate treatment or monitor adverse effects of drugs remain limited. Automated quantitative gait analysis can be useful for the acquisition of objective data for the evaluation and monitoring of ataxia in dogs. The aim of this prospective clinical study was to examine the gait characteristics of dogs with PB induced ataxia and compare them with healthy dogs using a computer- and treadmill-based gait analysis system. Six healthy dogs and five dogs with idiopathic epilepsy (IE) with PB-induced ataxia underwent video- and computer-assisted gait analysis during slow walking (maximum speed of 0.7 m/s) on a treadmill with four ground reaction force plates (one plate per limb). Kinetic and spatio-temporal gait parameters of dogs' locomotion were analyzed, including individually calculated coefficients of variation. Dogs with IE treated with PB showed higher variability in spatio-temporal but not in kinetic gait parameters. Double support phase of gait cycles was increased on the cost of single support and swing phases. Body weight standardized ground reaction forces in vertical, craniocaudal, and mediolateral direction were severely affected by ataxia. Compensatory mechanisms in locomotion of dogs with PB-induced ataxia included spatio-temporal and kinetic gait characteristics, most likely in order to compensate imbalance caused by limb incoordination.

Tuberculosis in prehistory in Eastern Central Europe (Hungary) - Chronological and geographical distribution.

Tuberculosis (TB) has long been a major scourge of humankind. Paleopathological and paleomicrobiological studies have revealed the past presence of the disease on a large spatial and temporal scale. The antiquity of the disease has extensively been studied in the Carpathian Basin, given its dynamic population and cultural changes since prehistory. These studies, however, have mainly focused on the populations living during the Common Era. The aim of this paper is to present the published and the recently discovered cases of prehistoric TB, from the Neolithic (6000-4500/4400 BCE) to the Bronze Age (2600/2500-800 BCE) Central Carpathian Basin (Hungary). We summarize 18 published cases and present new cases dating to the Neolithic period and introduce 3 newly discovered Bronze Age cases of TB. Despite extensive research, TB has not yet been identified from the Copper and Iron Ages in the Carpathian Basin. Considering the state of TB research, and supplemented by our prehistoric dataset, the spatio-temporal pattern of the disease can be further elucidated, thus advancing future molecular and paleopathological studies. Our dataset offers comprehensive spatial and temporal information on the spread of the disease in the Carpathian Basin, along with a detailed biological profile of the demonstrated cases and extensive paleopathological descriptions of the observed lesions, complemented by photographic evidence. This invaluable resource paves the way for enhanced understanding and progress in the field.

Sagittal suture morphological variation in human archaeological populations.

Cranial sutures join the many bones of the skull. They are therefore points of weakness and consequently subjected to the many mechanical stresses affecting the cranium. However, the way in which this impacts their morphological complexity remains unclear. We examine the intrinsic and extrinsic mechanisms of human sagittal sutures by quantifying the morphology from 107 individuals from archaeological populations spanning the Mesolithic to Middle ages, using standardized two-dimensional photographs. Results show that the most important factor determining sutural complexity appears to be the position along the cranial vault from the junction with the coronal suture at its anterior-most point to the junction with the lambdoid suture at its posterior-most point. Conversely, factors such as age and lifeways show few trends in complexity, the most significant of which is a lower complexity in the sutures of Mesolithic individuals who consumed a tougher diet. The simple technique used in this study therefore allowed us to identify that, taken together, structural aspects play a more important role in defining the complexity of the human sagittal suture than extrinsic factors such as the mechanical forces imposed on the cranium by individuals' diet.

Limb and back muscle activity adaptations to tripedal locomotion in dogs.

Alterations in muscle recruitment are key to the functional plasticity of the mammalian locomotor system. One particularly challenging situation quadrupeds may face is when the functionality of a limb is reduced or lost. To better understand how mammals manage in such situations and which muscular adaptations they exhibit when locomoting on three legs, we recorded the activity patterns of two limb and one back extensor muscle in nine dogs using surface electromyography. We compared the timing and the level of recruitment before and after the loss of a hindlimb was simulated. Both the intensity and the timing of the activity changed significantly in the m. vastus lateralis of the remaining hindlimb, consistent with this limb bearing a greater proportion of the body weight as well as with previously reported kinematic changes. In accordance with the greater body weight supported by the forelimbs, the m. triceps brachii showed first and foremost an increased level of excitation. The very asymmetrical changes in the timing and the level of activity in the m. longissimus dorsi reflects the highly asymmetrical functional requirements imposed on the trunk and the pelvis when one hindlimb is no longer involved in the production of locomotor work while the other hindlimb partially compensates the loss. Integration of our electromyographical findings with kinetic and kinematic results illustrates that dogs exhibited a well-coordinated response to the functional requirements of tripedalism and underlines the importance of moment-to-moment modulation in muscular recruitment for the functional plasticity of the mammalian locomotor system.

Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone.

The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.

Ontogenetic change of the weight support pattern in growing dogs.

Weight support patterns vary widely among mammals. Differences in how much of the body weight is supported by the fore- versus the hind-limbs are well documented among and within species. Intraindividual variation due to ontogenetic processes has been studied in several hindlimb-dominated species and consistently showed a caudal shift in the limbs' support roles. We hypothesized that forelimb-dominated species exhibit a cranial shift in their support pattern and tested this hypothesis by examining the vertical ground reaction forces in growing dogs. Six male Beagle siblings were studied from 9 to 51 postnatal weeks (PW) of age while they trotted on an instrumented treadmill. Ontogenetic shifting in fore-to-hind support was evaluated using vertical force ratios (i.e., peak and impulse) as well as the stance time ratio of the fore- and the hind-limbs. Because morphological and kinematic characteristics influence weight support patterns, changes in body shape (i.e., trunk shape), and average limb position were determined. As in adult dogs, the forelimbs carried a greater proportion of the body weight than the hindlimbs at all ages. When the dogs were younger, peak vertical force occurred earlier during stance in the hindlimbs but not the forelimbs. Both the increasing ratio of the vertical force and the increasing ratio of the stance times indicate an increasing weight support by the forelimbs (i.e., 59% at PW9 vs. 63% at PW51). The observed ontogenetic changes in trunk shape and average limb angle were consistent with this cranial shift in weight support.

Genome flux and stasis in a five millennium transect of European prehistory.

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe's genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.

Load redistribution in walking and trotting Beagles with induced forelimb lameness.

OBJECTIVE: To evaluate the load redistribution mechanisms in walking and trotting dogs with induced forelimb lameness. ANIMALS: 7 healthy adult Beagles. PROCEDURES: Dogs walked and trotted on an instrumented treadmill to determine control values for peak and mean vertical force as well as vertical impulse for all 4 limbs. A small sphere was attached to the ventral pad of the right forelimb paw to induce a reversible lameness, and recordings were repeated for both gaits. Additionally, footfall patterns were assessed to test for changes in temporal gait variables. RESULTS: During walking and trotting, peak and mean vertical force as well as vertical impulse were decreased in the ipsilateral forelimb, increased in the contralateral hind limb, and remained unchanged in the ipsilateral hind limb after lameness was induced. All 3 variables were increased in the contralateral forelimb during trotting, whereas only mean vertical force and vertical impulse were increased during walking. Stance phase duration increased in the contralateral forelimb and hind limb during walking but not during trotting. CONCLUSIONS AND CLINICAL RELEVANCE: Analysis of the results suggested that compensatory load redistribution mechanisms in dogs depend on the gait. All 4 limbs should be evaluated in basic research and clinical studies to determine the effects of lameness on the entire body. Further studies are necessary to elucidate specific mechanisms for unloading of the affected limb and to determine the long-term effects of load changes in animals with chronic lameness.