A distant city: Assessing the impact of Dutch socioeconomic developments on urban and rural health using respiratory disease as a proxy.

OBJECTIVES: To investigate the prevalence of respiratory disease in several populations from the Netherlands across different time periods and socioeconomic conditions. MATERIALS: We analyzed 695 adult individuals from six different Dutch contexts of urban and rural settlements dating to different time periods (i.e., early-medieval, late-medieval, post-medieval). METHODS: For each individual, the presence/absence of chronic maxillary sinusitis, otitis media, and inflammatory periosteal reaction on ribs was recorded macroscopically according to accepted methods. RESULTS: Statistically significant associations were found in the presence of sinusitis diachronically (early-medieval to late-medieval period, and early-medieval to post-medieval period) both in rural and urban environments. Differences in prevalence rates of otitis media were found statistically significant when comparing rural to urban environments in the early-medieval and late-medieval periods. CONCLUSION: Our results suggest that factors such as increased contact between towns and countryside, higher population densities, and intensification of agricultural production impacted the respiratory health of past populations both in rural and urban settings. SIGNIFICANCE: Our study provides new insights into the impact of environmental changes and urbanization on respiratory disease prevalence, shedding light on the relationship between health and changing social and environmental contexts. LIMITATIONS: Research limitations included the complex etiology of respiratory diseases, and the impact of uncontrollable factors such as hidden heterogeneity, selective mortality, and rural-to-urban migration. FUTURE RESEARCH: Further research in different contexts is advised in order to continue exploring urbanization and its impact on human health across both time and space.

Isotopic reconstruction of short to absent breastfeeding in a 19th century rural Dutch community.

Artificial feeding of young infants is considered a modern phenomenon. However, historical sources note its practice in some past European populations. This research explores factors that contributed to a short to absent period of breastfeeding in pre-modern Netherlands. Stable nitrogen and carbon isotope analysis is undertaken on 277 19th century individuals from Beemster, a, rural, mainly Protestant, dairy farming community. An intra-individual sampling approach for ≤6 year-olds compares newer metaphyseal to older diaphyseal long bone collagen to classify feeding status at death. Archivally identified individuals permit analyses of sex and year-of-death. Few infants have isotopic evidence for breastfeeding and, if present, it was likely of short duration or a minor source of dietary protein. From only a few weeks to months of age infants were fed cow's milk and paps with sugar. There is broad dietary homogeneity with no sex or temporal isotopic differences, but young infants (1-11 months) have the most ẟ15N and ẟ13C variation highlighting the effect of multiple dietary and physiological processes. Beemster had many factors associated with high rates of breastfeeding in other Dutch communities, yet, most mothers did not breastfeed, or not for long, showing that regional variation in infant feeding is influenced by community values and traditions. On top of child rearing and domestic chores, female dairy farmers were in charge of milking cattle and dairy production, an important income source, suggesting high workload was also a factor in short or absent breastfeeding periods, aided by the constant supply of fresh milk that could be fed to an infant by an older sibling.

Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology.

Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.

Quantifying cortical bone in fragmentary archeological second metacarpals.

OBJECTIVES: Skeletal variation in cortical bone thickness is an indicator of bone quality and health in archeological populations. Second metacarpal radiogrammetry, which measures cortical thickness at the shaft midpoint, is traditionally used to evaluate bone loss in bioarcheological and some clinical contexts. However fragmentary elements are regularly omitted because the midpoint cannot be determined. This methodological limitation reduces sample sizes and biases them against individuals prone to fracture, such as older individuals with low bone mass. This study introduces a new technique for measuring cortical bone in second metacarpals, the "Region of Interest" (ROI) method, which quantifies bone in archeological remains with less-than-ideal preservation while accounting for cortical heterogeneity. MATERIALS AND METHODS: The ROI method was adapted from digital X-ray radiogrammetry (DXR), a clinical method used to estimate bone mineral density, and tested using second metacarpals from Middenbeemster, Netherlands, a 19th century known age and sex skeletal collection. The ROI method quantifies cortical bone area within a 1.9 cm-long, mid-diaphyseal region, standardized for body size differences using total area (CAIROI ). CAIROI values were compared to traditional radiogrammetric cortical indices (CI) to assess the method's ability to identify age-related bone loss. RESULTS: CAIROI values have high intra- and interobserver replicability and are strongly and significantly correlated with CI values for both males (r[n = 39] = 0.906, p = 0.000) and females (r[n = 58] = 0.925, p = 0.000). CONCLUSION: The ROI method complements traditional radiogrammetry analyses and provides a reliable way to quantify cortical bone in incomplete second metacarpals, thereby maximizing sample sizes, allowing patterns in bone acquisition and loss to be more comprehensively depicted in archeological assemblages.

Coming of age in the Netherlands: An osteological assessment of puberty in a rural Dutch post-medieval community.

OBJECTIVES: The objective of this study is to apply pubertal stage estimation methods to a sample from a rural community: the post-medieval Dutch skeletal collection from Middenbeemster. Puberty is a key developmental period involving transition to physical adulthood with broad societal relevance through its impact on fertility, morbidity, and mortality. MATERIALS AND METHODS: Individuals (n = 55), including 27 of known sex and age-at-death, between the ages of 8 and 25 years were assessed for six skeletal markers indicative of pubertal growth spurt. Recent novel osteoarchaeological methods from Shapland and Lewis are used to reconstruct the timing and duration of pubertal stages. RESULTS: Pubertal acceleration occurred earlier in females (10.38 years, n = 8) than males (13.30 years, n = 6), whereas maturation occurred later in males (21.36 years, n = 11) than females (19.30 years, n = 5). Onset appears earlier and completion later compared to other archaeological skeletal samples with osteoarchaeological evidence of puberty. Age shortly after menarche was reconstructed at 20.45 years, substantially later than historic records and bioarchaeological research reports suggest. CONCLUSION: This early onset and late completion caused a "stretch" of the overall duration of puberty compared to other collections, especially of the last three stages. This prolonged development is reflected in historically known social expectations for the Netherlands, for example, that marriage and children should not occur before about 22-23 years of age. Increasing the range of past peoples with puberty stage reconstruction will permit more insightful interpretations of the biological and cultural patterns of this important life stage.

Getting Rid of Dichotomous Sex Estimations: Why Logistic Regression Should be Preferred Over Discriminant Function Analysis.

Sex estimation is an important part of creating a biological profile for skeletal remains in forensics. The commonly used methods for developing sex estimation equations are discriminant function analysis (DFA) and logistic regression (LogR). LogR equations provide a probability of the predicted sex, while DFA relies on cutoff points to segregate males and females, resulting in a rigid dichotomization of the sexes. This is problematic because sexual dimorphism exists along a continuum and there can be considerable overlap in trait expression between the sexes. In this study, we used humeral measurements to compare the performance of DFA and LogR and found them to be very similar under multiple conditions. The overall cross-validated (leave-one-out) accuracy of DFA (75.76-95.14%) was slightly higher than LogR (75.76-93.82%) for simple and multiple variable equations, and also performed better under varying sample sizes (94.03% vs. 93.78%). Three of five DFA equations outperformed LogR under the B index, while all five LogR equations outperformed the DFA equations under the Q index. Both methods saw an improvement in overall accuracy (DFA: 86.74-95.79%; LogR: 86.74-95.76%) when individuals with a classification probability lower than 0.80 were excluded. Additionally, we propose a method for calculating additional cutoff points (PMarks) based on posterior probability values. In conclusion, we recommend using LogR over DFA due to the increased flexibility, robusticity, and benefits for future users of the statistical models; however, if DFA is preferred, use of the proposed PMarks facilitates future analysis while avoiding unnecessary dichotomization.

Genomic insights into the early peopling of the Caribbean.

The Caribbean was one of the last regions of the Americas to be settled by humans, but where they came from and how and when they reached the islands remain unclear. We generated genome-wide data for 93 ancient Caribbean islanders dating between 3200 and 400 calibrated years before the present and found evidence of at least three separate dispersals into the region, including two early dispersals into the Western Caribbean, one of which seems connected to radiation events in North America. This was followed by a later expansion from South America. We also detected genetic differences between the early settlers and the newcomers from South America, with almost no evidence of admixture. Our results add to our understanding of the initial peopling of the Caribbean and the movements of Archaic Age peoples in the Americas.

Micro-CT assessment of dental mineralization defects indicative of vitamin D deficiency in two 17th-19th century Dutch communities.

OBJECTIVES: This study investigates vitamin D deficiency patterns in individuals from birth to the beginning of adolescence. Microscopic computed tomography (micro-CT) evaluation of interglobular dentine (IGD) in teeth provides information on the age of disease onset and the number of deficient periods per individual, which will increase our understanding of factors influencing vitamin D deficiency prevalence, including sociocultural practices and latitude. MATERIALS AND METHODS: Beemster and Hattem, two Dutch 17th-19th century communities, yielded relatively high prevalences of rickets (15-24%) and residual rickets (15-24%). From the affected individuals, a subsample of 20 teeth were selected for micro-CT scanning. Thin sections were made of 17 teeth, consisting of 6 teeth with and 11 teeth without observable IGD on micro-CT that were included for method comparison. RESULTS: About 19 out of 29 (65.5%) individuals (one tooth was deemed unobservable) presented with IGD on micro-CT. Eight of the 11 (72.7%) individuals without IGD on micro-CT demonstrated histologically visible IGD. In 40.7% (11/27) of the affected individuals (combined micro-CT and histology results), vitamin D deficiency was recurrent, and in four individuals, some episodes occurred at approximately annual intervals suggesting vitamin D deficiency was seasonal. In three individuals, IGD occurred in the dentine formed around birth, suggesting maternal vitamin D deficiency. DISCUSSION: Micro-CT analysis of IGD is found to be a valuable non-destructive method that can improve our understanding of the influence of sociocultural practices and latitude on disease development within age and sex groups in past communities.

The efficacy of whole human genome capture on ancient dental calculus and dentin.

OBJECTIVES: Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. MATERIALS AND METHODS: Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing. RESULTS: Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four-fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction. DISCUSSION: While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.

Gender-related vitamin D deficiency in a Dutch 19th century farming community.

The most common cause of vitamin D deficiency is inadequate dermal exposure to sunlight. Residual rickets is nonadult vitamin D deficiency still evident in an adult individual, whereas osteomalacia occurs in adulthood. Previous research on the Beemster population, a 19th century rural community in the Netherlands, identified rickets in 30.4% of the nonadults between the ages of two and four years (n=7/23). Because the sex of these nonadults was not known it was not possible to determine if there were differences between boys and girls. To overcome this gap in our knowledge, the aim of this paper is to determine if there are gender related differences in vitamin D deficiency in the Beemster skeletal collection, based on adults with residual rickets and osteomalacia. Out of 200 adults (100 females; 100 males) no cases of osteomalacia were detected. However, there were 29 cases of residual rickets (14.5%), with 21 of those cases in females (21.0%; 21/100). A complex interplay of multiple factors is proposed to have affected vitamin D levels in nonadults, including sociocultural variables such as gender-based labour norms. This research highlights the importance of continuing to explore gender-based health differences in past populations.

Columbus' environmental impact in the New World: Land use change in the Yaque River valley, Dominican Republic.

Columbus' arrival in the New World in AD 1492 on the northern coast of Hispaniola was followed by a suite of changes in land-use. We reconstruct environmental change from a 225-cm-long sediment core from site Los Indios from an abandoned and sediment-filled meander of the Yaque River, Cibao Valley, northeastern Dominican Republic. The sediment record starts ca. AD 195 (ca. 1755 cal. yr BP) and the history of the meander infill was monitored by changing grain size distributions, organic matter concentration and pollen from wetland plants. From ca. AD 200 to ca. AD 1525, the pollen record indicates a diverse forest assemblage; however, the presence of pollen from potential crop plants suggest nearby small-scale subsistence crop cultivation. More abundant charcoal after ca. AD 1410 shows Amerindians increasingly used fire. The record of grain size distributions shows that the meander was temporarily part of a low energetic drainage system in which bedload and suspended sediments accumulated. After European colonization of Hispaniola increasing spores of coprophilous fungi evidence that Europeans had introduced during the first decades of colonization cattle in the Cibao Valley which gradually resulted in more open forest. The charcoal record around ca. AD 1650 reflects intensive forest clearing, suggesting that small-scale Pre-Colonial practice of crop cultivation became replaced by large-scale agriculture on the moist and nutrient rich soils along the Yaque River. Further deforestation and signals of erosion suggest that the population of colonists and introduced enslaved labour force must have increased rapidly. After ca. AD 1740 charcoal influx decreased suggesting that last deforestation activities used selective cutting to produce fire wood and timber for construction, rather than burning forest in situ. Two centuries after European colonization, by the 18th century, land-use within the Cibao Valley had become a balance between substantial livestock and crop cultivation (pollen grains have evidenced cereals, maize, and potentially also sugar cane, amaranthaceous crops and tobacco). After ca. AD 1950, swamp vegetation of Typha and Cyperaceae decreased, pointing to an almost fully terrestrialized meander with only few bodies of standing water, reflecting the present-day setting. This multiproxy reconstruction of anthropogenic environmental change shows a clear differentiation between an immediate introduction of livestock and after some 150 years the development of a European style agriculture, providing a context for archaeological investigations.

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin.

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007-0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003-70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.

A probable case of metastatic carcinoma in the medieval Netherlands.

Despite recent considerable gains, our knowledge of cancer in antiquity is still limited. This paper discusses an adult individual from a Dutch medieval hospital site who demonstrates osteoblastic and osteolytic lesions on the ribs, scapula, clavicle, and vertebrae. The morphology, radiographic appearance, and distribution of the skeletal lesions suggest that this individual was affected by metastatic carcinoma. This case increases the number of publications that present an osteoblastic and osteolytic response to cancer and contributes to the body of evidence for archaeological neoplastic disease. For the Netherlands, this individual presents the first published case of probable metastatic carcinoma with mixed skeletal lesions.

Trabecular bone microarchitecture analysis, a way for an early detection of genetic dwarfism? Case study of a dwarf mother's offspring.

A 66 year-old woman with a disproportionate dwarfism and who bore seven children was discovered at the Middenbeemster archaeological site (The Netherlands). Three are perinates and show no macroscopic or radiological evidence for a FGFR3 mutation causing hypo-or achondroplasia. This mutation induces dysfunction of the growth cartilage, leading to abnormalities in the development of trabecular bone. Because the mutation is autosomal dominant, these perinates have a 50% risk of having been affected. This study determines whether trabecular bone microarchitecture (TBMA) analysis is useful for detecting genetic dwarfism. Proximal metaphyses of humeri were µCT-scanned with a resolution of 7-12 µm. Three volumes of interest were segmented from each bone with TIVMI© software. The TBMA was quantified in BoneJ© using six parameters on which a multivariate analysis was then performed. Two of the Middenbeemster perinates show a quantitatively different TBMA organization. These results and the family's medical history suggest a diagnosis of genetic dwarfism for this two perinates. This study provides evidence to support the efficacy of µCT for diagnosing early-stage bone disease.

Origins and genetic legacies of the Caribbean Taino.

The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher's Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.

Osteochondritis Dissecans of skeletal elements of the foot in a 19th century rural farming community from The Netherlands.

Osteochondritis Dissecans (OD) is a pathological condition of the subchondral bone and surrounding cartilage of synovial joints, associated with strenuous activity and/or trauma. Reports of OD in archaeological skeletal remains are few and the majority demonstrate low OD prevalence (<1%). A predominantly 19th century skeletal sample from Middenbeemster, the Netherlands, was assessed for OD. The sample included adult individuals of both sexes. There were no definitive OD lesions in non-pedal elements, yet 12.9% of individuals suffered from pedal OD. Few archaeological and clinical reports specify the prevalence of pedal OD. According to the few that do, the Middenbeemster pedal OD prevalence is distinctly high. Several factors could have contributed to this. First, the rural Beemster community was centered around cattle farming, requiring extensive outside work and animal maintenance; thus, increasing the chances of acute/repetitive trauma in the foot. Second, the footwear worn during that period in the Netherlands was the wooden clog. It is suggested that the hard and inflexible clog, which is poor at absorbing shock and limits the movement of the foot, could have resulted in repetitive microtrauma. These two factors combined may have caused a high frequency of OD.

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.

Unexpected evolutionary diversity in a recently extinct Caribbean mammal radiation.

Identifying general patterns of colonization and radiation in island faunas is often hindered by past human-caused extinctions. The insular Caribbean is one of the only complex oceanic-type island systems colonized by land mammals, but has witnessed the globally highest level of mammalian extinction during the Holocene. Using ancient DNA analysis, we reconstruct the evolutionary history of one of the Caribbean's now-extinct major mammal groups, the insular radiation of oryzomyine rice rats. Despite the significant problems of recovering DNA from prehistoric tropical archaeological material, it was possible to identify two discrete Late Miocene colonizations of the main Lesser Antillean island chain from mainland South America by oryzomyine lineages that were only distantly related. A high level of phylogenetic diversification was observed within oryzomyines across the Lesser Antilles, even between allopatric populations on the same island bank. The timing of oryzomyine colonization is closely similar to the age of several other Caribbean vertebrate taxa, suggesting that geomorphological conditions during the Late Miocene facilitated broadly simultaneous overwater waif dispersal of many South American lineages to the Lesser Antilles. These data provide an important baseline by which to further develop the Caribbean as a unique workshop for studying island evolution.

Osteological evidence of short-limbed dwarfism in a nineteenth century Dutch family: Achondroplasia or hypochondroplasia.

An opportunity to explore osteological features of a form of disproportionate dwarfism is presented by a recent archaeological discovery. Excavation of a predominately nineteenth century Dutch cemetery from the rural, agricultural village of Middenbeemster revealed an older adult female with skeletal changes consistent with achondroplasia. The most marked features are a rhizomelic pattern of shortened and thickened upper and lower limbs, frontal bossing and a moderately depressed nasal bridge, small lumbar neural canals with short pedicles, bowing of the femora and tibiae, and short stature (130.0±5cm). However, some common features of achondroplasia like cranial base reduction and shortened fingers and toes are absent. The alternative diagnosis of a more mild form of short-limbed dwarfism, hypochondroplasia, is explored and aided by archival identification of the individual and her offspring. Five offspring, including three perinates, a 10-year-old daughter, and a 21-year-old son, are analysed for evidence of an inherited skeletal dysplasia. The unique addition of family history to the paleopathological diagnostic process supports a differential outcome of hypochondroplasia. This combination of osteological and archival data creates a unique opportunity to track the inheritance and manifestation of a rare disease in a past population.