Biology subjects

Irish, J. D.

Publications and source records attributed to Irish, J. D..

9 recordsLinked to original sources

bioRxiv2026

DeMoDa: A global open access database for comparative research in human dental morphological variation

Human dental morphology is diverse and varies both within and between populations worldwide. Common variants include different numbers of cusps and roots, as well as different configurations in the fissures, ridges, and grooves on tooth crowns. Because teeth preserve well in taphonomic contexts and retain strong genetic signatures in their morphology, researchers across disciplines use dental form for research ranging from population affinity identification in forensic cases to the reconstruction of population history in archaeological and paleontological studies, and to explore the genetic underpinnings of dental development. However, these analyses are limited, as no publicly available comprehensive database of human dental morphological variation currently exists. Data are typically shared only within professional networks, excluding scientists outside those circles. Information is dispersed across repositories and the supplementary materials that accompany peer-reviewed publications, creating a fragmented and difficult-to-navigate data landscape. Although numberous dental anthropologists devoted their careers to collecting extensive datasets from thousands of individuals worldwide, their data have not yet been published in raw form nor made compatible. Here, we introduce the Dental Morphological Database (DeMoDa), an open access repository comprising 246 dental traits for 17,308 individuals across 32 major geographic regions worldwide spanning the past several thousand years. These data are from the legacy datasets of Turner, Hanihara, Scott, and Irish. Because these researchers used different scoring systems, we developed a scoring system with two steps that enables the three most-common scoring systems to be combined. We provide two versions of the data that correspond to these two steps: one with more nuanced trait scores at the cost of a smaller sample size, and another with less nuanced trait scores but broader sample coverage. We discuss the implications of publishing these legacy data and outline our decision-making process that guided their release in accordance with both the FAIR and CARE principles of open science.

evolutionary biology↗

bioRxiv2022

Imputed genomes and haplotype-based analyses of the Picts of early medieval Scotland reveal fine-scale relatedness between Iron Age, early medieval and the modern people of the UK.

The origins and ancestry of the Picts of early medieval Scotland (ca. AD 300-900) has been traditionally seen as a problem, prompted in part by exotic medieval origin myths, their enigmatic symbols and inscriptions, and the meagre textual evidence. The Picts, first mentioned in the late 3rd century AD resisted the Romans and went on to form a powerful kingdom that ruled over a large territory in northern Britain. In the 9th and 10th centuries Gaelic language, culture and identity became dominant, transforming the Pictish realm into Alba, the precursor to the medieval kingdom of Scotland. To date, no comprehensive analysis of Pictish genomes has been published, and questions about their biological relationships to other cultural groups living in Britain remain unanswered. Here we present two high-quality Pictish genomes (2.4 and 16.5X coverage) from central and northern Scotland dated from the 5th-7th century which we impute and co-analyse with >8,300 previously published ancient and modern genomes. Using allele frequency and haplotype-based approaches, we can firmly place the Pictish genomes within the Iron Age gene pool in Britain and demonstrate local biological affinity. We also demonstrate the presence of population structure within Pictish groups, with Orcadian Picts being genetically distinct from their mainland contemporaries. When investigating Identity-By-Descent (IBD) with present-day genomes, we observe broad affinities between the mainland Pictish genomes and the present-day people living in western Scotland, Wales, Northern Ireland and Northumbria, but less with the rest of England, the Orkney islands and eastern Scotland - where the political centres of Pictland were located. The pre-Viking Age Orcadian Picts evidence a high degree of IBD sharing across modern Scotland, Wales, Northern Ireland, and the Orkney islands, demonstrating substantial genetic continuity in the Orkney for the last ~2,000 years. Analysis of mitochondrial DNA diversity at the Pictish cemetery of Lundin Links (n = 7) reveals absence of female endogamy, with implications for broader social organisation. Overall, our study provides novel insights into the genetic affinities and population structure of the Picts and direct relationships between ancient and present-day groups of the UK.

genomics↗

bioRxiv2021

Dental caries in wild primates: interproximal cavities on anterior teeth

Dental caries has been reported in a variety of primates, although is still considered rare in wild populations. In this study, 11 catarrhine primates were studied for the presence of caries. A differential diagnosis of lesions found in interproximal regions of anterior teeth was undertaken, since they had been previously described as both carious and non-carious in origin. Each permanent tooth was examined macroscopically, with severity and position of lesions recorded. Two specimens were micro-CT scanned to assess demineralization. The differential diagnosis confirmed the cariogenic nature of interproximal cavities on anterior teeth (ICATs). Overall results show 3.3% of teeth are carious, with prevalence varying among species from 0% to over 7% of teeth affected. ICATs occurred in Pan troglodytes (9.8%), Gorilla gorilla gorilla (2.6%), Cercopithecus denti (22.4%), Presbytis femoralis (19.5%) and Cercopithecus mitis (18.3%). They make up 87.9% of carious lesions on anterior teeth. These results likely reflect dietary and food processing differences among species, but also between the sexes (e.g., 9.3% of teeth of female chimpanzees were carious vs. 1.8% in males). Processing cariogenic fruits and seeds with the anterior dentition (e.g., wadging) likely contributes to ICAT formation. Further research is needed on living populations to ascertain behavioral/dietary influences on caries occurrence in primates. Given the constancy of ICATs in frugivorous primates, their presence in archaeological and paleontological specimens may shed light on diet and food processing behaviors in fossil primates.

zoology↗

bioRxiv2021

Tooth chipping patterns in Paranthropus do not support regular hard food mastication

The paranthropines, including Paranthropus boisei and Paranthropus robustus, have often been considered hard-food specialists. The large post-canine teeth, thick enamel, and robust craniofacial features are often suggested to have evolved to cope with habitual mastication of hard foods. Yet, direct evidence for Paranthropus feeding behaviour often challenges these morphological interpretations. The main exception being antemortem tooth chipping which is still regularly used as evidence of habitual mastication of hard foods in this genus. In this study, data were compiled from the literature for six hominin species (including P. boisei and P. robustus) and 17 extant primate species, to analyse Paranthropus chipping patterns in a broad comparative framework. Severity of fractures, position on the dentition, and overall prevalence were compared among species. The results indicate that both Paranthropus species had a lower prevalence of tooth fractures compared to other fossil hominin species (P. boisei: 4%; P. robustus: 11%; Homo naledi: 37%; Australopithecus africanus: 17%; Homo neanderthalensis: 45%; Epipalaeolithic Homo sapiens: 29%); instead, their frequencies are similar to apes that masticate hard items in a non-regular frequency, including chimpanzees, gibbons, and gorillas (4%, 7% and 9% respectively). The prevalence is several times lower than in extant primates known to habitually consume hard items, such as sakis, mandrills, and sooty mangabeys (ranging from 28% to 48%). Comparative chipping analysis suggests that both Paranthropus species were unlikely habitual hard object eaters, at least compared to living durophage analogues.

paleontology↗

bioRxiv2020

Tooth size apportionment, Bayesian inference, and the phylogeny of Homo naledi

This study has three main objectives--two methodological and one summative, namely, further characterization of Homo naledi ([~]335-236 ka) to more firmly establish its evolutionary history. Using mathematically-corrected mesiodistal and buccolingual crown dimensions, the species was compared with samples of Pan troglodytes, Australopithecus africanus, A. afarensis, Paranthropus robustus, P. boisei, H. habilis, H. ergaster, H. erectus, H. heidelbergensis, H. neanderthalensis, and H. sapiens; the correction yields equivalently scaled samples unaffected by significant interspecific size differences. After initial cluster analysis, the data were used in tooth size apportionment analysis to determine how size is distributed relatively in each species dentition, while visualizing this variation in a sample scatterplot. The first main objective then, after quantitative coding, is evaluating the utility of these characters to estimate phylogenetic relationships, here using Bayesian inference with an Mkv model. The second objective, for the first time in paleoanthropological study, is estimating relationships using continuous characters, i.e., the scaled data, through Bayesian inference under a Brownian-motion model. This strategy facilitates maximum reception of potential phylogenetic signal. The final objective based on all analyses, though principally continuous Bayesian inference, is to elucidate the phylogeny of H. naledi. Relationships are largely congruent across methods and, with markedly higher node support, most of those inferred in prior systematic studies using qualitatively discretized traits. The present results place H. naledi as a sister taxon to H. habilis (node support [~]70-99%), with a plesiomorphic pattern of relative tooth size. It is nested within a clade comprising australopiths and early Homo dating 3.3 Ma to [~]800 ka, distinct from younger H. erectus through H. sapiens. This suggests that H. naledi originated well before the geological date range associated with the Dinaledi Chamber, from which the remains in this study were recovered, to represent a long-lived side branch in the genus.

paleontology↗

bioRxiv2019

Dental caries in human evolution: frequency of carious lesions in South African fossil hominins

Caries frequencies in South African fossil hominins were observed and compared with other hominin samples. Species studied include Paranthropus robustus, Homo naledi, Australopithecus africanus, early Homo and A. sediba. Teeth were viewed macroscopically with Micro-CT scans used to confirm lesions. Position and severity of each lesion were also noted and described. For all South African fossil hominin specimens studied, 16 have carious lesions, six of which are described for the first time in this study. These are from a minimum of six individuals, and include four P. robustus, one H. naledi, and one early Homo individual. No carious lesions were found on deciduous teeth, or any teeth assigned to A. africanus. Most are located interproximal, and only posterior teeth are affected. Caries frequency typically ranges between 1-5% of teeth in non-agricultural human samples, and this pattern seemingly holds true for at least the past two million years in the hominin lineage. Non-agricultural populations significantly above or below this threshold generally have a specialized diet, supporting other dietary evidence that A. africanus likely consumed large amounts of tough, non-cariogenic vegetation. Given the common occurrence of caries in the other hominin species, cariogenic bacteria and foods were evidently common in their collective oral environment. Along with recent research highlighting additional examples of caries in H. neanderthalensis, early Homo and Pleistocene H. sapiens, caries is clearly an ancient disease that was much more common than once maintained throughout the course of human evolution.View Full Text

paleontology↗

bioRxiv2019

Dental abscesses on the maxilla of a two million-year-old early Homo specimen

Abscesses and other periapical lesions are found in abundance in recent archeological samples, yet are scarce in the fossil hominin record. Periapical voids commonly develop after exposure of a tooth’s pulp chamber and are commonly associated with heavy crown wear, trauma or caries. In this study, all available maxilla and mandible fragments from the South African fossil hominin collections were studied, including specimens assigned to Homo naledi, Paranthropus robustus, Australopithicus africanus, A. sediba and early Homo. Only one specimen displayed voids consistent with periapical lesions, and a differential diagnosis of these voids was undertaken. The specimen, SK 847, is described as early Homo and has been dated to 2.3-1.65MA. There is one definite abscess, and likely at least two more with postmortem damage, all on the anterior aspect of the maxilla and associated with the incisors. The abscesses originate from the apices of the incisor roots and are therefore unlikely to represent a systemic disease such as multiple myeloma. They best fit the description of an abscess rather than a cyst or granuloma, with one showing a rounded thickened rim around the lesion. The abscesses highlight that this individual used their anterior dentition extensively, to the point that the pulp chambers were exposed on multiple teeth. This is one of the earliest hominin examples of a dental abscess and shows that this individual was able to cope with several concurrent abscesses, clearly surviving for an extended period. Therefore, this finding adds additional information to the history of dental pathology in our genus.View Full Text

paleontology↗

bioRxiv2019

Root caries on a Paranthropus robustus third molar from Drimolen

Objectives Dental caries is often perceived as a modern human disease. However, their presence is documented in many early human groups, various non-human primates and, increasingly, our hominin ancestors and relatives. In this study we describe an antemortem lesion on the root of a Paranthropus robustus third molar from Drimolen, South Africa, which likely represents another example of caries in fossil hominins.Materials and Methods The molar, DNH 40, is dated to 2.0–1.5 Ma and displays a lesion on the mesial root surface, extending from the cementoenamel junction 3 mm down toward the apex. The position and severity of the lesion was macroscopically recorded and micro-CT scanned to determine the extent of dentine involvement.Results A differential diagnosis indicates root caries, as the lesion is indistinguishable from clinical examples. Although necrotic in appearance, external tertiary dentine is evident on a micro CT scan. Gingival recession and/or continuous eruption of the tooth as a result of extensive occlusal wear would have occurred to facilitate caries formation. Therefore, the lesion is likely linked to relative old age of this individual.Discussion This new example increases the total number of carious lesions described in P. robustus teeth to 12, on occlusal, interproximal and, now, root surfaces. Beyond the consumption of caries-causing food(s), caries formation would have also required the presence of requisite intra-oral cariogenic bacteria in this individual and the species. Of interest, the presence of tertiary dentine on the outward surface suggests the DNH 40 lesion may have been arrested, i.e., no longer active, perhaps relating to a change in diet or oral microbiome just prior to the individual’s death.View Full Text

paleontology↗

bioRxiv2018

A probable genetic origin for pit defects on the molars of Paranthropus robustus

We report the frequencies of linear enamel hypoplasia (LEH) and, specifically, pitting enamel hypoplasia (PEH) defects in the teeth of Paranthropus robustus, for comparison with four other South African hominin species and three extant nonhuman primate species. Unlike LEH, the lesser known PEH is characterized by multiple circular depression defects across a tooth crown and is often difficult to interpret in terms of developmental timing and etiology. Teeth in all samples were examined macroscopically with type, position and number of defects recorded. Frequencies of teeth with LEH vary among hominin species, but the differences in PEH are considerable. That is, P. robustus has much higher rates of pitting defects, with 47% of deciduous teeth and 14% of permanent teeth affected, relative to 6.7% and 4.3%, respectively, for all other hominin teeth combined; none of the extant primate samples evidence comparable rates. The defects on P. robustus molars are unlike those in other species, with entire crowns often covered in small circular depressions. The PEH is most consistent with modern human examples of amelogenesis imperfecta. Additionally, the defects are: 1) not found on anterior teeth, 2) uniform in shape and size, and 3) similar in appearance/severity on all molars. A possible reason for this form of PEH is as a side effect of selection on another phenotype that shares the same coding gene(s), i.e., a genetic origin. Recent research on the ENAM gene provides one such possibility. Paranthropus likely underwent rapid evolution in the ENAM loci, with changes in this gene contributing to larger posterior teeth and thicker enamel. This same gene is associated with amelogenesis imperfecta; therefore, pleiotropy effects, relating to high selection on this gene during Paranthropus evolution, could have yielded this unique condition.

evolutionary biology↗