Charting a landmark-driven path forward for population genetics and ancient DNA research in Africa.

Population history-focused DNA and ancient DNA (aDNA) research in Africa has dramatically increased in the past decade, enabling increasingly fine-scale investigations into the continent's past. However, while international interest in human genomics research in Africa grows, major structural barriers limit the ability of African scholars to lead and engage in such research and impede local communities from partnering with researchers and benefitting from research outcomes. Because conversations about research on African people and their past are often held outside Africa and exclude African voices, an important step for African DNA and aDNA research is moving these conversations to the continent. In May 2023 we held the DNAirobi workshop in Nairobi, Kenya and here we synthesize what emerged most prominently in our discussions. We propose an ideal vision for population history-focused DNA and aDNA research in Africa in ten years' time and acknowledge that to realize this future, we need to chart a path connecting a series of "landmarks" that represent points of consensus in our discussions. These include effective communication across multiple audiences, reframed relationships and capacity building, and action toward structural changes that support science and beyond. We concluded there is no single path to creating an equitable and self-sustaining research ecosystem, but rather many possible routes linking these landmarks. Here we share our diverse perspectives as geneticists, anthropologists, archaeologists, museum curators, and educators to articulate challenges and opportunities for African DNA and aDNA research and share an initial map toward a more inclusive and equitable future.

Testing inter-observer error under a collaborative research framework for studying lithic shape variability.

Evaluating error that arises through the aggregation of data recorded by multiple observers is a key consideration in many metric and geometric morphometric analyses of stone tool shape. One of the most common approaches involves the convergence of observers for repeat trails on the same set of artefacts: however, this is logistically and financially challenging when collaborating internationally and/or at a large scale. We present and evaluate a unique alternative for testing inter-observer error, involving the development of 3D printed copies of a lithic reference collection for distribution among observers. With the aim of reducing error, clear protocols were developed for photographing and measuring the replicas, and inter-observer variability was assessed on the replicas in comparison with a corresponding data set recorded by a single observer. Our results demonstrate that, when the photography procedure is standardized and dimensions are clearly defined, the resulting metric and geometric morphometric data are minimally affected by inter-observer error, supporting this method as an effective solution for assessing error under collaborative research frameworks. Collaboration is becoming increasingly important within archaeological and anthropological sciences in order to increase the accessibility of samples, encourage dual-project development between foreign and local researchers and reduce the carbon footprint of collection-based research. This study offers a promising validation of a collaborative research design whereby researchers remotely work together to produce comparable data capturing lithic shape variability. Supplementary Information: The online version contains supplementary material available at 10.1007/s12520-022-01676-2.

Variation in Middle Stone Age mandibular molar enamel-dentine junction topography at Klasies River Main Site assessed by diffeomorphic surface matching.

The morphology and variability of the Middle Stone Age (MSA) hominin fossils from Klasies River Main Site have been the focus of investigation for more than four decades. The mandibular remains have figured prominently in discussions relating to robusticity, size dimorphism, and symphyseal morphology. Variation in corpus size between the robust SAM-AP 6223 and the diminutive SAM-AP 6225 mandibles is particularly impressive, and the difference between the buccolingual diameters of their M2s significantly exceeds recent human sample variation. SAM-AP 6223 and SAM-AP 6225 are the only Klasies specimens with homologous teeth (M2 and M3) that permit comparisons of crown morphology. While the differences in dental trait expression at the outer enamel surfaces of these molars are slight, diffeomorphic surface analyses of their underlying enamel-dentine junction (EDJ) topographies reveal differences that are well beyond the means of pairwise differences among comparative samples of Later Stone Age (LSA) Khoesan and recent African homologues. The EDJs of both SAM-AP 6225 molars and the SAM-AP 6223 M3 fall outside the envelopes that define the morphospace of these two samples. Although the radiocarbon dated LSA individuals examined here differ by a maximum of some 7000 years, and the two Klasies jaws may differ by perhaps as much as 18,000 years, it is difficult to ascribe their differences to time alone. With reference to the morphoscopic traits by which the SAM-AP 6223 and SAM-AP 6225 EDJs differ, the most striking is the expression of the protoconid cingulum. This is very weakly developed on the SAM-AP 6223 molars and distinct in SAM-AP 6225. As such, this diminutive fossil exhibits a more pronounced manifestation of what is likely a plesiomorphic feature, thus adding to the morphological mosaicism that is evident in the Klasies hominin assemblage. Several possible explanations for the variation and mosaicism in this MSA sample are discussed.

Seroprevalence of Toxoplasma gondii in American Black Bears (Ursus americanus) in Nevada, USA, using an Enzyme-linked Immunosorbent Assay.

Archived serum samples taken between 1997 and 2017 from 170 American black bears (Ursus americanus) in the Lake Tahoe area between California and Nevada, US, were tested for Toxoplasma antibodies to assess the seroprevalence of this agent. Samples were screened using a commercial porcine Toxoplasma (enzyme-linked immunosorbent assay [ELISA]) modified with Protein A/G peroxidase and compared to a traditional fluorescent antibody test. Results were analyzed to determine if there were differences in seroprevalence based on the test used, sex of bears, or habitat usage (urban-suburban vs. wildland). No significant differences in seroprevalence were attributable to any of these parameters. The overall seropositivity for bears was 36% (62/170), with urban-suburban bears scoring lower (31%; 37/119) than rural-wildland bears (40%; 18/45). Our results strongly support the use of a Protein A/G-modified ELISA for determining Toxoplasma exposure in black bears. We found somewhat lower levels of Toxoplasma antibodies in black bears from this region than in several reports from populations in the eastern US.

Application of Environment-Friendly Rhamnolipids against Transmission of Enveloped Viruses Like SARS-CoV2.

In the face of new emerging respiratory viruses, such as SARS-CoV2, vaccines and drug therapies are not immediately available to curb the spread of infection. Non-pharmaceutical interventions, such as mask-wearing and social distance, can slow the transmission. However, both mask and social distance have not prevented the spread of respiratory viruses SARS-CoV2 within the US. There is an urgent need to develop an intervention that could reduce the spread of respiratory viruses. The key to preventing transmission is to eliminate the emission of SARS-CoV2 from an infected person and stop the virus from propagating in the human population. Rhamnolipids are environmentally friendly surfactants that are less toxic than the synthetic surfactants. In this study, rhamnolipid products, 222B, were investigated as disinfectants against enveloped viruses, such as bovine coronavirus and herpes simplex virus 1 (HSV-1). The 222B at 0.009% and 0.0045% completely inactivated 6 and 4 log PFU/mL of HSV-1 in 5-10 min, respectively. 222B at or below 0.005% is also biologically safe. Moreover, 50 µL of 222B at 0.005% on ~1 cm2 mask fabrics or plastic surface can inactivate ~103 PFU HSV-1 in 3-5 min. These results suggest that 222B coated on masks or plastic surface can reduce the emission of SARS-CoV2 from an infected person and stop the spread of SARS-CoV2.

Viruses in unexplained encephalitis cases in American black bears (Ursus americanus).

Viral infections were investigated in American black bears (Ursus americanus) from Nevada and northern California with and without idiopathic encephalitis. Metagenomics analyses of tissue pools revealed novel viruses in the genera Circoviridae, Parvoviridae, Anelloviridae, Polyomaviridae, and Papillomaviridae. The circovirus and parvovirus were of particular interest due to their potential importance as pathogens. We characterized the genomes of these viruses and subsequently screened bears by PCR to determine their prevalence. The circovirus (Ursus americanus circovirus, UaCV) was detected at a high prevalence (10/16, 67%), and the chaphamaparvovirus (Ursus americanus parvovirus, UaPV) was found in a single bear. We showed that UaCV is present in liver, spleen/lymph node, and brain tissue of selected cases by in situ hybridization (ISH) and PCR. Infections were detected in cases of idiopathic encephalitis and in cases without inflammatory brain lesions. Infection status was not clearly correlated with disease, and the significance of these infections remains unclear. Given the known pathogenicity of a closely related mammalian circovirus, and the complex manifestations of circovirus-associated diseases, we suggest that UaCV warrants further study as a possible cause or contributor to disease in American black bears.

Human manual distal phalanges from the Middle Stone Age deposits of Klasies River Main Site, Western Cape Province, South Africa.

Two new distal manual phalanges from the Middle Stone Age deposits of Klasies River Main Site are described. One (SAM-AP 6387) likely derives from ray II or ray III, whereas the other (SAM-AP 6388) is from the thumb. Both derive from a late adolescent or fully adult individual. They were recovered by H. Deacon from the same stratigraphic unit (submember W or possibly submember R) of the Shell and Sand Member of Cave 1, which places them between 100 and 90 ka. Both are comparatively small elements, and the possibility that they came from the same hand cannot be discounted at this time. These bones add to the meager and all too fragmentary postcranial human fossil sample from the Late Pleistocene of South Africa. These two specimens provide some additional evidence pertaining to the morphological attributes of the distal phalanges of the Middle Stone Age inhabitants of South Africa. Together with the distal pollical phalanx from Die Kelders (SAM-AP 6402), they are relatively small in comparison with homologs from recent human samples as well as Late Pleistocene specimens from Eurasia. Given their small sizes, the distal pollical phalanges from Klasies and Die Kelders are not dissimilar to Holocene Khoesan homologs. As expected, the Klasies elements differ noticeably from Neandertal homologs, especially in the narrowness of their shafts and distal tuberosities.

Identification of gammaherpesvirus infection in free-ranging black bears (Ursus americanus).

Herpesvirus infection was investigated in black bears (Ursus americanus) with neurological signs and brain lesions of nonsuppurative encephalitis of unknown cause. Visible cytopathic effects (CPE) could only be observed on days 3-5 post-infection in HrT-18G cell line inoculated with bear tissue extracts. The observed CPE in HrT-18G cells included syncytia, intranuclear inclusions, and cell detachments seen in herpesvirus infection in vitro. Herpesvirus-like particles were observed in viral culture supernatant under the electron microscope, however, capsids ranging from 60 nm to 100 nm in size were often observed in viral cultures within the first two passages of propagation. Herpesvirus infection in the bear tissues and tissue cultures were detected by PCR using degenerate primers specific to the DNA polymerase gene (DPOL) and glycoprotein B gene (gB). DNA sequencing of the amplicon revealed that the detected herpesvirus has 94-95% identity to Ursid gammaherpesvirus 1 (UrHV-1) DNA sequences of DPOL. Phylogenetic analysis of DPOL sequences indicates that black bear herpesviruses and UrHV-1 are closely related and have small distances to members of Rhadinovirus. Interestingly, black bear herpesvirus infections were also found in bears without neurological signs. The DPOL DNA sequence of black bear herpesviruses detected in neurological bears were similar to the those detected in the non-neurological bears. However, the gB DNA sequence detected from the neurological bear is different from non-neurological bear and has only 64.5%-70% identity to each other. It is possible that at least two different types of gammaherpesviruses are present in the U. americanus population or several gammaherpesviruses exist in ursine species.

Questions of Khoesan continuity: dental affinities among the indigenous Holocene peoples of South Africa.

The present report follows up on the findings of previous research, including recent bioarchaeological study of well-dated Khoesan skeletal remains, that posits long term biological continuity among the indigenous peoples of South Africa after the Pleistocene. The Arizona State University Dental Anthropology System was used to record key crown, root, and intraoral osseous nonmetric traits in six early-through-late Holocene samples from the Cape coasts. Based on these data, phenetic affinities and an identification of traits most important in driving intersample variation were determined using principal components analysis and the mean measure of divergence distance statistic. To expand biological affinity comparisons into more recent times, and thus preliminarily assess the dental impact of disproportionate non-Khoesan gene flow into local peoples, dental data from historic Khoekhoe and San were also included. Results from the prehistoric comparisons are supportive of population continuity, though a sample from Matjes River Rockshelter exhibits slight phenetic distance from other early samples. This and some insignificant regional divergence among these coastal samples may be related to environmental and cultural factors that drove low-level reproductive isolation. Finally, a close affinity of historic San to all samples, and a significant difference of Khoekhoe from most early samples is reflective of documented population history following immigration of Bantu-speakers and, later, Europeans into South Africa.

Development and performance evaluation of calf diarrhea pathogen nucleic acid purification and detection workflow.

Calf diarrhea (scours) is a primary cause of illness and death in young calves. Significant economic losses associated with this disease include morbidity, mortality, and direct cost of treatment. Multiple pathogens are responsible for infectious diarrhea, including, but not limited to, Bovine coronavirus (BCV), bovine Rotavirus A (BRV), and Cryptosporidium spp. Identification and isolation of carrier calves are essential for disease management. Texas Veterinary Medical Diagnostic Laboratory current methods for calf diarrhea pathogen identification include electron microscopy (EM) for BCV and BRV and a direct fluorescent antibody test (DFAT) for organism detection of Cryptosporidium spp. A workflow was developed consisting of an optimized fecal nucleic acid purification and multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) for single tube concurrent detection of BCV, BRV, and Cryptosporidium spp., and an internal control to monitor nucleic acid purification efficacy and PCR reagent functionality. In "spike-in" experiments using serial dilutions of each pathogen, the analytical sensitivity was determined to be <10 TCID(50)/ml for BCV and BRV, and <20 oocysts for Cryptosporidium spp. Analytical specificity was confirmed using Canine and Feline coronavirus, Giardia spp., and noninfected bovine purified nucleic acid. Diagnostic sensitivity was ≥98% for all pathogens when compared with respective traditional methods. The results demonstrate that the newly developed assay can purify and subsequently detect BCV, BRV, and Cryptosporidium spp. concurrently in a single PCR, enabling simplified and streamlined calf diarrhea pathogen identification.

Characterization of Cervidpoxvirus isolates from Oregon, California, and eastern Canada.

The present report describes the analysis of 4 Deerpox virus isolates from California, Oregon, and Ontario, Canada. All 4 isolates were associated with cutaneous crusting lesions. Examination of selected samples by electron microscopy demonstrated that the viruses were morphologically similar to orthopoxviruses. Phylogenetic analysis of the A21 gene, which is found in all poxviruses, indicated that the 4 isolates form a lineage distinct from other members except for those belonging to the genus Cervidpoxvirus of the subfamily Chordopoxvirinae. Members of the Cervidpoxvirus lineage encode a set of genes not found in other poxviruses. These include homologs of genes encoding interleukin 1 receptor antagonists (IL-1Ra) and C-type lectin-like receptors (CTLR). In the current investigation, genes encoding homologs of IL-1Ra and CTLR were amplified from all the isolates and were found to be closely related to orthologs found in the Cervidpoxvirus genus, which further supports the inclusion of these isolates in the Cervidpoxvirus genus.

Disease surveillance in rural communities is compromised by address geocoding uncertainty: a case study of campylobacteriosis.

This study illustrates the impact of address geocoding uncertainty on rural estimates of reportable disease incidence using campylobacteriosis as an example. After all cases of campylobacteriosis notified from 1993 to 1997 had been geocoded, the minimum and maximum disease notification rates were calculated for rural and urban areas of New Zealand. The estimated maximum rural rates were four times higher than estimated minimum rural rates, whereas estimated minimum and maximum urban rates varied minimally. The impact of address geocoding on the estimation of disease notification rates across Public Health Service Regions showed considerable variation. The relative proportions of ungeocoded notifications to rural notifications ranged from 1.3:1 to 10.2:1, reflecting the range of uncertainty in estimated rural rates of campylobacteriosis. Unless the reliability of captured rural address data is improved significantly, disease surveillance systems will underestimate rural rates of disease and limit small area analyses.