Macaques at the margins: the biogeography and extinction of Macaca sylvanus in Europe

The genus Macaca (Primates: Cercopithecidae) originated in Africa, dispersed into Europe in the Late Miocene and resided there until the Late Pleistocene. In this contribution, we provide an overview of the evolutionary history of Macaca in Europe, putting it into context with the wider late Miocene, Pliocene and Pleistocene European monkey fossil record (also comprising Mesopithecus, Paradolichopithecus, Dolichopithecus and Theropithecus). The Pliocene and Pleistocene European Macaca fossil material is largely regarded as Macaca sylvanus, the same species as the extant Barbary macaque in North Africa. The M. sylvanus specimens found at West Runton in Norfolk (53°N) during the Middle Pleistocene are among the most northerly euprimates ever discovered. Our simple time-budget model indicates that short winter day lengths would have imposed a significant constraint on activity at such relatively high latitudes, so macaque populations in Britain may have been at the limit of their ecological tolerance. Two basic models using climatic and topographic data for the Last Interglacial and the Last Glacial Maximum alongside Middle and Late Pleistocene fossil distributions indicate that much of Europe may have been suitable habitat for macaques. The models also indicate that areas of southern Europe in the present day have a climate that could support macaque populations. However, M. sylvanus became locally extinct in the Late Pleistocene, possibly at a similar time as the straight-tusked elephant, Palaeoloxodon antiquus, and narrow-nosed rhinoceros, Stephanorhinus hemitoechus. Its extinction may be related to vegetation change or increased predation from Homo, although other factors (such as stochastic factors occurring as a result of small population sizes) cannot be ruled out. Notwithstanding the cause of extinction, the European macaque may thus be a previously overlooked member of the Late Pleistocene faunal turnover

Mongoose Manor: Herpestidae remains from the Early Pleistocene Cooper’s D locality in the Cradle of Humankind, Gauteng, South Africa

Mongooses (Herpestidae) are an important component of African ecosystems, and a common constituent of southern African fossil assemblages. Despite this, mongoose fossils from the Cradle of Humankind, Gauteng, South Africa, have received relatively little interest. This paper presents the diverse mongoose craniodental assemblage from the early Pleistocene fossil locality Cooper’s D. A total of 29 mongoose specimens from five genera were identified at Cooper’s, including numerous first appearances in the Cradle or in South Africa. The exceptional mongoose assemblage at Cooper’s likely reflects the effects of an unknown taphonomic process, although mongooses follow other carnivore groups in the Cradle in displaying an apparent preference for the southern part of the Cradle. This investigation shows the value of mongooses as palaeoecological indicators and supports previous interpretations of the environment at Cooper’s as grassland with a strong woody component near a permanent water source.Palaeontological Scientific Trust (PAST); DST-NRF Centre of Excellence, Palaeosciences (CoE-Pal); the South African National Research Foundation; and the University of the Witwatersrand Postgraduate Merit Award.JNC201

Scrubbing up: multi-scale investigation of woody encroachment in a southern African savannah

Changes in the extent of woody vegetation represent a major conservation question in many savannah systems around the globe. To address the problem of the current lack of broad-scale cost-effective tools for land cover monitoring in complex savannah environments, we use a multi-scale approach to quantifying vegetation change in Kruger National Park (KNP), South Africa. We test whether medium spatial resolution satellite data (Landsat, existing back to the 1970s), which have pixel sizes larger than typical vegetation patches, can nevertheless capture the thematic detail required to detect woody encroachment in savannahs. We quantify vegetation change over a 13-year period in KNP, examine the changes that have occurred, assess the drivers of these changes, and compare appropriate remote sensing data sources for monitoring change. We generate land cover maps for three areas of southern KNP using very high resolution (VHR) and medium resolution satellite sensor imagery from February 2001 to 2014. Considerable land cover change has occurred, with large increases in shrubs replacing both trees and grassland. Examination of exclosure areas and potential environmental driver data suggests two mechanisms: elephant herbivory removing trees and at least one separate mechanism responsible for conversion of grassland to shrubs, theorised to be increasing atmospheric CO2. Thus, the combination of these mechanisms causes the novel two-directional shrub encroachment that we observe (tree loss and grassland conversion). Multi-scale comparison of classifications indicates that although spatial detail is lost when using medium resolution rather than VHR imagery for land cover classification (e.g., Landsat imagery cannot readily distinguish between tree and shrub classes, while VHR imagery can), the thematic detail contained within both VHR and medium resolution classifications is remarkably congruent. This suggests that medium resolution imagery contains sufficient thematic information for most broad-scale land cover monitoring requirements in heterogeneous savannahs, while having the benefits of being cost-free and providing a longer historical archive of data than VHR sources. We conclude that monitoring of broad-scale land cover change using remote sensing has considerable potential as a cost-effective tool for both better informing land management practitioners, and for monitoring the future landscape-scale impacts of management policies in savannahs

Mustelid and viverrid remains from the Pleistocene site of Cooper’s D, Gauteng, South Africa

Fossil mustelids and viverrids are rare in the African Pleistocene fossil record. The careful examination of sieved sediments from the well-dated Cooper’s D locality in Gauteng has revealed six new mustelid and viverrid specimens. These represent three uncommon genera – two mustelids, Propoecilogale bolti and Mellivora capensis, and a viverrid, Civettictis cf. civetta. We describe and figure these six specimens here. Cooper’sD is only the fourth African locality at which P. bolti has been identified, and it is the first of the Witwatersrand sites to contain remains of the African civet.Palaeontological Scientific Trust NRF/DST Centre of Excellence in Palaeosciences South African National Research Foundation University of the Witwatersrand Postgraduate Merit Award Liverpool John Moores University Early Career Researcher Awar

‘Why so high?’ Examining discrepancies between the Sr biosphere map and archaeological tooth data from the Peak District, England

The analysis of 87Sr/86Sr isotope ratios in human and nonhuman tooth enamel is used worldwide for archaeological and forensic purposes to establish if an individual is likely to have grown up in the area from which their remains were excavated. The English Peak District has produced an unusually high proportion of archaeological humans who, based on Sr isotope ratios, appear to have come from elsewhere. We have used modern plant samples from the Peak to show that the current understanding of Sr isotope ratios for this area is incomplete – we found many plant samples growing on gritstone sediments had higher Sr values than would be expected based on the current literature. In addition we demonstrated that the taxonomy of the plant does not appear to affect the Sr isotope values (we also found that mycorrhizal type did not determine Sr isotope values in these plants), rather it is the substrate on which it is growing that is important. In terms of human movement, our work suggests it is likely that many archaeological individuals found in the Peak District are indeed local, rather than migrants. It is also possible that the expansion of blanket peat in the Peak has over time reduced the amount of Sr entering the food chain from mineral soils, reducing the radiogenic Sr isotope values in more recent teeth. While our case study is the Peak District, our findings have implications for anomalously high archaeological 87Sr/86Sr isotope values in other upland regions with similar geologies and blanket peats

The origins and persistence of Homo floresiensis on Flores: biogeographical and ecological perspectives

The finding of archaeological evidence predating 1 Ma and a small hominin species (Homo floresiensis) on Flores, Indonesia, has stimulated much research on its origins and ancestry. Here we take a different approach and examine two key questions – 1) how did the ancestors of H. floresiensis reach Flores and 2) what are the prospects and difficulties of estimating the likelihood of hominin persistence for over 1 million years on a small island? With regard to the first question, on the basis of the biogeography we conclude that the mammalian, avian, and reptilian fauna on Flores arrived from a number of sources including Java, Sulawesi and Sahul. Many of the terrestrial taxa were able to float or swim (e.g. stegodons, giant tortoises and the Komodo dragon), while the rodents and hominins probably accidentally rafted from Sulawesi, following the prevailing currents. The precise route by which hominins arrived on Flores cannot at present be determined, although a route from South Asia through Indochina, Sulawesi and hence Flores is tentatively supported on the basis of zoogeography. With regards to the second question, we find the archaeological record equivocal. A basic energetics model shows that a greater number of small-bodied hominins could persist on Flores than larger-bodied hominins (whether H. floresiensis is a dwarfed species or a descendent of an early small-bodied ancestor is immaterial here), which may in part explain their apparent long-term success. Yet the frequent tsunamis and volcanic eruptions in the region would certainly have affected all the taxa on the island, and at least one turnover event is recorded, when Stegodon sondaari became extinct. The question of the likelihood of persistence may be unanswerable until we know much more about the biology of H. floresiensis

The missing mushrooms: searching for fungi in ancient human dietary analysis

Fungi are a common part of modern human diets, but are rarely discussed in an archaeological context. Power et al. (2015) published data on bolete spores in human tooth calculus, suggesting that Upper Palaeolithic peoples ate mushrooms. Here we briefly consider the likelihood of mushroom consumption in the past, and examine whether or not stable isotopes may provide a way of seeing this in archaeological populations. We also consider the complexities of fungal stable isotopes using our own data and that from the literature. We conclude that fungi are highly variable isotopically, and are an additional dietary factor that should be considered when trying to interpret ‘terrestrial’ carbon isotope signatures combined with relatively high nitrogen isotope values in humans and other animals. Substantial mushroom ingestion could, in some cases, result in isotope values that may be interpreted as considerable meat consumption

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2–6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5–5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4–10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32–4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23–11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification

Identification of genetic variants associated with Huntington's disease progression: a genome-wide association study

Background Huntington's disease is caused by a CAG repeat expansion in the huntingtin gene, HTT. Age at onset has been used as a quantitative phenotype in genetic analysis looking for Huntington's disease modifiers, but is hard to define and not always available. Therefore, we aimed to generate a novel measure of disease progression and to identify genetic markers associated with this progression measure. Methods We generated a progression score on the basis of principal component analysis of prospectively acquired longitudinal changes in motor, cognitive, and imaging measures in the 218 indivduals in the TRACK-HD cohort of Huntington's disease gene mutation carriers (data collected 2008–11). We generated a parallel progression score using data from 1773 previously genotyped participants from the European Huntington's Disease Network REGISTRY study of Huntington's disease mutation carriers (data collected 2003–13). We did a genome-wide association analyses in terms of progression for 216 TRACK-HD participants and 1773 REGISTRY participants, then a meta-analysis of these results was undertaken. Findings Longitudinal motor, cognitive, and imaging scores were correlated with each other in TRACK-HD participants, justifying use of a single, cross-domain measure of disease progression in both studies. The TRACK-HD and REGISTRY progression measures were correlated with each other (r=0·674), and with age at onset (TRACK-HD, r=0·315; REGISTRY, r=0·234). The meta-analysis of progression in TRACK-HD and REGISTRY gave a genome-wide significant signal (p=1·12 × 10−10) on chromosome 5 spanning three genes: MSH3, DHFR, and MTRNR2L2. The genes in this locus were associated with progression in TRACK-HD (MSH3 p=2·94 × 10−8 DHFR p=8·37 × 10−7 MTRNR2L2 p=2·15 × 10−9) and to a lesser extent in REGISTRY (MSH3 p=9·36 × 10−4 DHFR p=8·45 × 10−4 MTRNR2L2 p=1·20 × 10−3). The lead single nucleotide polymorphism (SNP) in TRACK-HD (rs557874766) was genome-wide significant in the meta-analysis (p=1·58 × 10−8), and encodes an aminoacid change (Pro67Ala) in MSH3. In TRACK-HD, each copy of the minor allele at this SNP was associated with a 0·4 units per year (95% CI 0·16–0·66) reduction in the rate of change of the Unified Huntington's Disease Rating Scale (UHDRS) Total Motor Score, and a reduction of 0·12 units per year (95% CI 0·06–0·18) in the rate of change of UHDRS Total Functional Capacity score. These associations remained significant after adjusting for age of onset. Interpretation The multidomain progression measure in TRACK-HD was associated with a functional variant that was genome-wide significant in our meta-analysis. The association in only 216 participants implies that the progression measure is a sensitive reflection of disease burden, that the effect size at this locus is large, or both. Knockout of Msh3 reduces somatic expansion in Huntington's disease mouse models, suggesting this mechanism as an area for future therapeutic investigation