Unravelling the maternal evolutionary history of the African leopard (Panthera pardus pardus).

The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477-0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0-0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa.

Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size.

Low genomic diversity is generally indicative of small population size and is considered detrimental by decreasing long-term adaptability.1,2,3,4,5,6 Moreover, small population size may promote gene flow with congeners and outbreeding depression.7,8,9,10,11,12,13 Here, we examine the connection between habitat availability, effective population size (Ne), and extinction by generating a 40× nuclear genome from the extinct blue antelope (Hippotragus leucophaeus). Historically endemic to the relatively small Cape Floristic Region in southernmost Africa,14,15 populations were thought to have expanded and contracted across glacial-interglacial cycles, tracking suitable habitat.16,17,18 However, we found long-term low Ne, unaffected by glacial cycles, suggesting persistence with low genomic diversity for many millennia prior to extinction in ∼AD 1800. A lack of inbreeding, alongside high levels of genetic purging, suggests adaptation to this long-term low Ne and that human impacts during the colonial era (e.g., hunting and landscape transformation), rather than longer-term ecological processes, were central to its extinction. Phylogenomic analyses uncovered gene flow between roan (H. equinus) and blue antelope, as well as between roan and sable antelope (H. niger), approximately at the time of divergence of blue and sable antelope (∼1.9 Ma). Finally, we identified the LYST and ASIP genes as candidates for the eponymous bluish pelt color of the blue antelope. Our results revise numerous aspects of our understanding of the interplay between genomic diversity and evolutionary history and provide the resources for uncovering the genetic basis of this extinct species' unique traits.

Giraffe lineages are shaped by major ancient admixture events.

Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.

The association between cardiopulmonary exercise testing and postoperative outcomes in patients with lung cancer undergoing lung resection surgery: A systematic review and meta-analysis.

BACKGROUND: Exercise capacity should be determined in all patients undergoing lung resection for lung cancer surgery and cardiopulmonary exercise testing (CPET) remains the gold standard. The purpose of this study was to investigate associations between preoperative CPET and postoperative outcomes in patients undergoing lung resection surgery for lung cancer through a review of the existing literature. METHODS: A search was conducted on PubMed, Scopus, Cochrane Library and CINAHL from inception until December 2022. Studies investigating associations between preoperative CPET and postoperative outcomes were included. Risk of bias was assessed using the QUIPS tool. A random effect model meta-analysis was performed. I2 > 40% indicated a high level of heterogeneity. RESULTS: Thirty-seven studies were included with 6450 patients. Twenty-eight studies had low risk of bias. [Formula: see text] peak is the oxygen consumption at peak exercise and serves as a marker of cardiopulmonary fitness. Higher estimates of [Formula: see text] peak, measured and as a percentagege of predicted, showed significant associations with a lower risk of mortality [MD: 3.66, 95% CI: 0.88; 6.43 and MD: 16.49, 95% CI: 6.92; 26.07] and fewer complications [MD: 2.06, 95% CI: 1.12; 3.00 and MD: 9.82, 95% CI: 5.88; 13.76]. Using a previously defined cutoff value of > 15mL/kg/min for [Formula: see text] peak, showed evidence of decreased odds of mortality [OR: 0.55, 95% CI: 0.28-0.81] and but not decreased odds of postoperative morbidity [OR: 0.82, 95% CI: 0.64-1.00]. There was no relationship between [Formula: see text] slope, which depicts ventilatory efficiency, with mortality [MD: -9.60, 95% CI: -27.74; 8.54] however, patients without postoperative complications had a lower preoperative [Formula: see text] [MD: -2.36, 95% CI: -3.01; -1.71]. Exercise load and anaerobic threshold did not correlate with morbidity or mortality. There was significant heterogeneity between studies. CONCLUSIONS: Estimates of cardiopulmonary fitness as evidenced by higher [Formula: see text] peak, measured and as a percentage of predicted, were associated with decreased morbidity and mortality. A cutoff value of [Formula: see text] peak > 15mL/kg/min was consistent with improved survival but not with fewer complications. Ventilatory efficiency was associated with decreased postoperative morbidity but not with improved survival. The heterogeneity in literature could be remedied with large scale, prospective, blinded, standardised research to improve preoperative risk stratification in patients with lung cancer scheduled for lung resection surgery.

Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros.

The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.

Self-adherence to post-colonoscopy consults in patients undergoing diagnostic colonoscopy: Findings from a cross-sectional, quantitative survey at a South African quaternary hospital.

Post-colonoscopy consults empower patients to make informed decisions around their subsequent treatment, and non-compliance with these consults ("no-shows") hinders disease management. There is a paucity in the literature regarding self-adherence to post-colonoscopy consults in resource-limited settings such as South Africa. An understanding of self-adherence to post-colonoscopy consults in this setting is required to establish whether improved interventions are needed, and what specific elements of self-adherence should be addressed with these interventions. The objective of this hypothesis-generating, cross-sectional, quantitative survey was to conduct a baseline assessment of cognitive, motivational, social, and behavioural variables related to self-adherence to post-colonoscopy consults in patients who underwent diagnostic colonoscopy at a South African quaternary hospital. The Adherence Determinants Questionnaire (ADQ) was administered in 47 patients to establish a baseline assessment of elements related to self-adherence to post-colonoscopy consults, including interpersonal aspects of care, perceived utility, severity, susceptibility, subjective norms, intentions, and supports/barriers. ADQ scores were transformed to a percentage of the maximum score for each element (100.0%). The overall mean transformed ADQ score was 57.8%. The mean transformed scores for specific ADQ components were as follows: subjective norms (40.8%), perceived severity (55.4%), perceived utility (56.6%), intentions (59.4%), supports/barriers (59.9%), interpersonal aspects (62.2%), and perceived susceptibility (65.9%). There were no statistically significant differences in overall mean transformed ADQ scores and individual ADQ elements across categories of participant age (p-values ranging between 0.180 and 0.949 when compared between participants ≤40 years and >40 years old), gender (p-values ranging between 0.071 and 0.946 when compared between males and females), and race (p-values ranging between 0.119 and 0.774 when compared between Black Africans and non-Black Africans). Our findings suggest a general need for appropriate interventions to improve self-adherence to post-colonoscopy consults in our setting.

Large Bowel Perforation in Patients with Colorectal Cancer: A South African Perspective.

Introduction: Large bowel perforation (LBP) occurs in up to 10% of colorectal cancer (CRC) patients and is a potential surgical emergency. Data on LBP in CRC patients from resource-limited countries are required to improve the management of this condition in these settings. Our study aimed to describe LBP amongst CRC patients in KwaZulu-Natal, South Africa. Materials and Methods: This was a descriptive sub-analysis of LBP data from an ongoing CRC registry. This study explores free and contained perforations and describes LBP characteristics, surgical management, histological findings, overall survival, and CRC recurrence. Results: Ninety-four out of 2523 CRC patients had LBP (3.7%). The median age was 53.0 years (interquartile range: 43.0-64.0). The male-to-female ratio was 1.4:1. Thirty-three patients (35.1%) had a coexisting bowel obstruction. Tumor site perforations occurred in 87 patients (92.6%) and were mostly in the sigmoid colon (36.2%). Perforations were contained in 77 patients (81.9%). Eighty-nine patients (94.7%) underwent resection (elective resection: 76/89 patients, 85.4%). The post-operative inpatient mortality rate was 2.2%. Most patients had Stage III CRC (46 patients, 48.9%) and moderately differentiated tumors (77 patients, 81.9%). Overall survival at 12 months following CRC diagnosis was 55.4%. The early recurrence rate for CRC disease was 5.4%. Conclusion: Tumor site perforations predominated, and most were contained. Patients were younger when compared with the international literature. We reaffirm that diastatic-free and contained perforations are two distinct clinical entities.

Patient's attitudes and perceptions around attending oncology consultations following surgery for colorectal cancer: A qualitative study.

Background: The oncology consultation following surgery for colorectal cancer (CRC) is usually the first step in the receipt of chemotherapy. Non-compliance with this consultation results in non-receipt of recommended chemotherapy, when appropriate, and worse clinical outcomes. This study sought to explore South African patients' attitudes and perceptions around attending scheduled oncology consultations following their CRC surgery. Methods: Semi-structured qualitative interviews were conducted with patients who had surgery for CRC at a quaternary South African hospital and who had to decide whether they would return for an oncology consultation. The "Model of health services use" informed the design of the interview guide, which included questions on factors that impact health seeking behavior. Demographics of participants, CRC disease stage, and compliance with scheduled oncology consultations were also collected. Descriptive statistics were used to analyse the quantitative data, while deductive thematic analysis was used to analyse the qualitative data. Results: Seven participants were interviewed. The median age was 60.0 years and four participants (57.1%) were female. Black African, White, and Asian participants accounted for 85.7% of the study sample. Most participants had stage III CRC (71.4%). The oncology consultation no-show rate was 14.3%. Participant's knowledge and beliefs around CRC proved to be an important predisposing factor that influenced follow-up decisions. Family support and religion were cited as important enabling factors. Travel costs to the hospital and frustrations related to the clinic appointment booking/scheduling process were cited as important disabling factors. Lastly, the participant's self-perceived need for additional oncology care also appeared to influence their decision to return for ongoing oncology consultation after the initial surgery. Conclusion: Several contextual factors can potentially influence a patient's compliance with a scheduled oncology consultation following CRC surgery. A multipronged approach which addresses these factors is required to improve compliance with oncology consultations.

Molecular archaeology of human cognitive traits.

The brains and minds of our human ancestors remain inaccessible for experimental exploration. Therefore, we reconstructed human cognitive evolution by projecting nonsynonymous/synonymous rate ratios (ω values) in mammalian phylogeny onto the anatomically modern human (AMH) brain. This atlas retraces human neurogenetic selection and allows imputation of ancestral evolution in task-related functional networks (FNs). Adaptive evolution (high ω values) is associated with excitatory neurons and synaptic function. It shifted from FNs for motor control in anthropoid ancestry (60-41 mya) to attention in ancient hominoids (26-19 mya) and hominids (19-7.4 mya). Selection in FNs for language emerged with an early hominin ancestor (7.4-1.7 mya) and was later accompanied by adaptive evolution in FNs for strategic thinking during recent (0.8 mya-present) speciation of AMHs. This pattern mirrors increasingly complex cognitive demands and suggests that co-selection for language alongside strategic thinking may have separated AMHs from their archaic Denisovan and Neanderthal relatives.

Helicobacter pylori genomes reveal Paleolithic human migration to the east end of Asia.

A virulence bacterium, Helicobacter pylori, evolved parallel to its host human, therefore, can work as a marker for tracing the human migration. We found H. pylori strains indigenous in the southernmost islands of Japanese Archipelago, Okinawa, and defined them as hspOkinawa and hpRyukyu. Genome data of the strains revealed that hspOkinawa diverged from other East Asian strains about 20,000 years ago, and that hpRyukyu diverged about 45,000 years ago. The closest strains of hpRyukyu were found from Afghanistan, Punjab, and Nepal, which suggest this strain originated in the central Asia and traveled across the Eurasian continent during Paleolithic era. The divergence date of hpRyukyu corresponds with human fossil records in Okinawa. Although it is controversial from human DNA analyses whether descendants of the Paleolithic migrants remain in the modern Japanese population, this study reveals that the bacterium of Paleolithic origin remains in the stomachs of current Japanese.

Potential drivers of samango monkey (Cercopithecus albogularis) population subdivision in a highly fragmented mountain landscape in northern South Africa.

Forests affected by fragmentation are at risk of losing their primate populations over the long term. The impact of fragmentation on primate populations has been studied in several places in Africa, Asia and South America; however, there has been no discernible pattern of how primates react to forest disturbance and fragmentation. In fragmented habitats, the local extinction probability of a species increases due to a decrease in patch area and an increase in genetic isolation. Here we used microsatellite markers and mitochondrial DNA sequences to investigate how habitat fragmentation impacts on the genetic diversity and structure of a samango monkey population inhabiting forest patches in the Soutpansberg mountain range of northern South Africa. We sampled four local populations across the length of the mountain range and an additional outlying population from the Great Escarpment to the south. Our results indicate that local populations along the mountain range were historically more connected and less distinct than at present. In more recent times, a lack of contemporary gene flow is leading to a more pronounced genetic structure, causing population subdivision across the mountain and likely isolating the Soutpansberg population from the escarpment population to the south. Based on our results, we suggest that natural and anthropogenic fragmentation are driving population genetic differentiation, and that the matrix surrounding forests and their suitability for samango monkey utilisation play a role at the local scale. The degree of genetic isolation found for samango monkey populations in our study raises concerns about the long-term viability of populations across the mountain range.

Community disaster exposure and first onset of depression: A panel analysis of nationally representative South African data, 2008-2017.

Sub-Saharan Africa faces unprecedented disasters, with climate change expected to exacerbate the frequency and severity of unpredictable and stressful catastrophic events. Unlike developed nations, reconstruction in developing nations is hindered by resource constraints, with certain communities potentially experiencing multiple and enduring effects of disasters. Despite the potential danger of such cumulative community disaster exposure on mental health (e.g. depression), large-scale population-level evidence for the region is limited. We investigated the association between exposure to cumulative disaster and the first onset of depression in a nationally representative survey in South Africa. We used panel data from the South African National Income Dynamics Study (SA-NIDS) from 2008-2017, consisting of 17,255 adult study participants who were depression free at baseline. Risk of first depression onset between individuals exposed and unexposed to community disaster was measured, accounting for multiple disaster exposure over time by fitting generalized estimating equation (GEE) regression models. Data on the geographic location of disasters were obtained from the South African government gazette, and mapped with the government delineated SA-NIDS households' locations. Of the sampled individuals, 2,986 were exposed to disaster during the study duration (17.3%). Increased cumulative community disaster was significantly associated with the likelihood of depression onset (adjusted relative risk [aRR] = 1.20, p<0.01, 95% CI: 1.09-1.33), even after controlling for socio-demographic factors. In sub-group analyses, greater likelihood of depression onset was found among females [but not in men] (aRR = 1.23, p<0.01, 95% CI: 1.09-1.38), Black African [but not in other population group] (aRR = 1.21, p<0.01, 95% CI: 1.09-1.36), lower education attainment group [but not in tertiary and above educational attainment group] (aRR = 1.20, p<0.01, 95% CI: 1.08-1.33), and lower income attainment group [but not in the top income quartile group] (aRR = 1.24, p<0.01, 95% CI: 1.11-1.38), due to cumulative community disaster. Although cumulative community disaster exposure was significantly associated with the first onset of depression, its negative impact may be more pronounced among individuals considered chronically socially vulnerable (i.e. the groups above) in South Africa. Given that many individuals in South Africa rely on social, food parcel relief, and health services from government/public sector, timely access to community-based supportive intervention is needed for disaster survivors, prioritizing socially vulnerable groups to help mitigate problems associated with mental health challenges.

Independent evolution of intermediate bill widths in a seabird clade.

Interspecific introgression can occur between species that evolve rapidly within an adaptive radiation. Pachyptila petrels differ in bill size and are characterised by incomplete reproductive isolation, leading to interspecific gene flow. Salvin's prion (Pachyptila salvini), whose bill width is intermediate between broad-billed (P. vittata) and Antarctic (P. desolata) prions, evolved through homoploid hybrid speciation. MacGillivray's prion (P. macgillivrayi), known from a single population on St Paul (Indian Ocean), has a bill width intermediate between salvini and vittata and could also be the product of interspecies introgression or hybrid speciation. Recently, another prion population phenotypically similar to macgillivrayi was discovered on Gough (Atlantic Ocean), where it breeds 3 months later than vittata. The similarity in bill width between the medium-billed birds on Gough and macgillivrayi suggest that they could be closely related. In this study, we used genetic and morphological data to infer the phylogenetic position and evolutionary history of P. macgillivrayi and the Gough medium-billed prion relative other Pachyptila taxa, to determine whether species with medium bill widths evolved through common ancestry or convergence. We found that Gough medium-billed prions belong to the same evolutionary lineage as macgillivrayi, representing a new population of MacGillivray's prion that originated through a colonisation event from St Paul. We show that macgillivrayi's medium bill width evolved through divergence (genetic drift) and independently from that of salvini, which evolved through hybridisation (gene flow). This represents the independent convergence towards a similarly medium-billed phenotype. The newly discovered MacGillivray's prion population on Gough is of utmost conservation relevance, as the relict macgillivrayi population in the Indian Ocean is very small.

Predictors of treatment refusal in patients with colorectal cancer: A systematic review.

This systematic review was conducted to investigate predictors of treatment refusal in colorectal cancer (CRC) patients. An understanding of these predictors would inform statistical models for the identification of high-risk patients who might benefit from interventions that seek to improve treatment compliance. We performed a search of PubMed and Scopus to identify potentially relevant studies on predictors of treatment refusal in CRC patients that were published between January 1, 2000 and December 31, 2021. We screened manuscripts using predefined eligibility criteria. Information on study design, study location, patient characteristics, treatments, rates and predictors of treatment refusal, and the impact of treatment refusal on mortality or survival were collected from eligible studies. Study quality was assessed using the Newcastle-Ottawa score. The overall findings of the review process were summarized using descriptive statistics and a narrative synthesis. A total of 13 studies were included in this review. Ten studies reported on refusal of CRC surgery, refusal rate: 0.25%-3.26%; three studies reported on chemotherapy refusal (one of which reported on both surgery and chemotherapy refusal), refusal rate: 7.8%-41.5%; and one study reported on refusal of any cancer treatment, refusal rate: 8.7%. The bulk of the published literature confirmed the harmful association between treatment refusal and poor survival outcomes in CRC patients. Frequently cited predictors of treatment refusal included patient demographic characteristics (age, race, gender), clinical characteristics (disease stage, comorbidity), and factors that impact access to cancer care services (healthcare insurance, facility level). Potentially high rates of treatment refusal pose a challenge to CRC control. This review has identified several factors which must be considered when attempting to reduce treatment refusal in CRC patients. Furthermore, these factors should be tested as components of predictive risk models for this important outcome.

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.

Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum).

Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.

Helicobacter pylori's historical journey through Siberia and the Americas.

The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether ancient northern Eurasian populations persisted at high latitudes through the last glacial maximum and the relationships between present-day Siberians and Native Americans. A total of 556 strains were cultivated and genotyped by multilocus sequence typing, and 54 representative draft genomes were sequenced. The genetic diversity across Eurasia and the Americas was structured into three populations: hpAsia2, hpEastAsia, and hpNorthAsia. hpNorthAsia is closely related to the subpopulation hspIndigenousAmericas from Native Americans. Siberian bacteria were structured into five other subpopulations, two of which evolved through a divergence from hpAsia2 and hpNorthAsia, while three originated though Holocene admixture. The presence of both anciently diverged and recently admixed strains across Siberia support both Pleistocene persistence and Holocene recolonization. We also show that hspIndigenousAmericas is endemic in human populations across northern Eurasia. The evolutionary history of hspIndigenousAmericas was reconstructed using approximate Bayesian computation, which showed that it colonized the New World in a single migration event associated with a severe demographic bottleneck followed by low levels of recent admixture across the Bering Strait.

Patterns of multimorbidity and their association with hospitalisation: a population-based study of older adults in urban Tanzania.

BACKGROUND: while the HIV epidemic remains a considerable challenge in sub-Saharan Africa, a dramatic reduction in the associated mortality has led to a fundamental shift in the public health priorities aimed at tackling multimorbidity. Against the unprecedented level of urbanisation taking place in Tanzania, the burden of multimorbidity and its consequences among ageing adults, in the form of costly inpatient hospitalisation, remain unquantified. METHODS: we used data from one of Africa's largest urban population cohort, the Dar es Salaam Health and the Demographic Surveillance System, to quantity the extent of multimorbidity (occurrence of 2 ≥ health conditions) and discordant multimorbidity (occurrence of conditions in 2 ≥ domains in mental health, non-communicable and communicable health) among 2,299 adults aged ≥40 years in Dar es Salaam, Tanzania. We fitted logistic regression models to investigate the association between multimorbidity and inpatient hospitalisation. RESULTS: the prevalence of multimorbidity and discordant multimorbidity were 25.3 and 2.5%, respectively. Although the severe forms of multimorbidity (2.0% with ≥4 health conditions) and discordancy were low, hospitalisation was significantly higher based on the regression analyses. Household food insecurity was the only socio-economic variable that was significantly and consistently associated with a greater hospitalisation. CONCLUSION: we found an alarmingly high degree of multimorbidity among this ageing urban population where hospitalisation was driven by multimorbidity. As public health resources remain scarce, reducing costly inpatient hospitalisation requires multilevel interventions that address clinical- and structural-level challenges (e.g. food insecurity) to mitigate multimorbidity and promote long-term healthy independent living among older adults in Tanzania.

HIV viral load and pregnancy loss: results from a population-based cohort study in rural KwaZulu-Natal, South Africa.

OBJECTIVE: With ever-expanding antiretroviral therapy (ART) access among pregnant women in sub-Saharan Africa, it is more than ever important to address the gap in knowledge around ART effectiveness, as measured by HIV viral load, and pregnancy loss. DESIGN: A population-based cohort study. METHODS: The study sample consisted of 3431 pregnancies from 2835 women living with HIV aged 16-35 years old. All women participated in a population-based cohort conducted between 2004 and 2018 in rural KwaZulu-Natal, South Africa. Viral load data were collected at prior surveys and an HIV care registry. The closest available viral load to the date that each pregnancy ended was used and classified as either a pre- or postconception viral load. Logistic regression was used to investigate the association between high viral load (log10 viral load >4.0 copies/ml) and pregnancy loss, defined as either a miscarriage or stillbirth. RESULTS: Pregnancy loss occurred at a rate of 1.3 (95% confidence interval: 1.0-1.8) per 100 pregnancies. There were 1451 pregnancies (42.3%) with postconception viral load measurements. The median time between the viral load measurement and the pregnancy end date was 11.7 (interquartile range: 5.0-25.4) months. We found a higher likelihood of pregnancy loss in women who had high viral loads prior to the outcome of their pregnancy (adjusted odds ratio: 2.38, 95% confidence interval: 1.10-5.18). CONCLUSION: Given the significant relationship between high viral load and pregnancy loss, our study lends further credence to ensuring effective ART through enrolment and retention of pregnant women living with HIV in ART programs, treatment adherence interventions, and viral load monitoring during pregnancy.