An Ecological and Evolutionary Framework for Commensalism in Anthropogenic Environments

Acknowledgements We would like to thank Jean-Denis Vigne, members of the Searle lab, and SNEEB at Cornell University for a stimulating environment and many early discussions and comments. We would also like to thank Maeve McMahon for comments on the manuscript.Peer reviewedPublisher PD

Report to UNHCR Chad on proposals for livestock and animal owners in Eastern Chad.

Estimates of current livestock numbers owned by refugees in the 12 UNCHR camps in eastern Chad vary widely between 173,000 and 427,000 head, using data gathered by camp authorities. Finding adequate food for these animals is becoming an increasing challenge for their owners and is leading to increased tension between refugees and the host communities as they compete for already limited resources. The confinement of livestock within a relatively short distance from the camps is resulting in long-term environmental degradation resulting from over-exploitation of natural resources. Livestock mortality is very high due to high disease incidence exacerbated by poor nutrition. The application of traditional pastoralist management systems to an intensified livestock population is increasing the attrition of livestock, accelerating environmental degradation, increasing the risk of inter-ethnic conflict and, consequentially, failing to ensure that the most benefits possible in terms of added-value are being derived from the available livestock. Solutions to the problem of feeding the livestock belonging to refugees are made complex by the lack of incentive to invest in a region where camp dwellers have no land tenure rights and a strong desire to return home as soon as possible. In order to reduce conflict between refugees and the host community, solutions need to benefit both sectors.Due to the size of a camp and the concentration of dwellings in a small area, comparisons can be made with livestock keeping in a peri-urban environment. The over-grazing by the large numbers of livestock around the camps will result in degradation of the local environment and ultimately livestock may only be able to be kept by following a programme by refugee livestock owners of cutting and carrying available forage back to the immediate vicinity of the camps. An alternative, is that (as we shall later propose) fodder and crop residues are bought and brought in from outside the camp. However far more benefit would certainly derive from a planned programme of growing forage crops, either by the refugees, or endemic villagers who could then sell them to the refugees and gain a valuable additional income. However a balance has to be struck between what is currently an unsustainable situation, characterised by a excessive livestock population carrying out possibly long-term environmental degradation, versus support for an artificial system of livestock management, which will entail interventionary support and management, the planned and budgeted provision of supplementary feed and the perpetuation of a system which disconnects the refugees from their animal ownership and management traditions and knowledge. A series of recommendations will be made that are designed to reduce the overwhelming demand for forage in the short and medium term. If implemented, they should result in smaller, fitter herds of livestock that in the long term can be both more readily repatriated and readapted to the more favourable grazing conditions found in Western Sudan

Report to UNHCR Chad on proposals for livestock and animal owners in Eastern Chad.

Estimates of current livestock numbers owned by refugees in the 12 UNCHR camps in eastern Chad vary widely between 173,000 and 427,000 head, using data gathered by camp authorities. Finding adequate food for these animals is becoming an increasing challenge for their owners and is leading to increased tension between refugees and the host communities as they compete for already limited resources. The confinement of livestock within a relatively short distance from the camps is resulting in long-term environmental degradation resulting from over-exploitation of natural resources. Livestock mortality is very high due to high disease incidence exacerbated by poor nutrition. The application of traditional pastoralist management systems to an intensified livestock population is increasing the attrition of livestock, accelerating environmental degradation, increasing the risk of inter-ethnic conflict and, consequentially, failing to ensure that the most benefits possible in terms of added-value are being derived from the available livestock. Solutions to the problem of feeding the livestock belonging to refugees are made complex by the lack of incentive to invest in a region where camp dwellers have no land tenure rights and a strong desire to return home as soon as possible. In order to reduce conflict between refugees and the host community, solutions need to benefit both sectors.Due to the size of a camp and the concentration of dwellings in a small area, comparisons can be made with livestock keeping in a peri-urban environment. The over-grazing by the large numbers of livestock around the camps will result in degradation of the local environment and ultimately livestock may only be able to be kept by following a programme by refugee livestock owners of cutting and carrying available forage back to the immediate vicinity of the camps. An alternative, is that (as we shall later propose) fodder and crop residues are bought and brought in from outside the camp. However far more benefit would certainly derive from a planned programme of growing forage crops, either by the refugees, or endemic villagers who could then sell them to the refugees and gain a valuable additional income. However a balance has to be struck between what is currently an unsustainable situation, characterised by a excessive livestock population carrying out possibly long-term environmental degradation, versus support for an artificial system of livestock management, which will entail interventionary support and management, the planned and budgeted provision of supplementary feed and the perpetuation of a system which disconnects the refugees from their animal ownership and management traditions and knowledge. A series of recommendations will be made that are designed to reduce the overwhelming demand for forage in the short and medium term. If implemented, they should result in smaller, fitter herds of livestock that in the long term can be both more readily repatriated and readapted to the more favourable grazing conditions found in Western Sudan

Sperm competition as an under-appreciated factor in domestication

Humans created an environment that increased selective pressures on subgroups of those species that became domestic. We propose that the domestication process may in some cases have been facilitated by changes in mating behaviour and resultant sperm competition. By adapting to sperm competition, proto-domestic animals could potentially have outcompeted their wild counterparts in human-constructed niches. This could have contributed to the restriction of gene flow between the proto-domesticates and their wild counterparts, thereby promoting the fixation of other domestication characteristics. Further to this novel perspective for domestication, we emphasise the general potential of postcopulatory sexual selection in the restriction of gene flow between populations, and urge more studies

Exploring Rattus praetor (Rodentia, Muridae) as a possible species complex using geometric morphometrics on dental morphology

Taxonomic uncertainties in the Rattus genus persist due to among-species morphological conservatism coupled with within-species environmental variation in morphology. As a result, this genus contains a number of possible cryptic species. One important example can be found in R. praetor, where morphological studies indicate it is a possible species complex. Genetic studies of R. praetor (limited to analysis of mitochondrial DNA) have been inconclusive, but do indicate such subdivision. Here we use geometric morphometrics to explore this possible species complex by analysing the dental traits of 48 specimens from New Guinea and neighbouring regions. We find separate molar morphologies for Bougainsville Island, central New Guinea and west New Guinea which cannot be easily explained by different environmental factors (climate, precipitation and altitude), strongly suggesting the existence of a number of evolutionarily distinct taxa within what is currently called R. praetor thus supporting previous suggestions that R. praetor is a species complex. Our findings demonstrate the potential of advanced morphological analyses in identifying separate species, contrary to the claims of morphological conservatism. Future analyses should combine geometric morphometrics with genetic analyses over the species range and include sub-fossil specimens from the Bismarck archipelago and Solomon Islands to resolve the evolutionary history of R. praetor

Effect of pre-exposure use of hydroxychloroquine on COVID-19 mortality: a population-based cohort study in patients with rheumatoid arthritis or systemic lupus erythematosus using the OpenSAFELY platform.

BACKGROUND: Hydroxychloroquine has been shown to inhibit entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into epithelial cells in vitro, but clinical studies found no evidence of reduced mortality when treating patients with COVID-19. We aimed to evaluate the effectiveness of hydroxychloroquine for prevention of COVID-19 mortality, as opposed to treatment for the disease. METHODS: We did a prespecified observational, population-based cohort study using national primary care data and linked death registrations in the OpenSAFELY platform, which covers approximately 40% of the general population in England, UK. We included all adults aged 18 years and older registered with a general practice for 1 year or more on March 1, 2020. We used Cox regression to estimate the association between ongoing routine hydroxychloroquine use before the COVID-19 outbreak in England (considered as March 1, 2020) compared with non-users of hydroxychloroquine and risk of COVID-19 mortality among people with rheumatoid arthritis or systemic lupus erythematosus. Model adjustment was informed by a directed acyclic graph. FINDINGS: Between Sept 1, 2019, and March 1, 2020, of 194 637 people with rheumatoid arthritis or systemic lupus erythematosus, 30 569 (15·7%) received two or more prescriptions of hydroxychloroquine. Between March 1 and July 13, 2020, there were 547 COVID-19 deaths, 70 among hydroxychloroquine users. Estimated standardised cumulative COVID-19 mortality was 0·23% (95% CI 0·18 to 0·29) among users and 0·22% (0·20 to 0·25) among non-users; an absolute difference of 0·008% (-0·051 to 0·066). After accounting for age, sex, ethnicity, use of other immunosuppressive drugs, and geographical region, no association with COVID-19 mortality was observed (HR 1·03, 95% CI 0·80 to 1·33). We found no evidence of interactions with age or other immunosuppressive drugs. Quantitative bias analyses indicated that our observed associations were robust to missing information for additional biologic treatments for rheumatological disease. We observed similar associations with the negative control outcome of non-COVID-19 mortality. INTERPRETATION: We found no evidence of a difference in COVID-19 mortality among people who received hydroxychloroquine for treatment of rheumatological disease before the COVID-19 outbreak in England. Therefore, completion of randomised trials investigating pre-exposure prophylactic use of hydroxychloroquine for prevention of severe outcomes from COVID-19 are warranted. FUNDING: Medical Research Council

Post-glacial colonisation of Europe by the wood mouse, Apodemus sylvaticus : evidence of a northern refugium and dispersal with humans

The wood mouse Apodemus sylvaticus is an opportunistic rodent that is found throughout most of the European mainland. It is present on many islands around the margins of the continent and in northern Africa. The species has been the subject of previous phylogeographic studies but these have focussed on the more southerly part of its range. A substantial number of new samples, many of them from the periphery of the species’ range, contribute to an exceptional dataset comprising 981 mitochondrial cytochrome b sequences. These new data provide sufficient resolution to transform our understanding of the species’ survival through the last glaciation and its subsequent re-colonisation of the continent. The deepest genetic split we found is in agreement with previous studies and runs from the Alps to central Ukraine, but we further distinguish two separate lineages in wood mice to the north and west of this line. It is likely that this part of Europe was colonised from two refugia, putatively located in the Iberian peninsula and the Dordogne or Carpathian region. The wood mouse therefore joins the growing number of species with extant populations that appear to have survived the Last Glacial Maximum in northern refugia, rather than solely in traditionally recognised refugial locations in the southern European peninsulas. Furthermore, the existence of a northern refugium for the species was predicted in a study of mitochondrial variation in a specific parasite of the wood mouse, demonstrating the potential value of data from parasites to phylogeographic studies. Lastly, the presence of related haplotypes in widely disparate locations, often on islands or separated by substantial bodies of water, demonstrates the propensity of the wood mouse for accidental human-mediated transport

Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.Peer reviewe

Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets

Human-mediated biological exchange has had global social and ecological impacts. In subS-aharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species. Resolution of this longstanding debate requires new efforts, given the lack of well-dated fauna from high-precision excavations, and ambiguous osteomorphological identifications. We analysed faunal remains from 22 eastern African sites spanning a wide geographic and chronological range, and applied biomolecular techniques to confirm identifications of two Asian taxa: domestic chicken (Gallus gallus) and black rat (Rattus rattus). Our approach included ancient DNA (aDNA) analysis aided by BLAST-based bioinformatics, Zooarchaeology by Mass Spectrometry (ZooMS) collagen fingerprinting, and direct AMS (accelerator mass spectrometry) radiocarbon dating. Our results support a late, mid-first millennium CE introduction of these species. We discuss the implications of our findings for models of biological exchange, and emphasize the applicability of our approach to tropical areas with poor bone preservation

Inhaled corticosteroid use and risk COVID-19 related death among 966,461 patients with COPD or asthma: an OpenSAFELY analysis

AbstractBackgroundEarly descriptions of the coronavirus outbreak showed a lower prevalence of asthma and COPD than was expected for people diagnosed with COVID-19, leading to speculation that inhaled corticosteroids (ICS) may protect against infection with SARS-CoV-2, and development of serious sequelae. We evaluated the association between ICS and COVID-19 related death using linked electronic health records in the UK.MethodsWe conducted cohort studies on two groups of people (COPD and asthma) using the OpenSAFELY platform to analyse data from primary care practices linked to national death registrations. People receiving an ICS were compared to those receiving alternative respiratory medications. Our primary outcome was COVID-19 related death.FindingsWe identified 148,588 people with COPD and 817,973 people with asthma receiving relevant respiratory medications in the four months prior to 01 March 2020. People with COPD receiving ICS were at a greater risk of COVID-19 related death compared to those receiving a long-acting beta agonist (LABA) and a long-acting muscarinic antagonist (LAMA) (adjusted HR = 1.38, 95% CI = 1.08 – 1.75). People with asthma receiving high dose ICS were at an increased risk of death compared to those receiving a short-acting beta agonist (SABA) only (adjusted HR = 1.52, 95%CI = 1.08 – 2.14); the adjusted HR for those receiving low-medium dose ICS was 1.10 (95% CI = 0.82 – 1.49). Quantitative bias analyses indicated that an unmeasured confounder of only moderate strength of association with exposure and outcome could explain the observed associations in both populations.InterpretationThese results do not support a major role of ICS in protecting against COVID-19 related deaths. Observed increased risks of COVID-19 related death among people with COPD and asthma receiving ICS can be plausibly explained by unmeasured confounding due to disease severity.FundingThis work was supported by the Medical Research Council MR/V015737/1.</jats:sec