Dense sampling of bird diversity increases power of comparative genomics.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Restructuring of Palladium Nanoparticles during Oxidation by Molecular Oxygen.

An interplay between Pd and PdO and their spatial distribution inside the particles are relevant for numerous catalytic reactions. Using in situ time-resolved X-ray absorption spectroscopy (XAS) supported by theoretical simulations, a mechanistic picture of the structural evolution of 2.3 nm palladium nanoparticles upon their exposure to molecular oxygen is provided. XAS analysis revealed the restructuring of the fcc-like palladium surface into the 4-coordinated structure of palladium oxide upon absorption of oxygen from the gas phase and formation of core@shell Pd@PdO structures. The reconstruction starts from the low-coordinated sites at the edges of palladium nanoparticles. Formation of the PdO shell does not affect the average Pd‒Pd coordination numbers, since the decrease of the size of the metallic core is compensated by a more spherical shape of the oxidized nanoparticles due to a weaker interaction with the support. The metallic core is preserved below 200 °C even after continuous exposure to oxygen, with its size decreasing insignificantly upon increasing the temperature, while above 200 °C, bulk oxidation proceeds. The Pd‒Pd distances in the metallic phase progressively decrease upon increasing the fraction of the Pd oxide due to the alignment of the cell parameters of the two phases.

Determinants of contraceptive use among postpartum women in a county hospital in rural KENYA.

BACKGROUND: There is a high unmet need for limiting and spacing child births during the postpartum period. Given the consequences of closely spaced births, and the benefits of longer pregnancy intervals, targeted activities are needed to reach this population of postpartum women. Our objective was to establish the determinants of contraceptive uptake among postpartum women in a county referral hospital in rural Kenya. METHODS: Sample was taken based on a mixed method approach that included both quantitative and qualitative methods of data collection. Postpartum women who had brought their children for the second dose of measles vaccine between 18 and 24 months were sampled Participants were interviewed using structured questionnaires, data was collected about their socio-demographic characteristics, fertility, knowledge, use, and access to contraceptives. Chi square tests were used to determine the relationship between uptake of postpartum family planning and: socio demographic characteristics, contraceptive knowledge, use access and fertility. Qualitative data collection included focus group discussions (FDGs) with mothers and in-depth interviews with service providers Information was obtained from mothers' regarding their perceptions on family planning methods, use, availability, access and barriers to uptake and key informants' views on family planning counseling practices and barriers to uptake of family planning RESULTS: More than three quarters (86.3%) of women used contraceptives within 1 year of delivery, with government facilities being the most common source. There was a significant association (p ≤ 0.05) between uptake of postpartum family planning and lower age, being married, higher education level, being employed and getting contraceptives at a health facility. One third of women expressing no intention of having additional children were not on contraceptives. In focus group discussions women perceived that the quality of services offered at the public facilities was relatively good because they felt that they were adequately counseled, as opposed to local chemist shops where they perceived the staff was not experienced. CONCLUSION: Contraceptive uptake was high among postpartum women, who desired to procure contraceptives at health facilities. However, there was unmet need for contraceptives among women who desired no more children. Government health facility stock outs represent a missed opportunity to get family planning methods, especially long acting reversible contraceptives, to postpartum women.

Productivity declines threaten East African soda lakes and the iconic Lesser Flamingo.

Soda lakes are some of the most productive aquatic ecosystems.1 Their alkaline-saline waters sustain unique phytoplankton communities2,3 and provide vital habitats for highly specialized biodiversity including invertebrates, endemic fish species, and Lesser Flamingos (Phoeniconaias minor).1,4 More than three-quarters of Lesser Flamingos inhabit the soda lakes of East Africa5; however, populations are in decline.6 Declines could be attributed to their highly specialized diet of cyanobacteria7 and dependence on a network of soda lake feeding habitats that are highly sensitive to climate fluctuations and catchment degradation.8,9,10,11,12 However, changing habitat availability has not been assessed due to a lack of in situ water quality and hydrology data and the irregular monitoring of these waterbodies.13 Here, we combine satellite Earth observations and Lesser Flamingo abundance observations to quantify spatial and temporal trends in productivity and ecosystem health over multiple decades at 22 soda lakes across East Africa. We found that Lesser Flamingo distributions are best explained by phytoplankton biomass, an indicator of food availability. However, timeseries analyses revealed significant declines in phytoplankton biomass from 1999 to 2022, most likely driven by substantial rises in lake water levels. Declining productivity has reduced the availability of healthy soda lake ecosystems, most notably in equatorial Kenya and northern Tanzania. Our results highlight the increasing vulnerability of Lesser Flamingos and other soda lake biodiversity in East Africa, particularly with increased rainfall predicted under climate change.14,15,16 Without improved lake monitoring and catchment management practices, soda lake ecosystems could be pushed beyond their environmental tolerances. VIDEO ABSTRACT.

Observation of a black-cheeked waxbill (Brunhilda charmosyna) cleaning a Kirk's dik-dik (Madoqua kirkii).

The vast majority of interspecific interactions are competitive or exploitative. Yet, some positive interspecies interactions exist, where one (commensalism) or both (mutualism) species benefit. One such interaction is cleaning mutualisms, whereby a cleaner removes parasites from a client. In this note, we document the novel observation of a black-cheeked waxbill (Brunhilda charmosyna) appearing to clean a Kirk's dik-dik (Madoqua kirkii), at the Mpala Research Centre in Laikipia County, Kenya. The purported cleaning took place for over one minute and is notable firstly for the dik-dik remaining still for the duration of cleaning and secondly for involving two species that are much smaller than those traditionally involved in bird-mammal cleaning interactions. Unfortunately, no further cleaning events were subsequently observed, raising questions about whether this record was opportunistic or a regular occurrence. Future observations may reveal whether this behavior is widespread and whether it involves other small passerines.

Genomic Analyses of Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa.

Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.

Shade trees preserve avian insectivore biodiversity on coffee farms in a warming climate.

AIM: Coffee is an important export for many developing countries, with a global annual trade value of $100 billion, but it is threatened by a warming climate. Shade trees may mitigate the effects of climate change through temperature regulation that can aid in coffee growth, slow pest reproduction, and sustain avian insectivore diversity. The impact of shade on bird diversity and microclimate on coffee farms has been studied extensively in the Neotropics, but there is a dearth of research in the Paleotropics. LOCATION: East Africa. METHODS: We created current and future regional Maxent models for avian insectivores in East Africa using Worldclim temperature data and observations from the Global Biodiversity Information Database. We then adjusted current and future bioclimatic layers based on mean differences in temperature between shade and sun coffee farms and projected the models using these adjusted layers to predict the impact of shade tree removal on climatic suitability for avian insectivores. RESULTS: Existing Worldclim temperature layers more closely matched temperatures under shade trees than temperatures in the open. Removal of shade trees, through warmer temperatures alone, would result in reduction of avian insectivore species by over 25%, a loss equivalent to 50 years of climate change under the most optimistic emissions scenario. Under the most extreme climate scenario and removal of shade trees, insectivore richness is projected to decline from a mean of 38 to fewer than 8 avian insectivore species. MAIN CONCLUSIONS: We found that shade trees on coffee farms already provide important cooler microclimates for avian insectivores. Future temperatures will become a regionally limiting factor for bird distribution in East Africa, which could negatively impact control of coffee pests, but the effect of climate change can be potentially mediated through planting and maintaining shade trees on coffee farms.

Association between umbilical cord hygiene and neonatal sepsis among neonates presenting to a primary care facility in Nairobi County, Kenya: a case-control study.

Background: Three-quarters of all annual neonatal deaths in developing countries are attributable to neonatal sepsis. In primary care settings, poor cord hygiene due to improper handling of the infant's cord is a major contributor to the occurrence of neonatal sepsis. The objective of this study was to describe the umbilical cord practices among mothers attending a primary care facility, assess the relationship between umbilical cord hygiene and neonatal sepsis, its impact on the population, as well as the influence of other neonatal and maternal factors on this relationship. Methods: A case-control study was conducted to assess the umbilical cord hygiene-neonatal sepsis relationship among neonates attending a primary care facility between August and October 2018. All cases were selected, while controls were systematically random sampled, as per study eligibility criteria. Exposure variables were summarized using descriptive statistics. A multivariable logistic regression model was fitted to evaluate the association between umbilical cord hygiene and neonatal sepsis adjusting for the effect of potential confounders. Subsequently, a population attributable fraction (PAF) was estimated. Results: The proportion of mothers with improper hygiene was 35.3%: 72.1% among the cases and 16.3% among the controls' caregivers. The odds of neonatal sepsis were 13 times higher (OR=13.24; 95% CI: [7.5; 23.4]) among infants whose caregivers had improper hygiene compared to those who had proper hygiene. None of the neonatal and maternal covariates confounded the umbilical cord hygiene-neonatal sepsis association. This odds ratio gave a PAF of 66.7% (95% CI: 62.5; 69.0). Conclusions: Improper cord hygiene is prevalent in this low resource setting. Improper cord hygiene has a strong positive association with neonatal sepsis. Observing good cord care practices could avert up to 67% of newborn infections. This calls for inclusion of comprehensive cord care practices in the antenatal care educational package.

Monitoring the extraction of copper from chicken dung leachate using an aluminium electrode as an indicator.

Copper is found in several minerals in the earth's crust with varying the elemental and mineralogical composition. Several techniques of extraction have been investigated all in the effort of obtaining a cheaper and viable method. This paper reports on further works done on copper extraction using a wet chemical method. According to the method, reduction of copper (II) ions using hydrazones from chlorinated chicken waste leachate was stoichiometrically driven. The chicken dung leachate used was an impure bio-material in which the concentration could not be determined. It was, therefore, difficult to quantify the stoichiometric ratios of species in that reaction. This paper reports on a method of monitoring the extent of copper reduction by chlorinated chicken dung leachate using an aluminum electrode as an indicator. Mineral rocks were obtained from Maragwa Location in Tharaka Nithi County in Kenya. The samples were ground into a fine powder of 250 micro millimeters. The samples were then subjected to mineralogical analysis using X-ray diffraction (XRD). Chemical analysis was done using atomic absorption spectroscopy (AAS) and X-ray fluorescence spectroscopy (XRFS). Ground samples were leached using 1.0 M hydrochloric acid. The resulting leachate was treated with chicken dung leachate prepared from chicken dung in which chlorine gas was bubbled at a constant temperature of 28 °C. The pH of the resultant chicken dung leachate was adjusted from 4 to 12 using 1.0 M sodium hydroxide and then used as an electrolyte. An electrochemical cell was set up consisting of aluminum and graphite rods. The aluminum electrode was found not to corrode at pH above 11 while it was able to displace available copper ions. This property of the aluminum electrode was used to monitor when all copper ions were displaced. The recovered copper was analyzed using XRFS. The copper recovery rate from the samples ranged from 7.0 to 20.0 at level A and 7.4-26.8% at level B with a purity range of 84.9 level A to 88.6% level B. An overall positive potential in the reduction process confirmed the greater the tendency of copper reduction without an external source of electricity. The corrosion of the aluminium electrode in the process was not observed and therefore does not require frequent replacement. Therefore, a large scale extraction process needs to be investigated.

Enhancing the capacity and effectiveness of community health volunteers to improve maternal, newborn and child health: Experience from Kenya.

OBJECTIVE: To determine whether a simple monitoring and tracking tool, Mwanzo Mwema Monitoring and Tracking Tool (MMATT), would enable community health volunteers (CHVs) in Kenya to 1) plan their workloads and activities, 2) identify the women, newborns and children most in need of accessing critical maternal, newborn and child health (MNCH) interventions and 3) improve key MNCH indicators. METHODS: A mixed methods approach was used. Household surveys at baseline (n = 912) and endline (n = 1143) collected data on key MNCH indicators in the four subcounties of Taita Taveta County, Kenya. Eight focus group discussions were held with 40 CHVs to ascertain their perspectives on using the tool. RESULTS: Qualitative findings revealed that the CHVs found the MMATT to be useful in planning their activities and prioritizing beneficiaries requiring more support to access MNCH services. They also identified potential barriers to care at both the community and health system levels. At endline, previously pregnant women were more likely to have received four or more antenatal care visits, facility delivery, postnatal care within two weeks of delivery and a complete package of care than baseline respondents. Among women with children under 24 months, those at endline were more likely to report early breastfeeding and exclusive breastfeeding for the first six months. These results remained after adjustment for age, subcounty, gravida, mother's education and asset index. CONCLUSION: Our results demonstrate that simple tools enable CHVs to identify disparities in service delivery and health outcomes, and to identify barriers to MNCH care. Tools that enhance CHVs' ability to plan and prioritize the women and children most in need increase CHVs' potential impact.

A Bioacoustic Record of a Conservancy in the Mount Kenya Ecosystem.

BACKGROUND: Environmental degradation is a major threat facing ecosystems around the world. In order to determine ecosystems in need of conservation interventions, we must monitor the biodiversity of these ecosystems effectively. Bioacoustic approaches offer a means to monitor ecosystems of interest in a sustainable manner. In this work we show how a bioacoustic record from the Dedan Kimathi University wildlife conservancy, a conservancy in the Mount Kenya ecosystem, was obtained in a cost effective manner. A subset of the dataset was annotated with the identities of bird species present since they serve as useful indicator species. These data reveal the spatial distribution of species within the conservancy and also point to the effects of major highways on bird populations. This dataset will provide data to train automatic species recognition systems for birds found within the Mount Kenya ecosystem. Such systems are necessary if bioacoustic approaches are to be employed at the large scales necessary to influence wildlife conservation measures. NEW INFORMATION: We provide acoustic recordings from the Dedan Kimathi University wildlife conservancy, a conservancy in the Mount Kenya ecosystem, obtained using a low cost acoustic recorder. A total of 2701 minute long recordings are provided including both daytime and nighttime recordings. We present an annotation of a subset of the daytime recordings indicating the bird species present in the recordings. The dataset contains recordings of at least 36 bird species. In addition, the presence of a few nocturnal species within the conservancy is also confirmed.

A new species and new host records of the quill mites (Acari: Syringophilidae) associated with sunbirds (Passeriformes: Nectariniidae).

Neoaulonastus cinnyris sp. nov. (Acari: Prostigmata: Syringophilidae) parasitising Cinnyris mediocris (Passeriformes: Nectariniidae) from Tanzania is described. Additionally, Picobia oritis Skoracki et al. 2009 was recorded on four new hosts belonging to the family Nectariniidae from Ethiopian region: Cinnyris oustaleti (Bocage) from Angola, Cinnyris venustus (Shaw) from West Somalia, Cinnyris talatala Smith from Botswana and Zambia and Cinnyris erythrocercus (Hartlaub) from Uganda. All known quill mite species from family Nectariniidae are summarized in table.

Estimating the size of the female sex worker population in Kenya to inform HIV prevention programming.

BACKGROUND: The high burden of HIV infections among female sex workers (FSW) in sub-Saharan Africa has been long recognised, but effective preventive interventions have largely not been taken to scale. We undertook a national geographical mapping exercise in 2011/2012 to assess the locations and population size of FSW in Kenya, to facilitate targeted HIV prevention services for this population. METHODS AND FINDINGS: We used a geographical mapping approach, consisting of interviews with secondary key informants to identify "hot" spots frequented by FSW, their operational dynamics and the estimated numbers of FSW in those spots. This was followed by validation of the estimates through interviews with FSW at each spot identified. The mapping covered Nairobi, the capital city of Kenya, and 50 other major urban centres. In total, 11,609 secondary key informant interviews were conducted to identify FSW spots. Further, a total of 6,360 FSW were interviewed for spot validation purposes. A total of 10,670 spots where FSW congregate were identified. The estimated FSW population in all the towns mapped was 103,298 (range 77,878 to 128, 717). Size estimates in the towns mapped were extended to smaller towns that were not mapped, using a statistical model. The national urban FSW population estimate was 138,420 (range 107, 552 to 169, 288), covering all towns of over 5,000 population. We estimated that approximately 5% of the urban female population of reproductive age in Kenya could be sex workers, which is consistent with previous estimates from other sub-Saharan African countries. CONCLUSIONS: This study provides the first national level data on the size of the FSW population in Kenya. These data can be used to enhance HIV prevention programme planning and implementation for FSW, to form the basis for impact evaluations, and to improve programme coverage by directing efforts to locations with the greatest need.