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.

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3.1.1 Kenya's biodive rsity Kenya is rich in biological diversity. Around 2!\IH'M species of animal and 7,01)0 plants have SO far been recorded, along with at least 2,000 fungi and bacteria i'MK i iJW 2j An unormous range or species inhabits the country's varied habitab. I' rum its crowded and colourful coral reefs to icy alpine moorland. The biology of the vast majority of these organism*, is little known. UndoubtedK m,mv species have not even been named vet bv science. Their value to Kenya's human population, as sources ol useful genes, as food or medicine, or as vital parts oi ecological systems., has bareh been studied. \\ hat is . lear. htm ever, is thai Kenya's biodiversih ]«under serious threat. An expanding population is putting severe pressure on the environment. Impoverished people are torced to use resources unsustamably. Natural habitats continue to be cleared and converted. Land is degraded and water polluted; ecosystems are damaged and their functions impaired. Without concerted and caretulh focused action, we are likely to lose much of Kenya's diversity of life. I he wider consequences of this car, onk he guessed at. 1 he resourceto Mippovt ,ii Hon are -carce. however. We need to know where our biodiversity is and what state it is in. Which sites and habitats are the most important, which are the most threatened, and which therefore require the most urgent attention:Kenya alread\ has an extensive protected area system. Over 10% of the country's land area is presently gazetted as National Parks, National Reserves or Forest Reserves. Should this not be sufficient to conserve ourbiodh ersity? L'ntortunalek, it is not Mam protected areas (especially Forest Reserves) lace -en DUB conservation problems despite their status. Also, verj few of Kenya's protected areas were chosen to conserve biodiversity as such. Our parks and reserves exist tor a variety of reason--. I and ^as set aside because it contained good populations of 'big game' (i.e. large mammals I that might attract visitors, because it protected water catchments, because it supported valuable timber tor exploitation, or simply because at the lime ver\ tew people wanted to Jive there. There is no reason why sites selected in this way should contain exceptionally rich or distinctive fauna and flora. To select the most important sites tor biodiversih conservation, we need to focus clearly on biodiversity to begin with.Unfortunately, assessing biodiversity is difficult, expensive and extremely time-consuming (e.g. Lawton el til. 1998). By the time we obtained adequate information, it would be too late to make use of it We need to find workable ways to short-cut the process b\ using the data we already have. One wa\ to do this is to locus on birds. Using birds to assess conservation prioritiesThis directory is a contribution to identifving Kenya'? biodiversity conservation priorities, The Important Bird Areas process uses birds to select keysites for conservation. Important bird Areas {IBAs) are sites of global biodiversity conservation importance ...

1. Citizen science is gaining increasing prominence as a tool for science and engagement. However, despite being a potentially valuable tool for sustainable development, citizen science has little visibility in many developing countries.2. We undertook a collaborative prioritisation process with experts in conservation and the environment to assess the potential of environmental citizen science in East Africa, including its opportunities, benefits and barriers. This provided principles that are applicable across developing countries, particularly for large-scale citizen science.3. We found that there was great potential for citizen science to add to our scientific knowledge of natural resources and biodiversity trends. Many of the important benefits of citizen science were for people, as well as the environment directly.Major barriers to citizen science were mostly social and institutional, although projects should also consider access to suitable technology and language barriers. 4. Policy implications. Citizen science can provide data to support decision-making and reporting against international targets. Participation can also provide societal benefits, informing and empowering people, thus supporting the United Nations'This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

BackgroundThe 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 FindingsWe 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.ConclusionsThis 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.

BackgroundThere 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.MethodsSample 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 planningResultsMore 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.ConclusionContraceptive 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12889-017-4510-6) contains supplementary material, which is available to authorized users.

QUANTIFYING PEST CONTROL SERVICES BY BIRDS AND ANTS IN KENYAN COFFEE FARMS Megan MilliganEcosystem services, such as pest control and pollination, are critical benefits of biodiversity necessary for agricultural production. Predators, including insectivorous birds and ants, can provide important biological controls in agroecosystems, boosting crop yield and helping to offset the need for expensive inputs such as pesticides. With agricultural demand projected to increase in the future, two broad management strategies, termed land sparing and land sharing, have been proposed to conserve biodiversity while still meeting increased agricultural demand. Understanding the related impacts of habitat and landscape characteristics on the delivery of ecosystem services can better inform managers seeking to promote these benefits of biodiversity. In order to better understand these relationships, I conducted a sentinel pest experiment to investigate predation levels in response to a novel pest on coffee farms in central Kenya. The frequency of predation decreased significantly with increasing distance from adjacent forest fragments and was correlated with bird species richness. Predation was also significantly higher on shade compared to sun coffee farms. The mechanism through which the bird and ant communities are effecting pest removal is less clear, but encouraging particular preferential predators could positively influence pest control. In conclusion, a land sharing approach, via both the integration of shade trees and the conservation of small ii forest fragments within a farm, can support increased levels of pest control services provided by both birds and ants in Kenyan coffee farms.iii ACKNOWLEDGEMENTS