Extensive Population Structure Highlights an Apparent Paradox of Stasis in the Impala (Aepyceros melampus).

Impalas are unusual among bovids because they have remained morphologically similar over millions of years-a phenomenon referred to as evolutionary stasis. Here, we sequenced 119 whole genomes from the two extant subspecies of impala, the common (Aepyceros melampus melampus) and black-faced (A. m.

Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations.

The blue wildebeest (Connochaetes taurinus) is a keystone species in savanna ecosystems from southern to eastern Africa, and is well known for its spectacular migrations and locally extreme abundance. In contrast, the black wildebeest (C. gnou) is endemic to southern Africa, barely escaped extinction in the 1900s and is feared to be in danger of genetic swamping from the blue wildebeest.

Genomic prediction using machine learning: a comparison of the performance of regularized regression, ensemble, instance-based and deep learning methods on synthetic and empirical data.

Background: The accurate prediction of genomic breeding values is central to genomic selection in both plant and animal breeding studies. Genomic prediction involves the use of thousands of molecular markers spanning the entire genome and therefore requires methods able to efficiently handle high dimensional data. Not surprisingly, machine learning methods are becoming widely advocated for and used in genomic prediction studies.

Bird species richness and diversity responses to land use change in the Lake Victoria Basin, Kenya.

The increasing demand for cultivated lands driven by human population growth, escalating consumption and activities, combined with the vast area of uncultivated land, highlight the pressing need to better understand the biodiversity conservation implications of land use change in Sub-Saharan Africa. Land use change alters natural wildlife habitats with fundamental consequences for biodiversity. Consequently, species richness and diversity typically decline as land use changes from natural to disturbed.

Mapping brucellosis risk in Kenya and its implications for control strategies in sub-Saharan Africa.

In Sub-Saharan Africa (SSA), effective brucellosis control is limited, in part, by the lack of long-term commitments by governments to control the disease and the absence of reliable national human and livestock population-based data to inform policies. Therefore, we conducted a study to establish the national prevalence and develop a risk map for Brucella spp. in cattle to contribute to plans to eliminate the disease in Kenya by the year 2040.

Corrigendum/Erratum to "Livestock water and land productivity in Kenya and their implications for future resource us" [].

[This corrects the article DOI: 10.1016/j.heliyon.

Forecasting the Potential Effects of Climate Change on Malaria in the Lake Victoria Basin Using Regionalized Climate Projections.

Background: Malaria epidemics are increasing in East Africa since the 1980s, coincident with rising temperature and widening climate variability. A projected 1-3.5 °C rise in average global temperatures by 2100 could exacerbate the epidemics by modifying disease transmission thresholds.

Elevational distribution of montane Afrotropical butterflies is influenced by seasonality and habitat structure.

Determinants of elevational distribution of butterfly species richness and abundance in the tropics are poorly understood. Here we assess the combined effects, both additive and interactive, of seasonality and habitat structure on the elevational distribution of butterflies in the Uluguru Mountains, Tanzania. We sampled butterflies along a 1100 m elevational gradient that extended from 1540 to 2639 m using a time-constrained fixed-area method during the short to long rains and long to short rains transitions, and in habitat structure classified as closed or open.

Livestock water and land productivity in Kenya and their implications for future resource use.

Population growth and rising affluence increase the demand for agricultural commodities. Associated growth in production increases dependency on natural resources in countries that attempt to meet part or all of the new demand locally. This study assesses the impact of changing meat and milk production on natural resource use in Kenya under three plausible scenarios of socio-economic development, namely Business-As-Usual (BAU), Sustainable Development (SDP) and Kenya Vision 2030 (V2030) scenarios.

Long-term historical and projected herbivore population dynamics in Ngorongoro crater, Tanzania.

The Ngorongoro Crater is an intact caldera with an area of approximately 310 km2 located within the Ngorongoro Conservation Area (NCA) in northern Tanzania. It is known for the abundance and diversity of its wildlife and is a UNESCO World Heritage Site and an International Biosphere Reserve. Long term records (1963-2012) on herbivore populations, vegetation and rainfall made it possible to analyze historic and project future herbivore population dynamics.

Robust estimation of heritability and predictive accuracy in plant breeding: evaluation using simulation and empirical data.

Background: Genomic prediction (GP) is used in animal and plant breeding to help identify the best genotypes for selection. One of the most important measures of the effectiveness and reliability of GP in plant breeding is predictive accuracy. An accurate estimate of this measure is thus central to GP.

Cross-boundary human impacts compromise the Serengeti-Mara ecosystem.

Protected areas provide major benefits for humans in the form of ecosystem services, but landscape degradation by human activity at their edges may compromise their ecological functioning. Using multiple lines of evidence from 40 years of research in the Serengeti-Mara ecosystem, we find that such edge degradation has effectively "squeezed" wildlife into the core protected area and has altered the ecosystem's dynamics even within this 40,000-square-kilometer ecosystem. This spatial cascade reduced resilience in the core and was mediated by the movement of grazers, which reduced grass fuel and fires, weakened the capacity of soils to sequester nutrients and carbon, and decreased the responsiveness of primary production to rainfall.

Rainfall trends and variation in the Maasai Mara ecosystem and their implications for animal population and biodiversity dynamics.

Rainfall exerts a controlling influence on the availability and quality of vegetation and surface water for herbivores in African terrestrial ecosystems. We analyse temporal trends and variation in rainfall in the Maasai Mara ecosystem of East Africa and infer their implications for animal population and biodiversity dynamics. The data originated from 15 rain gauges in the Mara region (1965-2015) and one station in Narok Town (1913-2015), in Kenya's Narok County.

Wildlife Population Dynamics in Human-Dominated Landscapes under Community-Based Conservation: The Example of Nakuru Wildlife Conservancy, Kenya.

Wildlife conservation is facing numerous and mounting challenges on private and communal lands in Africa, including in Kenya. We analyze the population dynamics of 44 common wildlife species in relation to rainfall variation in the Nakuru Wildlife Conservancy (NWC), located in the Nakuru-Naivasha region of Kenya, based on ground total counts carried out twice each year from March 1996 to May 2015. Rainfall in the region was quasi-periodic with cycle periods dependent on the rainfall component and varying from 2.

Trade-offs for climate-resilient pastoral livelihoods in wildlife conservancies in the Mara ecosystem, Kenya.

Pastoralists in the wildlife-rich East African rangelands use diversification into conservation and tourism as a strategy to supplement livestock-based livelihoods and to spread risk. Tourism incomes are an important alternative source during drought, when livestock incomes decline. However, tourism may also reduce access to rangeland resources, and an abundant wildlife may destroy crops and injure, kill or transmit disease to livestock or people.

Comparing the Predictive Abilities of Phenotypic and Marker-Assisted Selection Methods in a Biparental Lettuce Population.

Breeding for traits with polygenic inheritance is a challenging task that can be done by phenotypic selection, marker-assisted selection (MAS) or genome-wide selection. We comparatively evaluated the predictive abilities of four selection models on a biparental lettuce ( L.) population genotyped with 95 single nucleotide polymorphisms and 205 amplified fragment length polymorphism markers.

Urban consumption of meat and milk and its green and blue water footprints-Patterns in the 1980s and 2000s for Nairobi, Kenya.

The Problem: Various studies show that the developing world experiences and will continue to experience a rise in consumption of animal proteins, particularly in cities, as a result of continued urbanization and income growth. Given the relatively large water footprint (WF) of animal products, this trend is likely to increase the pressure on already scarce water resources.

Aim: We estimate, analyse and interpret the changes in consumption of meat and milk between the 1980s and 2000s for three income classes in Nairobi, the ratio of domestic production to imports, and the WF (the volume of freshwater consumed) to produce these commodities in Kenya and abroad.

Extreme Wildlife Declines and Concurrent Increase in Livestock Numbers in Kenya: What Are the Causes?

There is growing evidence of escalating wildlife losses worldwide. Extreme wildlife losses have recently been documented for large parts of Africa, including western, Central and Eastern Africa. Here, we report extreme declines in wildlife and contemporaneous increase in livestock numbers in Kenya rangelands between 1977 and 2016.

How Rainfall Variation Influences Reproductive Patterns of African Savanna Ungulates in an Equatorial Region Where Photoperiod Variation Is Absent.

In high temperate latitudes, ungulates generally give birth within a narrow time window when conditions are optimal for offspring survival in spring or early summer, and use changing photoperiod to time conceptions so as to anticipate these conditions. However, in low tropical latitudes day length variation is minimal, and rainfall variation makes the seasonal cycle less predictable. Nevertheless, several ungulate species retain narrow birth peaks under such conditions, while others show births spread quite widely through the year.

Rubber yield prediction by meteorological conditions using mixed models and multi-model inference techniques.

Linear mixed models were developed and used to predict rubber (Hevea brasiliensis) yield based on meteorological conditions to which rubber trees had been exposed for periods ranging from 1 day to 2 months prior to tapping events. Predictors included a range of moving averages of meteorological covariates spanning different windows of time before the date of the tapping events. Serial autocorrelation in the latex yield measurements was accounted for using random effects and a spatial generalization of the autoregressive error covariance structure suited to data sampled at irregular time intervals.

Regularized group regression methods for genomic prediction: Bridge, MCP, SCAD, group bridge, group lasso, sparse group lasso, group MCP and group SCAD.

Background: Genomic prediction is now widely recognized as an efficient, cost-effective and theoretically well-founded method for estimating breeding values using molecular markers spread over the whole genome. The prediction problem entails estimating the effects of all genes or chromosomal segments simultaneously and aggregating them to yield the predicted total genomic breeding value. Many potential methods for genomic prediction exist but have widely different relative computational costs, complexity and ease of implementation, with significant repercussions for predictive accuracy.