Evaluation of spoor tracking to monitor cheetah abundance in central northern Namibia.

Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2007.The design, implementation, management and the evaluation of sound conservation practices, is often dependent on the availability of reliable estimates of animal abundance. Large carnivores often pose particular problems in this regard, due to their low densities and wide-ranging behaviour, so the true abundance of such species are seldom able to be reported in literature . As a result, the use of indices of abundance, mostly for relative abundance, has been investigated. However, before these indices can be reliably utilized for conservation purposes , there is a pressing need to calibrate them. As of yet, calibration studies have primarily been performed on demarcated conservation areas, where individuals could be individually identified. Not all these calibrations studies reported indices to be a function of true density. Nevertheless , spoor frequency has been reported to be a function of true density for carnivores in certain Parks in Namibia . Precisely , cheetah spoor density was reported to correlate with visuals in the Kgalagadi Transfrontier Park. The majority of these studies elucidate a species spatial organization, animal behaviour, as the paramount factor determining the relationship between densities estimated via different censusing methods. Thus, the efficiency of spoor frequency to estimate and monitor relative abundance for wild cheetahs is yet to be empirically tested . Despite the lack of a true density estimate for the free-ranging cheetahs in the study area, evaluated spoor tracking as a possible index to monitor relative cheetah abundance using radiotelemetry densities estimates as representative of true abundance for the area, for the 1995 to 2000 period. The study is considered to be opportunistic , and a pillar for future research, as transects where spoor tracking was conducted were layout primarily for ungulates strip counts. Least-linear regression and Spearman's correlation were used to evaluate the relationship between density estimates derived by the two methods. Percentages of change on annual densities were also regressed as a mean to test spoor frequency sensitivity to density changes. The calibration of spoor frequency with estimates of density produced using radio-telemetry, without the ascription of imprints to individual animals, was poor (rs=17.4, y=0.36+0.20). The sensitivity analysis also showed spoor tracking poor reliability to monitor cheetah population. This can be attributed, in order of importance, to the discrepancies on the spatial extent sampled by the two methods, the species large home ranges, substrate quality , habitat preferences, the availability of farm road networks and the transect design, i.e., cyclic. However, the paramount factor limiting the study conclusions was the lack of a more local density estimate at a farm level. Therefore, the use of spoor frequency to estimate wild cheetah relative abundance requires further research, particularly using a different sampling design, longer straight transects and the acquisition of local densities estimates

Metabarcoding of soil environmental DNA to estimate plant diversity globally

IntroductionTraditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. MethodsWe sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. ResultsLarge-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. DiscussioneDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region

Global diversity and distribution of nitrogen-fixing bacteria in the soil

Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria

Dataset on woody aboveground biomass, disturbance losses, and wood density from an African savanna ecosystem

This dataset comprises tree inventories and damage assessments performed in Namibia's semi-arid Zambezi Region. Data were sampled in savannas and savanna woodlands along steep gradients of elephant population densities to capture the effects of those (and other) disturbances on individual-level and stand-level aboveground woody biomass (AGB). The dataset contains raw data on dendrometric measures and processed data on specific wood density (SWD), woody aboveground biomass, and biomass losses through disturbance impacts. Allometric proxies (height, canopy diameters, and in adult trees also stem circumferences) were recorded for n = 6,179 tree and shrub individuals. Wood samples were taken for each encountered species to measure specific wood density. These measurements have been used to estimate woody aboveground biomass via established allometric models, advanced through our improved methodologies and workflows that accounted for tree and shrub architecture shaped by disturbance impacts. To this end, we performed a detailed damage assessment on each woody individual in the field. In addition to estimations of standing biomass, our new method also delivered data on biomass losses to different disturbance agents (elephants, fire, and others) on the level of plant individuals and stands. The data presented here have been used within a study published with Ecological Indicators (Kindermann et al., 2022) to evaluate the benefits of our improved methodology in comparison to a standard reference method of aboveground biomass estimations. Additionally, it has been employed in a study on carbon storage and sequestration in vegetation and soils (Sandhage-Hofmann et al., 2021). The raw data of dendrometric measurements can be subjected to other available allometric models for biomass estimation. The processed data can be used to analyze disturbance impacts on woody aboveground biomass, or for regional carbon storage estimates. The data on species-specific wood density can be used for application to other dendrometric datasets to (re-)estimate biomass through allometric models requiring wood density. It can further be used for plant functional trait analyses. (C) 2022 The Authors. Published by Elsevier Inc

Trends in cheetah <i>Acinonyx jubatus</i> density in north-central Namibia

Assessing trends in abundance and density of species of conservation concern is vital to inform conservation and management strategies. The remaining population of the cheetah (Acinonyx jubatus) largely exists outside of protected areas, where they are often in conflict with humans. Despite this, the population status and dynamics of cheetah outside of protected areas have received relatively limited attention across its range. We analyzed remote camera trapping data of nine surveys conducted from 2005 to 2014 in the Waterberg Conservancy, north-central Namibia, which included detections of 74 individuals (52 adult males, 7 adult females and 15 dependents). Using spatial capture–recapture methods, we assessed annual and seasonal trends in cheetah density. We found evidence of a stable trend in cheetah density over the study period, with an average density of 1.94/100 km2 (95% confidence interval 1.33–2.84). This apparent stability of cheetah density is likely the result of stable and abundant prey availability, a high tolerance to carnivores by farmers and low turnover rates in home range tenure. This study highlights the importance of promoting long-term surveys that capture a broad range of environmental variation that may influence species density and the importance of nonprotected areas for cheetah conservation.</p

Quantifying spatial ignorance in the effort to collect terrestrial fauna in Namibia, Africa

Effective conservation efforts and predictions of future impacts on biodiversity depend heavily on publicly available information about species distributions. However, data on species distributions is often patchy, especially in many countries of the Global South where resources for biological surveys have been historically limited. In this study, we use biodiversity ignorance scores to quantify and visualize gaps and biases in biodiversity data for Namibia, with a focus on five terrestrial taxa at a spatial scale of 10 x 10 km. We model the relationship between ignorance scores and socio-geographical variables using generalized additive models for location, scale and shape (GAMLSS). Our findings demonstrate that despite a high volume of occurrence records available on the Global Biodiversity Information Facility (GBIF), publicly available knowledge of Namibia's terrestrial biodiversity remains very limited, with large areas contributing few or no records for key taxa. The exception is birds that have benefitted from a massive influx of data from the citizen science platform eBird. Our study also highlights the importance of citizen science initiatives for biodiversity knowledge and reinforces the usefulness of ignorance scores as a simple intuitive indicator of the relative availability and distribution of species occurrence records. However, further research, biological surveys, and renewed efforts to make existing data held by museums and other institutions widely available are still necessary to enhance biodiversity data coverage in countries with patchy data

Global diversity and distribution of nitrogen-fixing bacteria in the soil

Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria