Genetic relatedness and disrupted social structure in a poached population of African elephants

We use genetic measures of relatedness and observations of female bonding to examine the demographic signature of historically heavy poaching of a population of free-ranging African elephants. We collected dung samples to obtain DNA and observed behaviour from 102 elephant families over a 25-month period in 2003–2005 in Mikumi National Park, Tanzania. Poaching reduced the population by 75% in the decade prior to the 1989 ivory trade ban; park records indicate that poaching dropped significantly in Mikumi following the ban. Using 10 microsatellite loci, DNA was genotyped in 203 elephants and pair-wise relatedness was calculated among adult females within and between groups. The Mikumi population is characterized by small group size, considerable variation in group relatedness, females with no first-order adult relatives and females that form only weak social bonds. We used gene-drop analysis and a model of a genetically intact pedigree to compare our observed Mikumi group relatedness to a simulated genetically intact unpoached expectation. The majority of groups in Mikumi contain 2 to 3 adults; of these, 45% were classified as genetically disrupted. Bonding, quantified with a pair-wise association index, was significantly correlated with relatedness; however only half of the females formed strong bonds with other females, and relatedness was substantially lower for a given bond strength as compared to an unpoached population. Female African elephants without kin demonstrated considerable behavioural plasticity in this disturbed environment, grouping with other females lacking kin, with established groups, or remaining alone, unable to form any stable adult female-bonds. We interpret these findings as the remaining effect of poaching disturbance in Mikumi, despite a drop in the level of poaching since the commercial trade in ivory was banned 15 years ago.     

Modelling the effectiveness of contraception for controlling introduced populations of elephant in South Africa

Re‐introduced African elephant (Loxodonta africana Blumenbach) populations are growing at very high rates in many of southern Africa’s reserves, have attained densities higher than previously thought possible and may be exhibiting irruptive growth. Active management of such populations is necessary to prevent the potentially negative effects on habitat and biodiversity that are associated with elephant overpopulation. One potentially feasible method of elephant management is immunocontraception, but very little is known about the long‐term effectiveness of this method. Using demographic data from three South African elephant populations, we made model projections of the effects of contraception on population growth rates to determine whether contraception may be a feasible management tool for elephant. In comparison with noncontracepted populations, realistic reductions in population growth rate after 20 years of contraception were projected to be up to c. 64%, with 50% being a very feasible target. Through its ability to reduce population growth rates, immunocontraception should be an effective tool for preventing or minimizing irruption in elephants and, perhaps, other introduced ungulate species.     

Heard but not seen: an acoustic survey of the African forest elephant population at Kakum Conservation Area, Ghana

This study, designed to survey forest elephants ( Loxodonta africana cyclotis ) at Kakum Conservation Area, Ghana, is the first to apply acoustic methods to elephant abundance estimation and to compare results with independent survey estimates. Nine acoustic sensors gathered sound continuously for 38 days. Low-frequency calling rates have been established as useful elephant abundance indices at a Namibian watering hole and a central African forest clearing. In this study, we estimated elephant population size by applying an abundance index model and detection function developed in central Africa to data from simultaneous sampling periods on Kakum sensors. The sensor array recorded an average of 1.81 calls per 20-min sampling period from an effective detection area averaging 10.27 km². The resulting estimate of 294 elephants (95% CI: 259–329) falls within confidence bounds of recent dung-based surveys. An extended acoustic model, estimating the frequency with which elephants are silent when present, yields an estimate of 350 elephants (95% CI: 315–384). Acoustic survey confidence intervals are at least half as wide as those from dung-based surveys. This study demonstrates that acoustic surveying is a valuable tool for estimating elephant abundance, as well as for detecting other vocal species and anthropogenic noises that may be associated with poaching.     

The influence of increasing population size and vegetation productivity on elephant distribution in the Kruger National Park

Decisions to reduce the impacts of large herbivores on biodiversity in protected areas are often based on controlling their numbers. However, numbers per se may not be the foremost consideration when managing impacts. This is because density‐related changes in distribution can also affect habitat utilization and hence, impact. In this study we tested whether changes in the distribution of African elephants are associated with increasing population size. We used spatially explicit count data collected during the dry seasons from 1998 to 2004 in South Africa's Kruger National Park. We did this at five spatial scales and in landscapes defined by vegetation, geology, climate and soils. We then investigated whether observed distributions and grid‐cell‐specific densities were associated with the remotely sensed Normalized Difference Vegetation Index (NDVI) as a measure of productivity and therefore food resource availability at the landscape scale. Consistent with density mediated changes, we found that elephant grid‐cell occupancy increased with population size, while grid‐cell‐specific density became less variable. In addition, the combined distribution of bull groups and breeding herds became less clumped with increasing population size. We further found that within landscapes elephants were present on grid‐cells with higher NDVI values, but that the influence of NDVI during the dry season on densities among landscapes may be weak. These results suggest that NDVI was more indicative of structural habitat choices such as woody vegetation than food availability per se. Our study highlights the need to consider factors other than population size alone when formulating management decisions to reduce large herbivore impacts on biodiversity in protected areas.     

Using naturally shed feathers for individual identification, genetic parentage analyses, and population monitoring in an endangered Eastern imperial eagle (Aquila heliaca) population from Kazakhstan

Genetic analyses on noninvasively collected samples have revolutionized how populations are monitored. Most noninvasive monitoring studies have used hair or scat for individual identification of elusive mammals, but here we utilize naturally shed feathers. The Eastern imperial eagle (EIE) is a species of conservation concern throughout Central Asia and, like most raptors, EIEs are inherently challenging to study because adults are difficult to capture and band using conventional techniques. Over 6 years, we noninvasively collected hundreds of adult feathers and directly sampled EIE chicks at a national nature reserve in Kazakhstan. All samples were genetically sexed and genotyped at a suite of microsatellite loci. Genetically profiled adult feathers identified and monitored the presence of individual eagles over time, enabling us to address a variety of issues related to the biology, demography, and conservation of EIEs. Specifically, we characterized (i) the genetic mating system, (ii) relatedness among mated pairs, (iii) chick sex ratios, and (iv) annual turnover in an adult breeding population. We show that EIEs are genetically monogamous and furthermore, there is no apparent relatedness-based system of mate choice (e.g. inbreeding avoidance). Results indicate that annual adult EIE survivorship (84%) is lower than expected for a long-lived raptor, but initial analyses suggest the current reproductive rate at our study site is sufficient to maintain a stable breeding population. The pristine habitat at our study site supports an EIE population that is probably the most demographically robust in the world; thus, our results caution that populations in marginal habitats may not be self-sustaining.     

Scope and utility of hydrogen exchange as a tool for mapping landscapes

The ability to determine conformational parameters of protein-folding landscapes is critical for understanding the link between conformation, function, and disease. Monitoring hydrogen exchange (HX) of labile protons at equilibrium enables direct extraction of thermodynamic or kinetic landscape parameters in two limiting extremes. Here, we establish a quantitative framework for relating HX behavior to landscape. We use this framework to demonstrate that the range of predicted global HX behavior for the majority of a set of characterized two-state proteins under near-native conditions does not readily span between both extremes. For most, stability may be quantitatively determined under physiological conditions, with semiquantitative boundaries on kinetics additionally determined using modest experimental perturbations to shift HX behavior. The framework and relationships derived in the simple context of two-state global folding highlight the importance of understanding HX across the entire continuum of behavior, in order to apply HX to map landscapes.     

Fluorescence spectroscopy as a tool for monitoring solubility and aggregation behavior of beta-lactoglobulin after heat treatment

Denaturation and aggregation of whey proteins are of interest to the food and pharmaceutical industry due to the importance of final structure in functionality, impact on food texture, and the chemical stability of the final product. In this study, we demonstrate the potential of fluorescence spectrometry combined with multivariate chemometric methods for quantifying solubility and aggregation behavior of beta-lactoglobulin (beta-LG); a major whey protein and a frequent food ingredient. Heat-induced aggregation of beta-LG was studied under different conditions including pH, temperature and heating durations. Results showed very good agreement between the fluorescence-based predictions and measurements obtained by HPLC and gravimetric analysis regardless of the conditions. Standard normal variate (SNV), a signal preprocessing and filtering tool, was found to enhance the predictive accuracy and robustness of the fluorescence-based model.     

Empirically testing the effectiveness of thermal imaging as a tool for identification of large mammals in the African bushveldt

Monitoring animal populations often relies on direct visual observations. This is problematic at night when spotlighting can cause misidentification and inaccurate counting. Using infrared thermography (IRT) could potentially solve these difficulties, but reliability is uncertain. Here, we test the accuracy of 24 observers, differing in experience and skill levels, in identifying antelope species from IRT photographs taken in the African bush. Overall, 38% of identifications were correct to species level, and 50% were correct to genus/subfamily level. Identification accuracy depended on the confidence and skill of the observer (positive relationship), the number of animals present (positive relationship), and the distance at which it was taken (negative relationship). Species with characteristic features, horn morphology, or posture were identified with ~80% accuracy (e.g. wildebeest, kudu and impala) while others were considerably lower (e.g. blesbok and waterbuck). Experience significantly improved identification accuracy but the effect was not consistent between species and even experienced observers struggled to identify red hartebeest, reedbuck and eland. Counting inaccuracies were commonplace, particularly when group size was large. We conclude that thermal characteristics of species and experience of observers can pose challenges for African field ecologists, but IRT can be used to identify and count some species accurately, especially <100 m.     

Secretomers as a new tool for the monitoring of CTL responses

Efforts to follow tumor-specific immune responses in patients are often thwarted by lack of knowledge of the appropriate tumor antigens and the CTL epitopes of those antigens. There is, therefore, a growing need for techniques to monitor tumor-specific immune responses in settings where tumor antigens, and antigenic epitopes, remain unidentified. Here we describe a novel system to follow tumor-specific CTL immune responses. A truncated, soluble murine class I MHC (H-2D^b) molecule was fused with a rat IgG_2a Fc, in order to allow secretion of the complex. Tumor-specific CTL could then be detected as a result of the complex fastening to specific T cell receptors (TCR). These constructs were inserted into the genome of a recombinant adenovirus vector. Infection of tumor cells with these adenovirus constructs results in the secretion of the complexes into the culture supernatant. These soluble divalent class I MHC molecules were used to detect and activate specific CTL populations.     

Citizen monitoring of invasive species: wing morphometry as a tool for detection of alien Tetropium species

The increasing threat of alien wood‐boring insect has resulted in the initiation of large‐scale monitoring programmes. These programmes are most often based on pheromone‐bailed traps, which allow the early detection and monitoring of invasive species. This approach is expensive because it entails the processing and accurate identification of large numbers of specimens. One of the most often suggested solutions to this problem is citizen participation in the monitoring of invasive species. Such an approach has the potential for reducing costs as well as providing data from a larger number of sites. However, citizens vary in taxonomic expertise and experience which can result in identification errors. This may be particularly important in the case of wood borers which include many morphologically similar species. In this study, we develop and discuss a semi‐automated method of identifying four morphologically similar and invasive Tetropium spp. wood borers as a potential tool for citizen‐based monitoring programmes. Identification is based on wing measurements and requires neither specialist knowledge nor expensive equipment. The method correctly identified the species of Tetropium with an error ranging from 1.3% for T. fuscum to 7.5% for T. cinnamopterum. We found that experience level of the individual user was not essential for correct identification; on average, inexperienced volunteers correctly identified the Tetropium species in 93% of cases. Further development of this method may be a significant step to overcoming the taxonomical impediment to citizen monitoring of taxonomically challenging groups of insects.     

Validation of a system for monitoring individual feeding and drinking behaviour and intake in young cattle

The objective of this study was to validate an electronic system for monitoring individual feeding and drinking behaviour and intake developed for young cattle housed in group. A total of 35 Holstein–Gyr crossbred heifers (BW: 180±52 kg; age: 121.5±32.5 days), fitted with an ear tag containing a unique passive transponder, were distributed in three groups of 12, 12 and 11 animals per period and had free access to 12 electronic feed bins and two electronic water bins (Intergado® Ltd). The dimensions of feed and water bins, as well as the sensors position were appropriate for young cattle. The system documented the visit frequency and duration, as well as the feed and water intakes, by recording the animal’s identification tag, bin number, initial and final times of visits and the difference of feed/water weight at the start and end of each bin visit. Feed bins were monitored using time-lapse video recording over 4 days and the water bins were monitored over 6 days. For each feed bin, two feeding events were monitored using manual weighings with an external scale immediately before and after the animal’s visit and the difference between them was assumed as feed intake (n=24 observations). For the water bins, 60 manual weighings were made. Video and manual weighing data were regressed on the electronic feeding and drinking behaviour and intake data to evaluate the system’s precision and accuracy. The system showed high specificity (98.98% and 98.56% for the feed and water bins, respectively) and sensitivity (99.25% and 98.74%, respectively) for identifying an animal’s presence or absence. Duration of feed and water bin visits as well as feed and water consumption per visit estimated by the system were highly correlated and precise compared with the observed video and manual weighing data (r²=0.917, 0.963, 0.973 and 0.986, respectively). It was concluded that Intergado® system is a useful tool for monitoring feeding and drinking behaviour as well as water and feed intakes in young cattle housed in groups.     

DNA barcoding of freshwater ichthyoplankton in the Neotropics as a tool for ecological monitoring

Quantifying and classifying ichthyoplankton is one of the most effective ways of monitoring the recruitment process in fishes. However, correctly identifying the fish based on morphological characters is extremely difficult, especially in the early stages of development. We examined ichthyoplankton from tributaries and reservoirs along the middle stretch of the Paranapanema River, one of the areas most impacted by hydroelectric projects in the Neotropics. Matching DNA sequences of the COI gene (628–648 bp) allowed us to identify 99.25% of 536 samples of eggs (293) and larvae (243) subjected to BOLD‐IDS similarity analysis with a species‐level threshold of 1.3%. The results revealed 37 species in 27 genera, 15 families and four orders, some 23.8% of documented fish species in the Paranapanema River. Molecular identification meant that we could include data from egg samples that accounted for about 30% of the species richness observed. The results in this study confirm the efficacy of DNA barcoding in identifying Neotropical ichthyoplankton and show how the data produced provide valuable information for preparing plans for conserving and managing inland waters.     

Near infrared spectroscopy compared to liquid chromatography coupled to mass spectrometry and capillary electrophoresis as a detection tool for peptide reaction monitoring

Peptide interaction is normally monitored by liquid chromatography (LC), liquid chromatography coupled to mass spectrometry (LC-MS), mass spectrometric (MS) methods such as MALDI-TOF/MS or capillary electrophoresis (CE). These analytical techniques need to apply either high pressure or high voltages, which can cause cleavage of newly formed bondages. Therefore, near infrared reflectance spectroscopy (NIRS) is presented as a rapid alternative to monitor the interaction of glutathione and oxytocin, simulating physiological conditions. Thereby, glutathione can act as a nucleophile with oxytocin forming four new conjugates via a disulphide bondage. Liquid chromatography coupled to UV (LC-UV) and mass spectrometry via an electrospray ionisation interface (LC-ESI-MS) resulted in a 82% and a 78% degradation of oxytocin at pH 3 and a 5% and a 7% degradation at pH 6.5. Capillary electrophoresis employing UV-detection (CE-UV) showed a 44% degradation of oxytocin. LC and CE in addition to the NIRS are found to be authentic tools for quantitative analysis. Nevertheless, NIRS proved to be highly suitable for the detection of newly formed conjugates after separating them on a thin layer chromatography (TLC) plate. The recorded fingerprint in the near infrared region allows for a selective distinct qualitative identification of conjugates without the need for expensive instrumentation such as quadrupole or MALDI-TOF mass spectrometers. The performance of the established NIRS method is compared to LC and CE; its advantages are discussed in detail.     

Life history and population dynamics of a tree species in tropical semi‐arid climate: A case study with Cordia oncocalyx

In semi‐arid climates, plant population dynamics are strongly influenced by the amount and temporal distribution of rainfall. We monitored a population of the tree species Cordia oncocalyx (Boraginaceae) for 24 months in the dry thorny woodland of semi‐arid northeastern Brazil, to investigate which life‐history traits allow this tree to be locally dominant. We used horizontal life tables and a Lefkovitch matrix and tested for relationships among demographic parameters of seedling, infant, juvenile, immature, virginile and reproductive ontogenetic stages with rainfall and canopy openness. Germination and recruitment occurred in the rainy months, and dry‐season mortality occurred only in seedlings (76% and 100%, first and second years, respectively) and infants (3% and 6%). Juveniles showed greater height growth under more open canopies (Spearman correlation coefficient = 0.24), suggesting that light availability influences growth. The population growth rate was λ = 1.0336, and the highest sensitivity occurred in the infant‐juvenile transition. Our results show light as a restrictive growth factor for plants in the juvenile stage and confirm the strong influence of rainfall on the dynamics of trees in a seasonally dry environment. The formation of a persistent seed bank with germination concentrated at the rainfall onset but spreading over the rainy season are strategies that hedge bets before establishment. The formation of a bank of infants, which can resume growth as soon as there is water, hedges bets after establishment. We attribute the positive population growth rate of Cordia oncocalyx to survival strategies allowing bet‐hedging both before and after establishment.