Romane Cristescu

Detecting bottlenecks using BOTTLENECK 1.2.02 in wild populations: the importance of the microsatellite structure

Reduced, or bottlenecked, populations are more prone to adverse events. Thus, the detection of genetic bottleneck signatures in wildlife is an important issue for conservation. BOTTLENECK 1.2.02 is a software commonly used for detecting genetic characteristics of past bottlenecks. Here we test the efficiency with which this software detects bottlenecks in two koala populations of known history. The sign test performed well for both populations, particularly under the infinite alleles model for mutation. This suggests this model could be the more realistic for marsupial microsatellites than other mutation models. Under the allele frequency distribution test, the two populations falsely appeared to be at mutation/drift equilibrium. However, this test could detect the bottleneck when only imperfect repeat microsatellites were included in the analysis. We thus recommend further investigation of imperfect repeat microsatellites, which could be more powerful for bottleneck detection. These results underline the cautious approach researchers and conservationists should take when studying the past of unknown populations.

Inbreeding and testicular abnormalities in a bottlenecked population of koalas (Phascolarctos cinereus)

Habitat destruction and fragmentation, interactions with introduced species or the relocation of animals to form new populations for conservation purposes may result in a multiplication of population bottlenecks. Examples are the translocations of koalas to French Island and its derivative Kangaroo Island population, with both populations established as insurance policies against koala extinction. In terms of population size, these conservation programs were success stories. However, the genetic story could be different. We conducted a genetic investigation of French and Kangaroo Island koalas by using 15 microsatellite markers, 11 of which are described here for the first time. The results confirm very low genetic diversity. French Island koalas have 3.8 alleles per locus and Kangaroo Island koalas 2.4. The present study found a 19% incidence of testicular abnormality in kangaroo Island animals. Internal relatedness, an individual inbreeding coefficient, was not significantly different in koalas with testicular abnormalities from that in other males, suggesting the condition is not related to recent inbreeding. It could instead result from an unfortunate selection of founder individuals carrying alleles for testicular abnormalities, followed by a subsequent increase in these alleles’ frequencies through genetic drift and small population-related inefficiency of selection. Given the low diversity and possible high prevalence of deleterious alleles, the genetic viability of the population remains uncertain, despite its exponential growth so far. This stands as a warning to other introductions for conservation reasons.

How Ebola impacts social dynamics in gorillas: a multistate modelling approach

Emerging infectious diseases can induce rapid changes in population dynamics and threaten population persistence. In socially structured populations, the transfers of individuals between social units, for example, from breeding groups to non-breeding groups, shape population dynamics. We suggest that diseases may affect these crucial transfers. We aimed to determine how disturbance by an emerging disease affects demographic rates of gorillas, especially transfer rates within populations and immigration rates into populations. We compared social dynamics and key demographic parameters in a gorilla population affected by Ebola using a long-term observation data set including pre-, during and post-outbreak periods. We also studied a population of undetermined epidemiological status in order to assess whether this population was affected by the disease. We developed a multistate model that can handle transition between social units while optimizing the number of states. During the Ebola outbreak, social dynamics displayed increased transfers from a breeding to a non-breeding status for both males and females. Six years after the outbreak, demographic and most of social dynamics parameters had returned to their initial rates, suggesting a certain resilience in the response to disruption. The formation of breeding groups increased just after Ebola, indicating that environmental conditions were still attractive. However, population recovery was likely delayed because compensatory immigration was probably impeded by the potential impact of Ebola in the surrounding areas. The population of undetermined epidemiological status behaved similarly to the other population before Ebola. Our results highlight the need to integrate social dynamics in host-population demographic models to better understand the role of social structure in the sensitivity and the response to disease disturbances.

Recovery Potential of a Western Lowland Gorilla Population following a Major Ebola Outbreak: Results from a Ten Year Study

Investigating the recovery capacity of wildlife populations following demographic crashes is of great interest to ecologists and conservationists. Opportunities to study these aspects are rare due to the difficulty of monitoring populations both before and after a demographic crash. Ebola outbreaks in central Africa have killed up to 95% of the individuals in affected western lowland gorilla (Gorilla gorilla gorilla) populations. Assessing whether and how fast affected populations recover is essential for the conservation of this critically endangered taxon. The gorilla population visiting Lokoué forest clearing, Odzala-Kokoua National Park, Republic of the Congo, has been monitored before, two years after and six years after Ebola affected it in 2004. This allowed us to describe Ebolas short-term and long-term impacts on the structure of the population. The size of the population, which included around 380 gorillas before the Ebola outbreak, dropped to less than 40 individuals after the outbreak. It then remained stable for six years after the outbreak. However, the demographic structure of this small population has significantly changed. Although several solitary males have disappeared, the immigration of adult females, the formation of new breeding groups, and several birth events suggest that the population is showing potential to recover. During the outbreak, surviving adult and subadult females joined old solitary silverbacks. Those females were subsequently observed joining young silverbacks, forming new breeding groups where they later gave birth. Interestingly, some females were observed joining silverbacks that were unlikely to have sired their infant, but no infanticide was observed. The consequences of the Ebola outbreak on the population structure were different two years and six years after the outbreak. Therefore, our results could be used as demographic indicators to detect and date outbreaks that have happened in other, non-monitored gorilla populations.

Experimental Evaluation of Koala Scat Persistence and Detectability with Implications for Pellet-Based Fauna Census

Establishing species distribution and population trends are basic requirements in conservation biology, yet acquiring this fundamental information is often difficult. Indirect survey methods that rely on fecal pellets (scats) can overcome some difficulties but present their own challenges. In particular, variation in scat detectability and decay rate can introduce biases. We studied how vegetation communities affect the detectability and decay rate of scats as exemplified by koalas Phascolarctos cinereus: scat detectability was highly and consistently dependent on ground layer complexity (introducing up to 16% non-detection bias); scat decay rates were highly heterogeneous within vegetation communities; exposure of scats to surface water and rain strongly accelerated scat decay rate and finally, invertebrates were found to accelerate scat decay rate markedly, but unpredictably. This last phenomenon may explain the high variability of scat decay rate within a single vegetation community. Methods to decrease biases should be evaluated when planning scat surveys, as the most appropriate method(s) will vary depending on species, scale of survey and landscape characteristics. Detectability and decay biases are both stronger in certain vegetation communities, thus their combined effect is likely to introduce substantial errors in scat surveys and this could result in inappropriate and counterproductive management decisions.

Accuracy and efficiency of detection dogs: a powerful new tool for koala conservation and management

Accurate data on presence/absence and spatial distribution for fauna species is key to their conservation. Collecting such data, however, can be time consuming, laborious and costly, in particular for fauna species characterised by low densities, large home ranges, cryptic or elusive behaviour. For such species, including koalas (Phascolarctos cinereus), indicators of species presence can be a useful shortcut: faecal pellets (scats), for instance, are widely used. Scat surveys are not without their difficulties and often contain a high false negative rate. We used experimental and field-based trials to investigate the accuracy and efficiency of the first dog specifically trained for koala scats. The detection dog consistently out-performed human-only teams. Off-leash, the dog detection rate was 100%. The dog was also 19 times more efficient than current scat survey methods and 153% more accurate (the dog found koala scats where the human-only team did not). This clearly demonstrates that the use of detection dogs decreases false negatives and survey time, thus allowing for a significant improvement in the quality and quantity of data collection. Given these unequivocal results, we argue that to improve koala conservation, detection dog surveys for koala scats could in the future replace human-only teams.

Is restoring flora the same as restoring fauna? Lessons learned from koalas and mining rehabilitation

Summary 1. Rehabilitation of degraded and disturbed landscapes has become critical for counteracting habitat loss. The success of rehabilitation projects, to date, has focused on abiotic and florabased criteria of success, leaving fauna unmonitored. This follows from the common paradigm that if flora recovers, fauna will recover too. However, we know very little about the extent to which this assumption is true. We addressed this issue by examining whether flora criteria used to assess mine rehabilitation reflected patterns in the recovery of an iconic species, the koala Phascolarctos cinereus, in eastern Australia. 2. We used rank tests to search for correlations between current mining flora criteria and fauna presence. We then developed a priori regression models to search for new abiotic and flora criteria that are biologically relevant to Phascolarctos cinereus. In a third step, we investigated correlations between rehabilitation success ranked on the best biologically relevant habitat variables and Phascolarctos cinereus recolonization. 3. We found that rehabilitation success based on current mining flora criteria (calculated at two different scales: rehabilitation blocks and monitoring plots) did not correlate with Phascolarctos cinereus presence. 4. In contrast to the current flora-based criteria, we found that variables that are biologically relevant to Phascolarctos cinereus had more influence on its presence. For instance, species richness in food trees favoured by Phascolarctos cinereus and tree canopy cover had a positive effect on its recolonization. However, correlations between biologically relevant habitat variables and fauna occurrence were still inconsistent. 5. Synthesis and applications. In our study, flora criteria for rehabilitation success did not correlate with fauna recolonization. We also found several additional difficulties in predicting fauna recolonization based on habitat variables, such as the choice of relevant scales and the geographic specificity of relevant variables. The choice between monitoring habitat proxies or fauna will ultimately be based on weighting costs and efficiency and will depend on the fauna species. However, we argue that in general, fauna species should be directly monitored to ensure the recolonization of i) species of interest (e.g. threatened and charismatic) and ii) fauna involved in long-term resilience of ecosystems.

The habitat and diet of koalas (Phascolarctos cinereus) in Queensland

Descriptions of koala (Phascolarctos cinereus) habitat and diet from 11 sites across Queensland are presented. Koala activity was recorded from 49 regional ecosystems across nine land zones and five bioregions. Thirty-four tree species were identified from an examination of leaf cuticle fragments in faecal pellets. Although the species were from three families and seven genera, 44% of browse species (15) belonged to the myrtaceous subgenus Symphomyrtus. Eleven of these contributed most of the koala diet across all sites. However, most species were present in minor or trace dietary elements. There was also a large number of unidentified species or dietary elements, all of which were usually present in trace amounts. The importance of these minor and trace components is not known. Diet at some sites was founded on a single eucalypt species. Here the likelihood of those sites’ browse resources being lost or degraded by stochastic events, as climate variability increases, raises questions about the persistence of the resident koala populations.

What faecal pellet surveys can and can’t reveal about the ecology of koalas Phascolarctos cinereus

Previous approaches to indirect detection of koala presence have been proposed, however, the present paper identifies issues of bias, pellet detectability and over-analysis of information inherent in those prior techniques. We recommend an approach that reduces bias, can be consistently applied and enables information on presence of koalas Phascolarctos cinereus to be used to inform larger survey programs, ‘ground-truth’ predictive habitat mapping, etc. We describe a rapid assessment methodology based on indirect signs that provides a reproducible, statistically valid, time-efficient and resource-efficient protocol for determining the presence of this species. The application, advantages and limitations of this ‘koala rapid assessment method’ (KRAM) are discussed with reference to its role in the design of detailed and landscape scale P. cinereus surveys.

Effective population size of koala populations under different population management regimes including contraception

Context. The management of wildlife populations aiming to control population size should also consider the preservation of genetic diversity. Some overabundant koala populations, for example, have low genetic variation. Different management strategies will affect population genetic variation differently. Aims. Here, we compare four strategies with respect to their effects on the effective population size, Ne , and therefore on genetic variation. Methods. The four strategies of interest are: (1) sterilisation or culling (which have the same effect on genetic variation); (2) random contraception of females with replacement; (3) random contraception of females without replacement; and (4) regular contraception, giving every female equal opportunity to reproduce. We develop mathematical models of these alternative schemes to evaluate their impact on Ne . We also consider the effect of changing population sizes by investigating a model with geometric population growth in which females are removed by sterilisation or culling. Key results. We find that sterilisation/culling at sexual maturity has the most detrimental effect on Ne , whereas regular contraception has no impact on Ne . Random contraception lies between these two extremes, leading to a moderate reduction in Ne . Removal of females from a growing population results in a higher Ne than the removal of females from a static population. Conclusions. Different strategies for controlling a population lead to different effective population sizes. Implications. To preserve genetic diversity in a wildlife population under control, the effective population size should be kept as large as possible. We suggest that a suitable approach in managing koala populations may be to prevent reproduction by all females older than a particular age.