Find research datasets worth reusing

opencc-zeroJan 2021View details →

Data from: Changes in soil microbial communities in post mine ecological restoration: implications for monitoring using high throughput DNA sequencing

<p>The ecological restoration of ecosystem services and biodiversity is a key intervention used to reverse the impacts of anthropogenic activities such as mining. Assessment of the performance of restoration against completion criteria relies on biodiversity monitoring. However, monitoring usually overlooks soil microbial communities (SMC), despite increased awareness of their pivotal role in many ecological functions. Recent advances in cost, scalability and technology has led to DNA sequencing being considered as a cost-effective biological monitoring tool, particularly for otherwise difficult to survey groups such as microbes. However, such approaches for monitoring complex restoration sites such as post-mined landscapes have not yet been tested. Here we examine bacterial and fungal communities across chronosequences of mine site restoration at three locations in Western Australia to determine if there are consistent changes in SMC diversity, community composition and functional capacity. Although we detected directional changes in community composition indicative of microbial recovery, these were inconsistent between locations and microbial taxa (bacteria or fungi). Assessing functional diversity provided greater understanding of changes in site conditions and microbial recovery than could be determined through assessment of community composition alone. These results demonstrate that <span>high-throughput amplicon sequencing of environmental DNA (eDNA)</span> is an effective approach for monitoring the complex changes in SMC following restoration. Future monitoring of mine site restoration using eDNA should consider archiving samples to provide improved understanding of changes in communities over time. Expansion to include other biological groups (e.g. soil fauna) and substrates would also provide a more holistic understanding of biodiversity recovery. </p>

Data from: Monitoring a Norwegian freshwater crayfish tragedy - eDNA snapshots of invasion, infection and extinction

1.The European Noble crayfish (Astacus astacus) is threatened by crayfish plague caused by the oomycete Aphanomyces astaci, which is spread by the invasive North American crayfish (e.g. signal crayfish, Pacifastacus leniusculus). Surveillance of crayfish plague status in Norway has traditionally relied on the monitoring survival of cage‐held noble crayfish, a method of ethical concern. Additionally, trapping is used in crayfish population surveillance. Here we test whether environmental DNA (eDNA) monitoring could provide a suitable alternative to the cage‐method, and a supplement to trapping. 2.We took advantage of an emerging crayfish plague outbreak in a Norwegian watercourse following illegal introduction of disease‐carrying signal crayfish, and initiated simultaneous eDNA‐monitoring and cage‐based surveillance, supplemented with trapping. A total of 304 water samples were filtered from several sampling stations over a four year period. eDNA data (species‐specific qPCR) for the presence of A. astaci, noble and signal crayfish within the water samples were compared to cage mortality and trapping. 3.This is the first study comparing eDNA‐monitoring and cage‐surveillance during a natural crayfish plague outbreak. We show that eDNA‐monitoring corresponds well with the biological status measured in terms of crayfish mortality and trapping results. eDNA analysis also reveals the presence of A. astaci in the water up to 2.5 weeks in advance of the cage‐method. eDNA estimates of A. astaci concentration and noble crayfish numbers increased markedly during mortality, and vanished quickly thereafter. eDNA provides a snapshot of the presence, absence or disappearance of crayfish regardless of season, and constitutes a valuable supplement to the trapping‐method that relies on season and legislation. 4.Synthesis and applications. Simultaneous eDNA‐monitoring of Aphanomyces astaci (crayfish plague) and relevant native and invasive freshwater crayfish species is well‐suited for early‐warning of invasion or infection, risk assessments, habitat evaluation and surveillance regarding pathogen and invasive/native crayfish status. This non‐invasive, animal‐welfare friendly method excludes the need for cage‐held susceptible crayfish in disease‐monitoring. Further, eDNA‐monitoring is less likely to spread A. astaci than traditional methods. This study resulted in the implementation of eDNA‐monitoring for Norwegian crayfish plague and crayfish surveillance programmes, and we believe other countries could improve management strategies for freshwater crayfish using a similar approach.

Data from: Camera-based occupancy monitoring at large scales: power to detect trends in grizzly bears across the Canadian Rockies

Monitoring carnivores is critical for conservation, yet challenging because they are rare and elusive. Few methods exist for monitoring wide-ranging species over large spatial and sufficiently long temporal scales to detect trends. Remote cameras are an emerging technology for monitoring large carnivores around the world because of their low cost, non-invasive methodology, and their ability to capture pictures of species of concern that are difficult to monitor. For species without uniquely identifiable spots, stripes, or other markings, cameras collect detection/non-detection data that are well suited for monitoring trends in occupancy as its own independent useful metric of species distribution, as well as an index for abundance. As with any new monitoring method, prospective power analysis is essential to ensure meaningful trends can be detected. Here we test camera-based occupancy models as a method to monitor changes in occupancy of a threatened species, grizzly bears (Ursus arctos), at large landscape scales, across 5 Canadian national parks (~21,000 km2). With n = 183 cameras, the top occupancy model estimated regional occupancy to be 0.79 across all 5 parks. We evaluate the statistical power to detect simulated 5–40% declines in occupancy between two sampling years and test applied questions of how power is affected by the spatial scale of interest (park level vs. regional level), the number of cameras deployed, and duration of camera deployment. We also explore several ecological mechanisms (i.e., spatial patterns) of decline in occupancy, and examine how power changes when focusing only on grizzly bears family groups. As hypothesized, statistical power increased with the number of cameras and with the number of days deployed. Power was unaffected, however, by the ecological mechanisms of decline, indicating that our systematic sampling design can detect a decline regardless of whether occupancy declined due to range edge attrition, ecological trap or other mechanisms. Despite their lower occupancy, power was similarly high for grizzly bear family groups compared to grizzly bears in general. We highlight which study design attributes contributed to high power and we provide advice for establishing cost-effective camera-based programs for monitoring large carnivore occupancy at large spatial scales.

Data from: The use and utility of surrogates in biodiversity monitoring programmes

Monitoring programmes are intended to inform effective biodiversity conservation and management (Legge et al. 2018). Well‐designed programmes can establish baseline conditions, determine trends in threatened species populations, quantify the effects of management, and provide warning of ecosystem changes (Magurran et al. 2010). For these reasons, biodiversity monitoring underpins the activities of land management agencies worldwide. However, it is not always possible to directly monitor key variables at ideal spatio‐temporal resolutions, due to resourcing or logistic constraints. For example, direct monitoring of koalas (Phascolarctos cinereus) can be cost‐ and time‐intensive as koalas are cryptic, occur at low densities, and are difficult to reliably observe in dense forest canopies (McAlpine et al. 2006).

opencc-zeroDec 2012View details →

Data from: Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards

Recent conceptual, technological, and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here we showcase an organismal system for a data-rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex), a widespread group distributed throughout Southeast Asia and southern India, have been the subject of numerous taxonomic treatments, which have drawn recent attention due to the possibility of undocumented species diversity. To date, studies of this group have relied on purportedly diagnostic morphological characters, with no attention given to the genetic underpinnings of species diversity. Using a 5-gene dataset, we estimated phylogeny and used multilocus genetic networks, analysis of population structure, and a Bayesian coalescent approach to infer species boundaries. Our results contradict previous systematic hypotheses, reveal surprising relationships between island and mainland lineages, and uncover novel, cryptic evolutionary lineages (i.e. new putative species). Our study contributes to a growing body of literature suggesting that, used in concert with other sources of data (e.g., morphology, ecology, biogeography), multilocus genetic data can be highly informative to systematists and biodiversity specialists when attempting to estimate species diversity and identify conservation priorities. We recommend holding in abeyance taxonomic decisions until multiple, converging lines of evidence are available to best inform taxonomists, evolutionary biologists, and conservationists.

Data from: An environmental DNA-based method for monitoring spawning activity: a case study, using the endangered Macquarie perch (Macquaria australasica)

Determining the timing and location of reproductive events is critical for efficient management of species. However, methods currently used for aquatic species are costly, time intensive, biased and often require destructive or injurious sampling. Hence, developing a non-invasive sampling method to accurately determine the timing and location of reproduction for aquatic species would be extremely valuable. We conducted an experimental and field study to determine the influence of spawning, and the mass release of spermatozoa in particular, on environmental DNA (eDNA) concentrations. Using a quantitative PCR approach we monitored changes in nuclear and mitochondrial eDNA concentrations over time. The data from the experimental study and the field survey supported our hypothesis that spawning events are characterized by higher concentrations of nuclear relative to mitochondrial eDNA. Outside of the reproductive period, we find that nuclear and mitochondrial DNA fragments are equally abundant in environmental water samples. We have shown that changes in the relative abundance of nuclear and mitochondrial eDNA can be used to monitor spawning activity of the endangered Macquarie perch. Our method is likely to be transferrable to other aquatic species and can be particularly useful to increase our understanding of the spawning biology of cryptic, rare or threatened species as well as design and evaluate environmental management actions and determine species establishment.

Data from: Monitoring vultures in the 21st century: the need for standardized protocols

This article calls on scientists, managers and organizations focused on vulture conservation to promote and use standardized monitoring programs based on sampling of molted feathers.

Data from: Acoustic monitoring of coastal dolphins and their response to naval mine neutralization exercises

To investigate the potential impacts of naval mine neutralization exercises (MINEX) on odontocete cetaceans, a long-term passive acoustic monitoring study was conducted at a US Navy training range near Virginia Beach, USA. Bottom-moored acoustic recorders were deployed in 2012–2016 near the epicentre of MINEX training activity and were refurbished every 2–4 months. Recordings were analysed for the daily presence/absence of dolphins, and dolphin acoustic activity was quantified in detail for the hours and days before and after 31 MINEX training events. Dolphins occurred in the area year-round, but there was clear seasonal variability, with lower presence during winter months. Dolphins exhibited a behavioural response to underwater detonations. Dolphin acoustic activity near the training location was lower during the hours and days following detonations, suggesting that animals left the area and/or reduced their signalling. Concurrent acoustic monitoring farther away from the training area suggested that the radius of response was between 3 and 6 km. A generalized additive model indicated that the predictors that explained the greatest amount of deviance in the data were the day relative to the training event, the hour of the day and circumstances specific to each training event.

Data from: Opportunities to integrate herders' indicators into formal rangeland monitoring: an example from Mongolia

Despite increasing calls for knowledge integration around the world, traditional knowledge is rarely used in formal, Western science-based monitoring and resource management. To better understand indicators herders use and their relationship to researcher-measured indicators, we conducted in-depth field interviews with 26 herders in three ecological zones of Mongolia. We asked each herder to 1) assess the overall condition of three different sites located along a livestock-use gradient from their winter camp using a numeric scale, 2) describe the indicators they used in their assessment, and 3) explain what caused their pastures to remain healthy or become degraded. At each site, we collected field data on vegetation variables and compared these with herders' ratings and indicators using linear regression. We used classification and ordination to understand how herders' assessment scores related to plant community composition, and determine how well multivariate analysis of factors determining plant community composition aligned with herders' observations of factors causing rangeland change. Across all ecological zones, herders use indicators similar to those used in formal monitoring. Herders' assessment scores correlated significantly and positively with measured total foliar cover in all three ecological zones, and with additional measured variables in the steppe and desert steppe. Ordination revealed that herder assessment scores were correlated with the primary ordination axis in each zone, and the main factors driving plant community composition in each zone were the same as those identified by herders as the primary causes of rangeland change in that zone. These results show promise for developing integrated indicators and monitoring protocols and highlight the importance of developing a common language of monitoring terminology shared by herders, government monitoring agencies, and researchers. We propose a new model for integrating herder knowledge and participation into formal monitoring in Mongolia, with implications for rangelands and pastoral people globally. We suggest practical ways of involving herders in formal monitoring that have potential broad application for promoting local and indigenous people's participation in implementing international agreements such as the UN Convention to Combat Desertification and the UN Convention on Biological Diversity, both of which call for involvement of local people and indigenous/traditional knowledges.

opencc-zeroApr 2020View details →

Rapid and accurate species identification for ecological studies and monitoring using CRISPR-based SHERLOCK

<p>One of the most foundational aspects of ecological studies and monitoring is accurate species identification, but cryptic speciation and observer error can confound phenotype-based identification. The CRISPR-Cas toolkit has facilitated remarkable advances in many scientific disciplines, but the fields of ecology and conservation biology have yet to fully embrace this powerful technology. The recently developed CRISPR-Cas13a platform SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) enables highly accurate taxonomic identification and has all the characteristics needed to transition to ecological and environmental disciplines. Here we conducted a series of proof of principle experiments to characterize SHERLOCK's ability to accurately, sensitively, and rapidly distinguished three fish species (two with protected status and one non-native) co-occurring in the San Francisco Estuary which are easily misidentified in the field. We improved SHERLOCK's ease of field deployment by combining its rapid isothermal amplification and CRISPR genetic identification with a minimally invasive and extraction-free DNA collection protocol as well as the option of instrument-free lateral flow detection. This approach opens the door for redefining how, where and by whom genetic identifications occur in the future.</p>

opencc-zeroMar 2020View details →

Afognak Lake sockeye salmon stock monitoring project (2017–2019)

<p>The Afognak River (Litnik) has historically supported one of the largest sockeye salmon subsistence fisheries for Kodiak Archipelago residents. In the 2000s, the number of sockeye salmon returning to Afognak River had diminished substantially resulting in closures to commercial, sport, and subsistence fishing in Afognak Bay. Local subsistence users, represented by the Kodiak-Aleutians Regional Advisory Council, Kodiak Fish and Game Advisory Committee, and Kodiak Tribal Council, stressed the importance of the Afognak River system to local subsistence users and contended that continued closures would make it more difficult for local residents to meet their sockeye salmon needs and shift fishing efforts to small nearby sockeye salmon runs. The Afognak Lake Sockeye Salmon Stock Monitoring Project enumerates adult sockeye salmon into Afognak Lake through a weir located on the Afognak River, describes run-timing, or proportional daily passage, of sockeye salmon through the weir, estimates the age and sex composition of adult sockeye salmon returns, and estimates the average length (mm) by age and sex of sockeye salmon passing through the weir. Data collected from this project provide salmon management biologists the ability to make in-season decisions to execute commercial and sport fisheries. In addition, the information that is gathered from these projects refine the escapement goals and improve preseason run forecasts to allow for maximum sustainable yield and prevent unnecessary restrictions of federal and state subsistence fisheries.</p>

Data from: Using local ecological knowledge to monitor threatened Mekong megafauna in Lao PDR

Pressures on freshwater biodiversity in Southeast Asia are accelerating yet the status and conservation needs of many of the region's threatened fish species are unclear. This impacts the ability to implement conservation activities and to understand the effects of infrastructure developments and other hydrological changes. We used Local Ecological Knowledge from fishing communities on the Mekong River in the Siphandone waterscape, Lao PDR to estimate mean and mode last capture dates of eight rare or culturally significant fish species in order to provide conservation monitoring baselines. One hundred and twenty fishermen, from six villages, were interviewed. All eight species had been captured, by at least one of the interviewees, within the waterscape within the past year. However the mean and mode last capture dates varied between the species. Larger species, and those with higher Red List threat status, were caught less recently than smaller species of less conservation concern. The status of the Critically Endangered Pangasius sanitwongsei (mean last capture date 116.4 months) is particularly worrying suggesting severe population decline although cultural issues may have caused this species to have been under-reported. This highlights that studies making use of Local Ecological Knowledge need to understand the cultural background and context from which data is collected. Nevertheless we recommend our approach, of stratified random interviews to establish mean last capture dates, may be an effective methodology for monitoring freshwater fish species of conservation concern within artisanal fisheries. If fishing effort remains relatively constant, or if changes in fishing effort are accounted for, differences over time in mean last capture dates are likely to represent changes in the status of species. We plan to repeat our interview surveys within the waterscape as part of a long-term fish-monitoring program.

Data from: Long-term monitoring data provide evidence of declining species richness in a river valued for biodiversity conservation

Free-flowing river segments provide refuges for many imperiled aquatic biota that have been extirpated elsewhere in their native ranges. These biodiversity refuges are also foci of conservation concerns because species persisting within isolated habitat fragments may be particularly vulnerable to local environmental change. We have analyzed long-term (14- and 20-year) survey data to assess evidence of fish species declines in two southeastern U.S. rivers where managers and stakeholders have identified potentially detrimental impacts of current and future land uses. The Conasauga River (Georgia and Tennessee) and the Etowah River (Georgia) form free-flowing headwaters of the extensively dammed Coosa River system. These rivers are valued in part because they harbor multiple species of conservation concern, including three federally endangered and two federally threatened fishes. We have used data sets comprising annual surveys for fish species at multiple, fixed sites located at river shoals to analyze occupancy dynamics and temporal changes in species richness. Our analyses incorporate repeated site-specific surveys in some years to estimate and account for incomplete species detection, and test for species-specific (rarity, mainstem-restriction) and year-specific (elevated frequencies of low- or high-flow days) covariates on occupancy dynamics. In the Conasauga River, analysis of 26 species at 13 sites shows evidence of temporal declines in colonization rates for nearly all taxa, accompanied by declining species richness. Four taxa (including one federally endangered species) have reduced occupancy across the Conasauga study sites, with three of these taxa apparently absent for at least the last 5 years of the study. In contrast, a similar fauna of 28 taxa at 10 sites in the Etowah River shows no trends in species persistence, colonization or occupancy. None of the tested covariates show strong effects on persistence or colonization rates in either river. Previous studies and observations identify contaminants, nutrient loading, or changes in benthic habitat as possible causes for fish species declines in the Conasauga River. Our analysis provides baseline information that could be used to assess effectiveness of future management actions in the Conasauga or Etowah rivers, and illustrates the use of dynamic occupancy models to evaluate evidence of faunal decline from time-series data.

Data from: Insights into the introduction history and population genetic dynamics of the Nile monitor (Varanus niloticus) in Florida

Invasive species are widely recognized as important drivers of the ongoing biodiversity crisis. The US state of Florida is especially susceptible to the proliferation of invasive reptiles, and nonnative lizards currently outnumber native lizard species. At present, there are three documented breeding populations of the Nile monitor (Varanus niloticus) in different regions of Southern Florida, and these populations are considered potential dangers to threatened, fossorial endemics, such as burrowing owls, American crocodiles, and gopher tortoises. Nevertheless, at present, both the introduction histories of these populations and the degree to which they are connected by gene flow are not known. To address these issues, we genotyped V. niloticus from Cape Coral, Homestead Air Reserve Base, and West Palm Beach at 17 microsatellite loci and conducted a variety of analyses to assess both intra-population genetic diversity, the degree of gene flow between populations, and the most likely introduction scenario. The results of our analyses demonstrate that all three populations have limited genetic diversity (mean number of effective alleles across loci in all three populations ~ 2.00) and are highly differentiated from one another (GST = 0.268; G''ST = 0.628). Our results also suggest that these populations resulted from independent introduction events that occurred within the past few decades. Consequently, we advise that wildlife managers focus management efforts on containment of existing populations and intensification of monitoring efforts on potential migration corridors.

Data from: Long-term environmental monitoring for assessment of change: measurement inconsistencies over time and potential solutions

The importance of long-term environmental monitoring and research for detecting and understanding changes in ecosystems and human impacts on natural systems is widely acknowledged. Over the last decades a number of critical components for successful long-term monitoring have been identified. One basic component is quality assurance/quality control protocols to ensure consistency and comparability of data. In Norway, the authorities require environmental monitoring of the impacts of the offshore petroleum industry on the Norwegian continental shelf, and in 1996 a large-scale regional environmental monitoring program was established. As a case study, we used a sub-set of data from this monitoring to explore concepts regarding best practices for long-term environmental monitoring. Specifically, we examined data from physical and chemical sediment samples and benthic macro-invertebrate assemblages from 11 stations from six sampling occasions during the period 1996-2011. Despite the established quality assessment and quality control protocols for this monitoring program, we identified several data challenges, such as, missing values and outliers, discrepancies in variable and station names, changes in procedures without calibration, and different taxonomic resolution. Furthermore, we show that the use of different laboratories over time makes it difficult to draw conclusions with regard to some of the observed changes. We offer recommendations to facilitate comparison of data over time. We also present a new procedure to handle different taxonomic resolution so valuable historical data is not discarded. These topics have a broader relevance and application than for our case study.

Data from: Non-invasive genetic monitoring involving citizen science enables reconstruction of current pack dynamics in a re-establishing wolf population

Background: Carnivores are re-establishing in many human-populated areas, where their presence is often contentious. Reaching consensus over management decisions is often hampered by a dispute about the size of the local carnivore population. Understanding the reproductive dynamics and individual movements of the carnivores can provide support for management decisions, but individual-level information can be difficult to obtain from elusive, wide-ranging species. Non-invasive genetic sampling can yield such information, but makes subsequent reconstruction of population history challenging due to incomplete population coverage and error-prone data. Here, we combine a collaborative, volunteer-based sampling scheme with Bayesian pedigree reconstruction to describe the pack dynamics of an establishing grey wolf (Canis lupus) population in south-west Finland, where wolf breeding was recorded in 2006 for the first time in over a century. Results: Using DNA extracted mainly from faeces collected since 2008, we identified 81 individual wolves and assigned credible full parentages to 70 of these and partial parentages to a further 9, revealing 7 breeding pairs. Individuals used a range of strategies to obtain breeding opportunities, including dispersal to established or new packs, long-distance migration and inheriting breeding roles. Gene flow occurred between all packs but inbreeding events were rare. Conclusions: These findings demonstrate that characterizing ongoing pack dynamics can provide detailed, locally-relevant insight into the ecology of contentious species such as the wolf. Involving various stakeholders in data collection makes these results more likely to be accepted as unbiased and hence reliable grounds for management decisions.

opencc-zeroNov 2019View details →

Occupancy in dynamic systems: accounting for multiple scales and false positives using environmental DNA to inform monitoring

<div class="page"> <div class="section"> <p>Occupancy is an important metric to understand current and future trends in populations that have declined globally. In addition, occupancy can be an efficient tool for conducting landscape-scale and long-term monitoring. A challenge for occupancy monitoring programs is to determine the appropriate spatial scale of analysis and to obtain precise occupancy estimates for elusive species. We used a multi-scale occupancy model to assess occupancy of Columbia spotted frogs in the Great Basin, USA, based on environmental DNA (eDNA) detections. We collected three replicate eDNA samples at 220 sites across the Great Basin. We estimated and modeled ecological factors that described watershed and site occupancy at multiple spatial scales simultaneously while accounting for imperfect detection. Additionally, we conducted visual and dipnet surveys at all sites and used our paired detections to estimate the probability of a false positive detection for our eDNA sampling. We applied the estimated false positive rate to our multi-scale occupancy dataset and assessed changes in model selection. We had higher naïve occupancy estimates for eDNA (0.37) than for traditional survey methods (0.20). We estimated our false positive detection rate per qPCR replicate at 0.023 (95% CI: 0.016-0.033). When the false positive rate was applied to the multi-scale dataset, we did not observe substantial changes in model selection or parameter estimates. Conservation and resource managers have an increasing need to understand species occupancy in highly variable landscapes where the spatial distribution of habitat changes significantly over time due to climate change and human impact. A multi-scale occupancy approach can be used to obtain regional occupancy estimates that can account for spatially dynamic differences in availability over time, especially when assessing potential declines. Additionally, this study demonstrates how eDNA can be used as an effective tool for improved occupancy estimates across broad geographic scales for long-term monitoring.</p> </div> </div>

opencc-zeroDec 2013View details →

Data from: Disease, predation and demography: assessing the impacts of bovine tuberculosis on African buffalo by monitoring at individual and population levels

1. Understanding the effects of disease is critical to determining appropriate management responses, but estimating those effects in wildlife species is challenging. We used bovine tuberculosis (BTB) in the African buffalo Syncerus caffer population of Kruger National Park, South Africa, as a case study to highlight the issues associated with estimating chronic disease effects in a long-lived host. 2. We used known and radiocollared buffalo, aerial census data, and a natural gradient in pathogen prevalence to investigate if: (i) at the individual level, BTB infection reduces reproduction; (ii) BTB infection increases vulnerability to predation; and (iii) at the population level, increased BTB prevalence causes reduced population growth. 3. There was only a marginal reduction in calving success associated with BTB infection, as indexed by the probability of sighting a known adult female with or without a calf ( P = 0·065). 4. Since 1991, BTB prevalence increased from 27 to 45% in the southern region and from 4 to 28% in the central region of Kruger National Park. The prevalence in the northern regions was only 1·5% in 1998. Buffalo population growth rates, however, were neither statistically different among regions nor declining over time. 5. Lions Panthera leo did not appear to preferentially kill test-positive buffalo. The best (Akaike's Information Criterion corrected for small sample size) AIC c model with BTB as a covariate [exp( β ) = 0·49; 95% CI = (0·24–1·02)] suggested that the mortality hazard for positive individuals was no greater than for test-negative individuals. 6. Synthesis and applications . Test accuracy, time-varying disease status, and movement among populations are some of the issues that make the detection of chronic disease impacts challenging. For these reasons, the demographic impacts of bovine tuberculosis in the Kruger National Park remain undetectable despite 6 years of study on known individuals and 40 years of population counts. However, the rainfall and forage conditions during this study were relatively good and the impacts of many chronic diseases may be a non-linear function of environmental conditions such that

Data from: Stock enhancement or sea ranching? Insights from monitoring the genetic diversity, relatedness and effective size in a seeded great scallop population (Pecten maximus)

The mass release of hatchery-propagated stocks raises numerous questions concerning its efficiency in terms of local recruitment and effect on the genetic diversity of wild populations. A seeding program, consisting of mass release of hatchery-produced juveniles in the local naturally occurring population of great scallops (Pecten maximus L.), was initiated in the early 1980s in the Bay of Brest (France). The present study aims at evaluating whether this seeding program leads to actual population enhancement, with detectable effects on genetic diversity and effective population size, or consists of sea ranching with limited genetic consequences on the wild stock. To address this question, microsatellite-based genetic monitoring of three hatchery-born and naturally recruited populations was conducted over a 5-year period. Results showed a limited reduction in allelic richness but a strong alteration of allelic frequencies in hatchery populations, while genetic diversity appeared very stable over time in the wild populations. A temporal increase in relatedness was observed in both cultured stock and wild populations. Effective population size (Ne) estimates were low and variable in the wild population. Moreover, the application of the Ryman-Laikre model suggested a high contribution of hatchery-born scallops to the reproductive output of the wild population. Overall, the data suggest that the main objective of the seeding program, which is stock enhancement, is fulfilled. Moreover, gene flow from surrounding populations and/or the reproductive input of undetected sub-populations within the bay may buffer the Ryman-Laikre effect and ensure the retention of the local genetic variability.