Individual identification of animals from DNA in field-collected faecal samples is becoming an increasingly important tool in wildlife population monitoring. A major issue relevant to the application of this technique is the reliability of the genotypes obtained. I investigated the effect of sample age and season of collection on amplification rates and reliability of microsatellite genotypes amplified from faecal DNA of a marsupial herbivore, the brush-tailed rock-wallaby (Petrogale penicillata) and a eutherian carnivore, the red fox (Vulpes vulpes). Comparison of DNA profiles from 1 day to 6 months for both species suggests that as the age of the faeces increases there is less good-quality DNA present on the surface of the faeces, resulting in significantly decreasing amplification rates and increasing genotyping error rates over time. No microsatellite PCR products were obtained from samples older than 3 months from any faecal DNA extract in either season. For both species, faeces collected during the summer trial yielded high-quality DNA for up to one week. Faeces collected in winter had significantly lower amplification rates and higher genotyping errors than the summer-collected samples. Computer simulations were used to estimate the probability of obtaining false genotypes when genotyping faecal samples of various ages. These revealed that three replicates is sufficient to prevent identification of false individuals for P. penicillata from faeces up to one week old in both summer and winter but more replicates may be required for older samples, particularly in winter. In contrast, up to eight replicates may be required for fox faeces collected in winter, particularly if more than one week old. These results also suggest that it is difficult to visually identify faecal age for V. vulpes, and any study using fox faeces would need to account for the likely inclusion of older faeces in a field collection. For P. penicillata, faecal age could be accurately assessed, particularly when less than one week old and targeting faeces that match the two most reliable appearance classes described here would be an efficient sampling strategy. It is recommended that the appropriate PCR replication protocol for any given study should be tailored to the error rates expected for the oldest samples likely to be collected. This study is the first to thoroughly investigate the effects of sample age and season of collection on microsatellite genotyping from faecal samples and provides guidelines for sampling and PCR repetition strategies for field-based non-invasive DNA studies.

Conservation monitoring programs are critical for identifying many elements of species ecology and for detecting changes in populations. However, without articulating how monitoring information will trigger relevant conservation actions, programs that monitor species until they become extinct are at odds with the primary goal of conservation: avoiding biodiversity loss. Here, we outline cases in which species were monitored until they suffered local, regional, or global extinction in the absence of a preplanned intervention program, and contend that conservation monitoring programs should be embedded within a management plan and characterized by vital attributes to ensure their effectiveness. These attributes include: (1) explicit articulation of how monitoring information will inform conservation actions, (2) transparent specification of trigger points within monitoring programs at which strategic interventions will be implemented, and (3) rigorous quantification of the ability to achieve early detection of change.

Understanding the scale of marine population connectivity is critical for the conservation and sustainable management of marine resources. For many marine species adults are benthic and relatively immobile, so patterns of larval dispersal and recruitment provide the key to understanding marine population connectivity. Contrary to previous expectations, recent studies have often detected unexpectedly low dispersal and fine-scale population structure in the sea, leading to a paradigm shift in how marine systems are viewed. Nonetheless, the link between fine-scale marine population structure and the underlying physical and biological processes has not been made. Here we show that patterns of genetic structure and population connectivity in the broadcast-spawning and long-distance dispersing sea urchin Centrostephanus rodgersii are influenced by physical oceanographic and geographic variables. Despite weak genetic differentiation and no isolation-by-distance over thousands of kilometers among samples from eastern Australia and northern New Zealand, fine-scale genetic structure was associated with sea surface temperature (SST) variability and geography along the southeastern Australian coast. The zone of high SST variability is characterized by periodic shedding of eddies from the East Australian Current, and we suggest that ocean current circulation may, through its influence on larval transport and recruitment, interact with the genetic consequences of large variance in individual reproductive success to generate patterns of fine-scale patchy genetic structure. If proven consistent across species, our findings suggest that the optimal scale for fisheries management and reserve design should vary among localities in relation to regional oceanographic variability and coastal geography.

Abstract.Obtaining useful information about elusive or endangered species can be logistically difficult, particularly if relying entirely on field signs such as hair, feathers or faeces. However, recent developments in molecular technology add substantially to the utility of such 'non-invasive' samples, which provide a source of DNA that can be used to identify not only species but also individuals and their gender. This provides great potential to improve the accuracy of abundance estimates and determine behavioural parameters, such as home-range size, individual habitat and dietary preferences, and even some forms of social interaction. Non-invasive samples can also be a useful alternative to blood or tissue samples (the collection of which traditionally has required trapping of animals) as genetic material for applications such as relatedness, population genetic and phylogenetic analyses. Despite the huge potential of non-invasive genetic sampling, the current technology does have limitations. The low quantity and quality of DNA often obtained from such sources results in an increased risk of genotyping errors, which may lead to incorrect inferences, particularly false identification of individuals. Appropriate precautions and pilot studies are required to minimise these risks, and in some cases it may be wise to employ traditional methods when they are adequate.