Maxine P. Piggott

Oceanic variability and coastal topography shape genetic structure in a long-dispersing sea urchin.

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.

Effect of sample age and season of collection on the reliability of microsatellite genotyping of faecal DNA

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.

A Multiplex Pre-Amplification Method that Significantly Improves Microsatellite Amplification and Error Rates for Faecal DNA in Limiting Conditions

Maxine P. Piggott*, Eva Bellemain, Pierre Taberlet & Andrea C. Taylor School of Biological Sciences, Monash University, Victoria, 3800, Australia; Laboratoire d’Ecologie Alpine, Génomique des Populations et Biodiversité, CNRS UMR 5553, Université Joseph Fourier, B.P. 53, 38041, Grenoble, Cedex 9, France and Department of Ecology and Natural Resource Management, Agricultural University of Norway, Postbox 5003, NO-1432 AS, Norway; Laboratoire d’Ecologie Alpine, Génomique des Populations et Biodiversité, CNRS UMR 5553, Université Joseph Fourier, B.P. 53, 38041, Grenoble, Cedex 9, France (*Author for correspondence: fax: +61-3-99055613; e-mail: Maxine.Piggott @sci.monash.edu.au)

Sex and sociality in a disconnected world: a review of the impacts of habitat fragmentation on animal social interactions

Despite the extensive literature describing the impacts of habitat fragmentation on the distribution and abundance of species, fragmentation effects on life-history strategies have been relatively understudied. Social interactions are important life-history attributes that have fitness consequences for individuals and have been observed to differ among populations in relation to geographic and demographic variability. Therefore, habitat fragmentation is expected to affect social interactions, and these social impacts or responses may contribute to population viability and broad-scale patterns of distribution and abundance in fragmented landscapes. Here we review the emerging literature on this issue. We focus on the impacts of habitat fragmentation that are expected to, or have been observed to, affect social strategies. These include altered resource distribution (e.g., habitat quality, spatial configuration of patches), interspecific interactions (e.g., predator–prey and host–parasite dynamics, human di...

Counting the books while the library burns: why conservation monitoring programs need a plan for action

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.

Extensive evaluation of faecal preservation and DNA extraction methods in Australian native and introduced species

We evaluated and compared sixteen combinations of commonly used storage and extraction methods for faecal DNA from two Australian marsupial herbivores, two marsupial carnivores and an introduced carnivorous mammal. For all species the highest amplification and lowest genotyping error rates were achieved using dried faeces extracted via a surface wash followed by spin column purification. The highest error rates were seen in the two Dasyurus spp. and the lowest in Vulpes vulpes. The rates observed for each species were incorporated into computer simulations to identify the number of PCR replicates required to achieve accurate genotyping of DNA isolated via the optimised protocol. Three replicates per sample were sufficient for V. vulpes, Thylogale billardierii and Petrogale penicillata. However, further replicates may be required for marsupial carnivores, as their faeces yielded DNA that amplified substantially less often and less reliably, for all preservation and extraction methods tested, than did the other species. Although pilot studies remain vital for evaluating the feasibility of non-invasive sampling prior to undertaking any in-depth study the availability of a thoroughly tested storage and DNA extraction combination protocol known to be optimal for five different species should make that process much simpler.

Comparison of methods to detect rare and cryptic species: a case study using the red fox (Vulpes vulpes)

Choosing the appropriate method to detect and monitor wildlife species is difficult if the species is rare or cryptic in appearance or behaviour. We evaluated the effectiveness of the following four methods for detecting red foxes (Vulpes vulpes) on the basis of equivalent person hours in a rural landscape in temperate Australia: camera traps, hair traps (using morphology and DNA from hair follicles), scats from bait stations (using DNA derived from the scats) and spotlighting. We also evaluated whether individual foxes could be identified using remote collection of their tissues. Genetic analysis of hair samples was the least efficient method of detection among the methods employed because of the paucity of samples obtained and the lack of follicles on sampled hairs. Scat detection was somewhat more efficient. Scats were deposited at 17% of bait stations and 80% of scats were amplified with a fox-specific marker, although only 31% of confirmed fox scats could be fully genotyped at all six microsatellite loci. Camera trapping and spotlighting were the most efficient methods of detecting fox presence in the landscape. Spotlighting success varied seasonally, with fox detections peaking in autumn (80% of spotlighting transects) and being lowest in winter (29% of transects). Cameras detected foxes at 51% of stations; however, there was limited seasonality in detection, and success rates varied with camera design. Log-linear models confirmed these trends. Our results showed that the appropriate technique for detecting foxes varies depending on the time of the year. It is suggested that wildlife managers should consider both seasonal effects and species biology when attempting to detect rare or elusive species.

Genetic structure of a recent climate change-driven range extension.

The life‐history strategies of some species make them strong candidates for rapid exploitation of novel habitat under new climate regimes. Some early‐responding species may be considered invasive, and negatively impact on ‘naïve’ ecosystems. The barrens‐forming sea urchin Centrostephanus rodgersii is one such species, having a high dispersal capability and a high‐latitude range margin limited only by a developmental temperature threshold. Within this species’ range in eastern Australian waters, sea temperatures have increased at greater than double the global average rate. The coinciding poleward range extension of C. rodgersii has caused major ecological changes, threatening reef biodiversity and fisheries productivity. We investigated microsatellite diversity and population structure associated with range expansion by this species. Generalized linear model analyses revealed no reduction in genetic diversity in the newly colonized region. A ‘seascape genetics’ analysis of genetic distances found no spatial genetic structure associated with the range extension. The distinctive genetic characteristic of the extension zone populations was reduced population‐specific FST, consistent with very rapid population expansion. Demographic and genetic simulations support our inference of high connectivity between pre‐ and post‐extension zones. Thus, the range shift appears to be a poleward extension of the highly‐connected rangewide population of C. rodgersii. This is consistent with advection of larvae by the intensified warm water East Australian current, which has also increased Tasmanian Sea temperatures above the species’ lower developmental threshold. Thus, ocean circulation changes have improved the climatic suitability of novel habitat for C. rodgersii and provided the supply of recruits necessary for colonization.

Evaluating the effects of laboratory protocols on eDNA detection probability for an endangered freshwater fish.

Abstract The effectiveness and accuracy of detection using environmental DNA (eDNA) is dependent on understanding the influence laboratory methods such as DNA extraction and PCR strategies have on detection probability. Ideally choice of sampling and extraction method will maximize eDNA yield and detection probability. Determining the survey effort required to reach a satisfactory detection probability (via increased PCR replicates or more sampling) could compensate for a lower eDNA yield if the sampling and extraction method has other advantages for a study, species or system. I analysed the effect of three different sampling and extraction methods on eDNA yield, detection probability and PCR replication for detecting the endangered freshwater fish Macquaria australasica from water samples. The impact of eDNA concentration, PCR strategy, target amplicon size and two marker regions: 12S (a mitochondrial gene) and 18S (a nuclear gene) was also assessed. The choice of sampling and extraction method and PCR strategy, rather than amplicon size and marker region, had the biggest effect on detection probability and PCR replication. The PCR replication effort required to achieve a detection probability of 0.95, ranged from 2 to 6 PCR replicates depending on the laboratory method used. As all methods yielded eDNA from which M. australasica was detected using the three target amplicons, differences in eDNA yield and detection probability between the three methods could be mitigated by determining the appropriate PCR replication effort. Evaluating the effect sampling and extraction methods will have on the detection probability and determining the laboratory protocols and PCR replication required to maximize detection and minimize false positives and negatives is a useful first step for eDNA occupancy studies.

Geographical Variation in Body Size and Sexual Size Dimorphism in an Australian Lizard, Boulenger's Skink (Morethia boulengeri)

Ecogeographical rules help explain spatial and temporal patterns in intraspecific body size. However, many of these rules, when applied to ectothermic organisms such as reptiles, are controversial and require further investigation. To explore factors that influence body size in reptiles, we performed a heuristic study to examine body size variation in an Australian lizard, Boulengers Skink Morethia boulengeri from agricultural landscapes in southern New South Wales, south-eastern Australia. We collected tissue and morphological data on 337 adult lizards across a broad elevation and climate gradient. We used a model-selection procedure to determine if environmental or ecological variables best explained body size variation. We explored the relationship between morphology and phylogenetic structure before modeling candidate variables from four broad domains: (1) geography (latitude, longitude and elevation), (2) climate (temperature and rainfall), (3) habitat (vegetation type, number of logs and ground cover attributes), and (4) management (land use and grazing history). Broad phylogenetic structure was evident, but on a scale larger than our study area. Lizards were sexually dimorphic, whereby females had longer snout-vent length than males, providing support for the fecundity selection hypothesis. Body size variation in M. boulengeri was correlated with temperature and rainfall, a pattern consistent with larger individuals occupying cooler and more productive parts of the landscape. Climate change forecasts, which predict warmer temperature and increased aridity, may result in reduced lizard biomass and decoupling of trophic interactions with potential implications for community organization and ecosystem function.