Older forests function as energetic and demographic refugia for a climate-sensitive species.

More frequent and extreme heat waves threaten climate-sensitive species. Structurally complex, older forests can buffer these effects by creating cool microclimates, although the mechanisms by which forest refugia mitigate physiological responses to heat exposure and subsequent population-level consequences remain relatively unexplored. We leveraged fine-scale movement data, doubly labeled water, and two decades of demographic data for the California spotted owl (Strix occidentalis occidentalis) to (1) assess the role of older forest characteristics as potential energetic buffers for individuals and (2) examine the subsequent value of older forests as refugia for a core population in the Sierra Nevada and a periphery population in the San Bernardino Mountains. Individuals spent less energy moving during warmer sampling periods and the presence of tall canopies facilitated energetic conservation during daytime roosting activities. In the core population, where tall-canopied forest was prevalent, temperature anomalies did not affect territory occupancy dynamics as warmer sites were both less likely to go extinct and less likely to become colonized, suggesting a trade-off between foraging opportunities and temperature exposure. In the peripheral population, sites were more likely to become unoccupied following warm summers, presumably because of less prevalent older forest conditions. While individuals avoided elevated energetic expenditure associated with temperature exposure, behavioral strategies to conserve energy may have diverted time and energy from reproduction or territory defense. Conserving older forests, which are threatened due to fire and drought, may benefit individuals from energetic consequences of exposure to stressful thermal conditions.

Landscape heterogeneity provides co-benefits to predator and prey.

Predator populations are imperiled globally, due in part to changing habitat and trophic interactions. Theoretical and laboratory studies suggest that heterogeneous landscapes containing prey refuges acting as source habitats can benefit both predator and prey populations, although the importance of heterogeneity in natural systems is uncertain. Here, we tested the hypothesis that landscape heterogeneity mediates predator-prey interactions between the California spotted owl (Strix occidentalis occidentalis)-a mature forest species-and one of its principal prey, the dusky-footed woodrat (Neotoma fuscipes)-a younger forest species-to the benefit of both. We did so by combining estimates of woodrat density and survival from live trapping and very high frequency tracking with direct observations of prey deliveries to dependent young by owls in both heterogeneous and homogeneous home ranges. Woodrat abundance was ~2.5 times higher in owl home ranges (14.12 km2 ) featuring greater heterogeneity in vegetation types (1805.0 ± 50.2 SE) compared to those dominated by mature forest (727.3 ± 51.9 SE), in large part because of high densities in young forests appearing to act as sources promoting woodrat densities in nearby mature forests. Woodrat mortality rates were low across vegetation types and did not differ between heterogeneous and homogeneous home ranges, yet all observed predation by owls occurred within mature forests, suggesting young forests may act as woodrat refuges. Owls exhibited a type 1 functional response, consuming ~2.5 times more woodrats in heterogeneous (31.1/month ± 5.2 SE) versus homogeneous (12.7/month ± 3.7 SE) home ranges. While consumption of smaller-bodied alternative prey partially compensated for lower woodrat consumption in homogeneous home ranges, owls nevertheless consumed 30% more biomass in heterogeneous home ranges-approximately equivalent to the energetic needs of producing one additional offspring. Thus, a mosaic of vegetation types including young forest patches increased woodrat abundance and availability that, in turn, provided energetic and potentially reproductive benefits to mature forest-associated spotted owls. More broadly, our findings provide strong empirical evidence that heterogeneous landscapes containing prey refuges can benefit both predator and prey populations. As anthropogenic activities continue to homogenize landscapes globally, promoting heterogeneous systems with prey refuges may benefit imperiled predators.

Disease-related population declines in bats demonstrate non-exchangeability in generalist predators.

The extent to which persisting species may fill the functional role of extirpated or declining species has profound implications for the structure of biological communities and ecosystem functioning. In North America, arthropodivorous bats are threatened on a continent-wide scale by the spread of white-nose syndrome (WNS), a disease caused by the fungus Pseudogymnoascus destructans. We tested whether bat species that display lower mortality from this disease can partially fill the functional role of other bat species experiencing population declines. Specifically, we performed high-throughput amplicon sequencing of guano from two generalist predators: the little brown bat (Myotis lucifugus) and big brown bat (Eptesicus fuscus). We then compared changes in prey consumption before versus after population declines related to WNS. Dietary niches contracted for both species after large and abrupt declines in little brown bats and smaller declines in big brown bats, but interspecific dietary overlap did not change. Furthermore, the incidence and taxonomic richness of agricultural pest taxa detected in diet samples decreased following bat population declines. Our results suggest that persisting generalist predators do not necessarily expand their dietary niches following population declines in other predators, providing further evidence that the functional roles of different generalist predators are ecologically distinct.

Land use and life history constrain adaptive genetic variation and reduce the capacity for climate change adaptation in turtles.

BACKGROUND: Rapid anthropogenic climate change will require species to adapt to shifting environmental conditions, with successful adaptation dependent upon current patterns of genetic variation. While landscape genomic approaches allow for exploration of local adaptation in non-model systems, most landscape genomics studies of adaptive capacity are limited to exploratory identification of potentially important functional genes, often without a priori expectations as to the gene functions that may be most important for climate change responses. In this study, we integrated targeted sequencing of genes of known function and genotyping of single-nucleotide polymorphisms to examine spatial, environmental, and species-specific patterns of potential local adaptation in two co-occuring turtle species: the Blanding's turtle (Emydoidea blandingii) and the snapping turtle (Chelydra serpentina). RESULTS: We documented divergent patterns of spatial clustering between neutral and putatively adaptive genetic variation in both species. Environmental associations varied among gene regions and between species, with stronger environmental associations detected for genes involved in stress response and for the more specialized Blanding's turtle. Land cover appeared to be more important than climate in shaping spatial variation in functional genes, indicating that human landscape alterations may affect adaptive capacity important for climate change responses. CONCLUSIONS: Our study provides evidence that responses to climate change will be contingent on species-specific adaptive capacity and past history of exposure to human land cover change.

Using the ecological significance of animal vocalizations to improve inference in acoustic monitoring programs.

Recent bioacoustic advances have facilitated large-scale population monitoring for acoustically active species. Animal sounds, however, can of information that is underutilized in typical approaches to passive acoustic monitoring (PAM) that treat sounds simply as detections. We developed 3 methods of extracting additional ecological detail from acoustic data that are applicable to a broad range of acoustically active species. We conducted landscape-scale passive acoustic surveys of a declining owl species and an invasive congeneric competitor in California. We then used sex-specific vocalization frequency to inform multistate occupancy models; call rates at occupied sites to characterize interactions with interspecific competitors and assess habitat quality; and a flexible multivariate approach to differentiate individuals based on vocal characteristics. The multistate occupancy models yielded novel estimates of breeding status occupancy rates that were more robust to false detections and captured known habitat associations more consistently than single-state occupancy models agnostic to sex. Call rate was related to the presence of a competitor but not habitat quality and thus could constitute a useful behavioral metric for interactions that are challenging to detect in an occupancy framework. Quantifying multivariate distance between groups of vocalizations provided a novel quantitative means of discriminating individuals with ≥20 vocalizations and a flexible tool for balancing type I and II errors. Therefore, it appears possible to estimate site turnover and demographic rates, rather than just occupancy metrics, in PAM programs. Our methods can be applied individually or in concert and are likely generalizable to many acoustically active species. As such, they are opportunities to improve inferences from PAM data and thus benefit conservation.

Uso de la Importancia Ecológica de las Vocalizaciones Animales para Mejorar la Inferencia en los Programas de Monitoreo Acústico Resumen Los avances bioacústicos recientes han facilitado el monitoreo a gran escala de poblaciones de especies acústicamente activas. Sin embargo, los sonidos de animales pueden transmitir cantidades sustanciales de información que queda utilizada insuficientemente en las estrategias comunes de monitoreo acústico pasivo (MAP) que tratan a los sonidos como simples detecciones. Desarrollamos tres métodos de extracción de detalles ecológicos adicionales de los datos acústicos que son aplicables a una gama amplia de especies acústicamente activas. Realizamos censos acústicos pasivos a escala de paisaje para una especie de búho en declinación y para un competidor congenérico invasivo en California. Después utilizamos la frecuencia de vocalizaciones específicas por sexo para orientar los modelos multiestado de ocupación; las tasas de llamados en sitios ocupados para caracterizar las interacciones con los competidores interespecíficos y evaluar la calidad de su hábitat; y una estrategia multivariada flexible para diferenciar a los individuos con base en sus características vocales. Los modelos multiestado de ocupación brindaron estimaciones novedosas para las tasas de ocupación por estado reproductivo que fueron más sólidas ante las detecciones falsas y capturaron el número de asociaciones de hábitat más sistemáticamente que los modelos de estado único agnósticos al sexo. La tasa de llamados estuvo relacionada con la presencia de un competidor pero no con la calidad del hábitat y por lo tanto podría constituir una medida conductual útil para las interacciones que son difíciles de detectar en un marco de trabajo de ocupación. La cuantificación de la distancia multivariada entre los grupos de vocalizaciones proporcionó un medio cuantitativo novedoso para discriminar a los individuos con ≥20 vocalizaciones y una herramienta flexible para balancear los errores del tipo I y del tipo II. Por lo tanto, parecer que hay posibilidad de estimar las tasas demográficas y de rotación, en lugar de sólo las medidas de ocupación, en los programas MAP. Nuestros métodos pueden aplicarse individualmente o de manera conjunta y es probable poder generalizarlas para muchas especies acústicamente activas. Dicho así, son oportunidades para mejorar las inferencias de los datos MAP y por lo tanto, beneficiar a la conservación.

Predator preferences shape the diets of arthropodivorous bats more than quantitative local prey abundance.

Although most predators are generalists, the majority of studies on the association between prey availability and prey consumption have focused on specialist predators. To investigate the role of highly generalist predators in a complex food web, we measured the relationships between prey consumption and prey availability in two common arthropodivorous bats. Specifically, we used high-throughput amplicon sequencing coupled with a known mock community to characterize seasonal changes in little brown and big brown bat diets. We then linked spatiotemporal variation in prey consumption with quantitative prey availability estimated from intensive prey community sampling. We found that although quantitative prey availability fluctuated substantially over space and time, the most commonly consumed prey items were consistently detected in bat diets independently of their respective abundance. Positive relationships between prey abundance and probability of consumption were found only among prey groups that were less frequently detected in bat diets. While the probability of prey consumption was largely unrelated to abundance, the community structure of prey detected in bat diets was influenced by the local or regional abundance of prey. Observed patterns suggest that while little brown and big brown bats maintain preferences for particular prey independently of quantitative prey availability, total dietary composition may reflect some degree of opportunistic foraging. Overall, our findings suggest that generalist predators can display strong prey preferences that persist despite quantitative changes in prey availability.

The demography of a resource specialist in the tropics: Cecropia trees and the fitness of three-toed sloths.

Resource specialists persist in a narrow range of resources. Consequently, the abundance of key resources should drive vital rates, individual fitness, and population viability. While Neotropical forests feature both high levels of biodiversity and numbers of specialist species, no studies have directly evaluated how the variation of key resources affects the fitness of a tropical specialist. Here, we quantified the effect of key tree species density and forest cover on the fitness of three-toed sloths ( Bradypus variegatus), an arboreal folivore strongly associated with Cecropia trees in Costa Rica, using a multi-year demographic, genetic, and space-use dataset. We found that the density of Cecropia trees was strongly and positively related to both adult survival and reproductive output. A matrix model parametrized with Cecropia-demography relationships suggested positive growth of sloth populations, even at low densities of Cecropia (0.7 trees ha-1). Our study shows the first direct link between the density of a key resource to demographic consequences of a tropical specialist, underscoring the sensitivity of tropical specialists to the loss of a single key resource, but also point to targeted conservation measures to increase that resource. Finally, our study reveals that previously disturbed and regenerating environments can support viable populations of tropical specialists.

An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals.

DNA analysis of predator faeces using high-throughput amplicon sequencing (HTS) enhances our understanding of predator-prey interactions. However, conclusions drawn from this technique are constrained by biases that occur in multiple steps of the HTS workflow. To better characterize insectivorous animal diets, we used DNA from a diverse set of arthropods to assess PCR biases of commonly used and novel primer pairs for the mitochondrial gene, cytochrome oxidase C subunit 1 (COI). We compared diversity recovered from HTS of bat guano samples using a commonly used primer pair "ZBJ" to results using the novel primer pair "ANML." To parameterize our bioinformatics pipeline, we created an arthropod mock community consisting of single-copy (cloned) COI sequences. To examine biases associated with both PCR and HTS, mock community members were combined in equimolar amounts both pre- and post-PCR. We validated our system using guano from bats fed known diets and using composite samples of morphologically identified insects collected in pitfall traps. In PCR tests, the ANML primer pair amplified 58 of 59 arthropod taxa (98%), whereas ZBJ amplified 24-40 of 59 taxa (41%-68%). Furthermore, in an HTS comparison of field-collected samples, the ANML primers detected nearly fourfold more arthropod taxa than the ZBJ primers. The additional arthropods detected include medically and economically relevant insect groups such as mosquitoes. Results revealed biases at both the PCR and sequencing levels, demonstrating the pitfalls associated with using HTS read numbers as proxies for abundance. The use of an arthropod mock community allowed for improved bioinformatics pipeline parameterization.

Behavioral mechanisms leading to improved fitness in a subsidized predator.

General mechanisms underlying the distribution and fitness of synanthropic predators in human-influenced landscapes remain unclear. Under the consumer resource-matching hypothesis, synanthropes are expected to distribute themselves among habitats according to resource availability, such that densities are greater in human-subsidized habitats, but mean individual fitness is equal among habitats because of negative density dependence. However, "under-matching" to human food resources can occur, because dominant individuals exclude subordinates from subsidized habitats and realize relatively high fitness. We integrated physiological, behavioral, and demographic information to test resource-matching hypotheses in Steller's jays (Cyanocitta stelleri), a synanthropic nest predator, to understand how behavior and social systems can influence how synanthropes respond to food subsidies. Jays consumed more human foods at subsidized (park campground) sites than jays at unsubsidized (interior forest) sites based on stable isotope analyses. Jays that occurred at higher densities were in better body condition (based on feather growth bars and lipid analyses), and had greater reproductive output at subsidized than unsubsidized sites. Jays with breeding territories in subsidized sites maintained relatively small home ranges that overlapped with multiple conspecifics, and exhibited a social system where dominant individuals typically won contests over food. Thus, jays appeared to be under-matched to prevalent resource subsidies despite high densities and behaviors expected to lead to resource matching. Our results also indicate that local resource subsidies within protected areas can result in source habitats for synanthropes, potentially impacting sensitive species over broader spatial scales.

Cophylogenetics and biogeography reveal a coevolved relationship between sloths and their symbiont algae.

Specialized species, like arboreal folivores, often develop beneficial relationships with symbionts to exploit ecologically constrained lifestyles. Although coevolution can drive speciation by specialization of a symbiont to a host, a symbiotic relationship is not indicative of coevolution between host and symbiont. We tested for coevolved relationships between highly specialized two- and three-toed sloths (Choloepus spp. and Bradypus spp., respectively) and their symbiotic algae using cophylogenies and phylogeography. Our phylogeographic analysis showed a biogeographic pattern for the sloth distribution that was not found in the algal phylogeny. We found support for congruence between the sloth and algae phylogenies, implying cospeciation, only in the Bradypus lineage. Algae host-switching occurred from Bradypus spp. to Choloepus spp. Our results support a previously hypothesized symbiotic relationship between sloths and the algae in their fur and indicate that coevolution may have played a role in algae diversification. More broadly, convergent evolution may facilitate host switching between deeply diverged host lineages.

Genetic effects of landscape, habitat preference and demography on three co-occurring turtle species.

Expanding the scope of landscape genetics beyond the level of single species can help to reveal how species traits influence responses to environmental change. Multispecies studies are particularly valuable in highly threatened taxa, such as turtles, in which the impacts of anthropogenic change are strongly influenced by interspecific differences in life history strategies, habitat preferences and mobility. We sampled approximately 1500 individuals of three co-occurring turtle species across a gradient of habitat change (including varying loss of wetlands and agricultural conversion of upland habitats) in the Midwestern USA. We used genetic clustering and multiple regression methods to identify associations between genetic structure and permanent landscape features, past landscape composition and landscape change in each species. Two aquatic generalists (the painted turtle, Chrysemys picta, and the snapping turtle Chelydra serpentina) both exhibited population genetic structure consistent with isolation by distance, modulated by aquatic landscape features. Genetic divergence for the more terrestrial Blanding's turtle (Emydoidea blandingii), on the other hand, was not strongly associated with geographic distance or aquatic features, and Bayesian clustering analysis indicated that many Emydoidea populations were genetically isolated. Despite long generation times, all three species exhibited associations between genetic structure and postsettlement habitat change, indicating that long generation times may not be sufficient to delay genetic drift resulting from recent habitat fragmentation. The concordances in genetic structure observed between aquatic species, as well as isolation in the endangered, long-lived Emydoidea, reinforce the need to consider both landscape composition and demographic factors in assessing differential responses to habitat change in co-occurring species.

Linking Genetic Kinship and Demographic Analyses to Characterize Dispersal: Methods and Application to Blanding's Turtle.

Characterizing how frequently, and at what life stages and spatial scales, dispersal occurs can be difficult, especially for species with cryptic juvenile periods and long reproductive life spans. Using a combination of mark-recapture information, microsatellite genetic data, and demographic simulations, we characterize natal and breeding dispersal patterns in the long-lived, slow-maturing, and endangered Blanding's turtle (Emydoidea blandingii), focusing on nesting females. We captured and genotyped 310 individual Blanding's turtles (including 220 nesting females) in a central Wisconsin population from 2010 to 2013, with additional information on movements among 3 focal nesting areas within this population available from carapace-marking conducted from 2001 to 2009. Mark-recapture analyses indicated that dispersal among the 3 focal nesting areas was infrequent (<0.03 annual probability). Dyads of females with inferred first-order relationships were more likely to be found within the same nesting area than split between areas, and the proportion of related dyads declined with increasing distance among nesting areas. The observed distribution of related dyads for nesting females was consistent with a probability of natal dispersal at first breeding between nearby nesting areas of approximately 0.1 based on demographic simulations. Our simulation-based estimates of infrequent female dispersal were corroborated by significant spatial genetic autocorrelation among nesting females at scales of <500 m. Nevertheless, a lack of spatial genetic autocorrelation among non-nesting turtles (males and females) suggested extensive local connectivity, possibly mediated by male movements or long-distance movements made by females between terrestrial nesting areas and aquatic habitats. We show here that coupling genetic and demographic information with simulations of individual-based population models can be an effective approach for untangling the contributions of natal and breeding dispersal to spatial ecology.

Arboreal Folivores Limit Their Energetic Output, All the Way to Slothfulness.

By exploiting unutilized resources, organisms expand into novel niches, which can lead to adaptive radiation. However, some groups fail to diversify despite the apparent opportunity to do so. Although arising multiple times, arboreal folivores are rare and have not radiated, presumably because of energetic constraints. To explore this hypothesis, we quantified the field metabolic rate (FMR), movement, and body temperature for syntopic two- and three-toed sloths, extreme arboreal folivores that differ in their degree of specialization. Both species expended little energy, but three-toed sloths (162 kJ/day*kg(0.734)) possessed the lowest FMR recorded for any mammal. Three-toed sloths were more heterothermic and moved less than two-toed sloths. We then compared FMRs and basal metabolic rates (BMRs) for 19 species of arboreal folivores along a spectrum of specialization. Overall, arboreal folivores had lower BMRs and FMRs than other mammals, and increasing specialization led to lower FMRs but not BMRs. Thus, reduced energetic expenditure in specialized species was the result of thermoregulatory and behavioral strategies, rather than simply a proportionate reduction in BMR. Altogether, our findings support the concept that arboreal folivores are tightly constrained by nutritional energetics and help to explain the lack of radiation among species exploiting a lifestyle in the trees.

Finding the right coverage: the impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates.

Restriction-enzyme-based sequencing methods enable the genotyping of thousands of single nucleotide polymorphism (SNP) loci in nonmodel organisms. However, in contrast to traditional genetic markers, genotyping error rates in SNPs derived from restriction-enzyme-based methods remain largely unknown. Here, we estimated genotyping error rates in SNPs genotyped with double digest RAD sequencing from Mendelian incompatibilities in known mother-offspring dyads of Hoffman's two-toed sloth (Choloepus hoffmanni) across a range of coverage and sequence quality criteria, for both reference-aligned and de novo-assembled data sets. Genotyping error rates were more sensitive to coverage than sequence quality and low coverage yielded high error rates, particularly in de novo-assembled data sets. For example, coverage ≥5 yielded median genotyping error rates of ≥0.03 and ≥0.11 in reference-aligned and de novo-assembled data sets, respectively. Genotyping error rates declined to ≤0.01 in reference-aligned data sets with a coverage ≥30, but remained ≥0.04 in the de novo-assembled data sets. We observed approximately 10- and 13-fold declines in the number of loci sampled in the reference-aligned and de novo-assembled data sets when coverage was increased from ≥5 to ≥30 at quality score ≥30, respectively. Finally, we assessed the effects of genotyping coverage on a common population genetic application, parentage assignments, and showed that the proportion of incorrectly assigned maternities was relatively high at low coverage. Overall, our results suggest that the trade-off between sample size and genotyping error rates be considered prior to building sequencing libraries, reporting genotyping error rates become standard practice, and that effects of genotyping errors on inference be evaluated in restriction-enzyme-based SNP studies.

Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths.

Symbiotic microbial communities are critical to the function and survival of animals. This relationship is obligatory for herbivores that engage gut microorganisms for the conversion of dietary plant materials into nutrients such as short-chain organic acids (SCOAs). The constraint on body size imposed by their arboreal lifestyle is thought to make this symbiosis especially important for sloths. Here, we use next-generation sequencing to identify the bacteria present in the fore and distal guts of wild two- and three-toed sloths, and correlate these communities with both diet and SCOAs. We show that, unlike other mammalian herbivores, sloth gut communities are dominated by the bacterial phyla Proteobacteria and Firmicutes. Specifically, three-toed sloths possess a highly conserved, low-diversity foregut community with a highly abundant Neisseria species associated with foregut lactate. In contrast, two-toed sloths have a more variable and diverse foregut microbiota correlated with a variety of SCOAs. These differences support the hypothesis that feeding behaviour selects for specific gut bacterial communities, as three-toed sloths subsist primarily on Cecropia tree leaves while two-toed sloths have a more generalist diet. The less diverse diet and gut microbiota of three-toed sloths may render them more susceptible to habitat loss and other diet-altering conditions.

A syndrome of mutualism reinforces the lifestyle of a sloth.

Arboreal herbivory is rare among mammals. The few species with this lifestyle possess unique adaptions to overcome size-related constraints on nutritional energetics. Sloths are folivores that spend most of their time resting or eating in the forest canopy. A three-toed sloth will, however, descend its tree weekly to defecate, which is risky, energetically costly and, until now, inexplicable. We hypothesized that this behaviour sustains an ecosystem in the fur of sloths, which confers cryptic nutritional benefits to sloths. We found that the more specialized three-toed sloths harboured more phoretic moths, greater concentrations of inorganic nitrogen and higher algal biomass than the generalist two-toed sloths. Moth density was positively related to inorganic nitrogen concentration and algal biomass in the fur. We discovered that sloths consumed algae from their fur, which was highly digestible and lipid-rich. By descending a tree to defecate, sloths transport moths to their oviposition sites in sloth dung, which facilitates moth colonization of sloth fur. Moths are portals for nutrients, increasing nitrogen levels in sloth fur, which fuels algal growth. Sloths consume these algae-gardens, presumably to augment their limited diet. These linked mutualisms between moths, sloths and algae appear to aid the sloth in overcoming a highly constrained lifestyle.

More precisely biased: increasing the number of markers is not a silver bullet in genetic bottleneck testing.

In response to our review of the use of genetic bottleneck tests in the conservation literature (Peery et al. 2012,Molecular Ecology, 21, 3403­3418), Hoban et al. (2013, Molecular Ecology, in press) conducted population genetic simulations to show that the statistical power of genetic bottleneck tests can be increased substantially by sampling large numbers of microsatellite loci, as they suggest is now possible in the age of genomics. While we agree with Hoban and co-workers in principle, sampling large numbers of microsatellite loci can dramatically increase the probability of committing type 1 errors(i.e. detecting a bottleneck in a stable population) when the mutation model is incorrectly assumed. Using conservative values for mutation model parameters can reduce the probability of committing type 1 errors, but doing so can result in significant losses in statistical power. Moreover, we believe that practical limitations associated with developing large numbers of high-quality microsatellite loci continue to constrain sample sizes, a belief supported by a literature review of recent studies using next generation sequencing methods to develop microsatellite libraries. conclusion, we maintain that researchers employing genetic bottleneck tests should proceed with caution and carefully assess both statistical power and type 1 error rates associated with their study design.

Estimating population impacts via dynamic occupancy analysis of Before-After Control-Impact studies.

Estimating environmental impacts on populations is one of the main goals of wildlife monitoring programs, which are often conducted in conjunction with management actions or following natural disturbances. In this study we investigate the statistical power of dynamic occupancy models to detect changes in local survival and colonization from detection-nondetection data, while accounting for imperfect detection probability, in a Before-After Control-Impact (BACI) framework. We simulated impacts on local survival and/or detection probabilities, and asked questions related to: (1) costs and benefits of different analysis models, (2) confounding changes in detection with changes in local survival, (3) sampling design trade-offs, and (4) species with low vs. high rates of turnover. Estimating seasonal effects on local survival and colonization, as opposed to estimating Before-After effects, had little effect on the power to detect changes in local survival. Estimating a parameter that accounted for pretreatment differences in local survival between Control and Impact sites decreased power by 50%, but it was critical to include when such differences existed. When the experimental treatment had a negative impact on species detectability but analysis assumed constant detection, the Type I error rates were dramatically inflated (0.20 0.33). In general, there was low power (< 0.5) to detect a 50% decrease in local survival for all combinations of sites (N = 50 vs. 100), seasons sampled (8 vs. 12), and visits per site per season (4 vs. 6). Unbalanced designs performed worse than balanced designs, with the exception of the case of treatments being implemented in different seasons at different sites. Adding more control sites improved the ability to detect changes in local survival. Surveying more seasons after impact resulted in modest power gains, but at least three seasons before impact were required to successfully implement BACI occupancy studies. Turnover rates had a low impact on power. Occupancy studies conducted in a BACI design offer the opportunity to detect environmental impacts on wildlife populations without the costs of intensive studies. However, given the low power to detect small changes (20%) in local survival, these studies should be used when researchers are confident that major treatment impacts will occur or very large sample sizes are obtainable.