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A prominent challenge for managing migratory species is the development of conservation plans that accommodate spatiotemporally varying distributions throughout the year. Migratory networks are spatially‐explicit models that incorporate migratory assignment and seasonal abundance data to define patterns of connectivity between stages of the annual cycle. These models are particularly useful for widespread application because different types of migratory data can be used to quantify individual and population‐level movement across the annual cycle of migratory species. While there are clear benefits of combining migratory assignment and abundance data for the development of conservation strategies, there is a concurrent need for corresponding user‐friendly software to facilitate the integration of these data for conservation.Here, we present mignette (migratory network tools ensemble), an R package for developing migratory network models to estimate network connectivity among migratory populations. We demonstrate the functionality of mignette with three empirical examples that highlight the use of different types of tracking data for migratory assignment.mignette facilitates the modelling of migratory networks by providing R functions to: (1) define breeding and nonbreeding nodes, (2) assemble abundance and assignment data and (3) model the migratory network. Additionally, mignette provides R functions to visualize modelled migratory networks.With increasing availability of migratory assignment and abundance data, mignette represents a valuable tool for developing effective conservation strategies for migratory species. [ABSTRACT FROM AUTHOR]

The preference-performance hypothesis explains host specificity in phytophagous insects, positing that host plants chosen by adults confer the greatest larval fitness. However, adults sometimes oviposit on plants supporting low larval success because the components of host specificity (adult preference, plant palatability, and larval survival) are non-binary and not necessarily correlated. Palatability (willingness to eat) is governed by chemical cues and physical barriers such as trichomes, while survival (ability to complete development) depends upon nutrition and toxicity. Absence of a correlation between the components of host specificity results in low-performance hosts supporting limited larval development. Most studies of specificity focus on oviposition behavior leaving the importance and basis of palatability and survival under-explored. We conducted a comprehensive review of 127 plant species that have been claimed or tested to be hosts for the monarch butterfly Danaus plexippus to classify them as non-hosts, low performance, or high performance. We performed a meta-analysis to test if performance status could be explained by properties of neurotoxic cardenolides or trichome density. We also conducted a no-choice larval feeding experiment to identify causes of low performance. We identified 34 high performance, 42 low performance, 33 non-hosts, and 18 species with unsubstantiated claims. Mean cardenolide concentration was greater in high- than low-performance hosts and a significant predictor of host status, suggesting possible evolutionary trade-offs in monarch specialization. Other cardenolide properties and trichome density were not significant predictors of host status. In the experiment, we found, of the 62% of larvae that attempted to eat low-performance hosts, only 3.5% survived to adult compared to 85% of those on the high-performance host, demonstrating that multiple factors affect larval host plant specificity. Our study is the first to classify all known host plants for monarchs and has conservation implications for this threatened species. [ABSTRACT FROM AUTHOR]

During long‐distance spring migrations, birds may rest and refuel at numerous stopover sites while minimizing the time to reach the breeding grounds. If habitat is limited along the migration route, pre‐breeding birds optimize flight range by having longer stopovers at higher quality sites compared to poorer quality sites. Stopover duration also depends on distance remaining to breeding grounds, ecological barriers and individual characteristics.We assessed spring migration tactics and connectivity of a Nearctic–Neotropical migratory shorebird, the semipalmated sandpiper Calidris pusilla, at two sites with known relative habitat quality on the northern Gulf of Mexico (NGOM) coast, the first land encountered after crossing the Gulf of Mexico (GOM).We used automated radio telemetry (Motus) to estimate stopover duration and probability of departure. Migration speed was estimated for individuals detected at subsequent receivers on the Motus network. To measure migratory connectivity, we used morphometrics and the Motus network to assign general breeding regions. Additionally, feather stable isotope ratios of C and N provided coarse information about overwintering regions.Stopover duration declined with higher fuel loads at capture as expected under a time‐minimizing strategy. After accounting for fuel load, stopover duration was approximately 40% longer at the higher quality site. We found no detectable effect of age, sex or breeding location on stopover behaviour. The probability of departure was strongly affected by humidity and also by tailwind and weather conditions. Birds stopping at the higher quality site had earlier apparent arrival to the breeding grounds. The Louisiana coast is an apparent stopover hub for this species, since the individuals were departing to range‐wide breeding regions and isotope values suggested birds were also using widespread wintering regions.Our study shows how high‐quality, coastal wetlands along the NGOM coast serve a critical role in the annual cycle of a migratory shorebird. Stopover behaviour indicated that high‐quality habitat may be limited for this species during spring migration. As threats to the GOM coast increase, protection of these already limited wetlands is vitally important. [ABSTRACT FROM AUTHOR]

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Light‐level geolocator tags use ambient light recordings to estimate the whereabouts of an individual over the time it carried the device. Over the past decade, these tags have emerged as an important tool and have been used extensively for tracking animal migrations, most commonly small birds.Analysing geolocator data can be daunting to new and experienced scientists alike. Over the past decades, several methods with fundamental differences in the analytical approach have been developed to cope with the various caveats and the often complicated data.Here, we explain the concepts behind the analyses of geolocator data and provide a practical guide for the common steps encompassing most analyses – annotation of twilights, calibration, estimating and refining locations, and extraction of movement patterns – describing good practices and common pitfalls for each step.We discuss criteria for deciding whether or not geolocators can answer proposed research questions, provide guidance in choosing an appropriate analysis method and introduce key features of the newest open‐source analysis tools.We provide advice for how to interpret and report results, highlighting parameters that should be reported in publications and included in data archiving.Finally, we introduce a comprehensive supplementary online manual that applies the concepts to several datasets, demonstrates the use of open‐source analysis tools with step‐by‐step instructions and code and details our recommendations for interpreting, reporting and archiving. [ABSTRACT FROM AUTHOR]

Blue crabs, Callinectes sapidus Rathbun, 1896, are ubiquitous along the Atlantic and Gulf coasts of the USA. These organisms play an integral role in the ecosystems of the Gulf of Mexico (GOM), where not only are they a keystone species, but are also socioeconomically important. The survival of embryonated eggs is necessary to ensure adequate recruitment into the next generation. Because the 2010 Deepwater Horizon oil spill (DWH) occurred during the peak of the blue crab spawning season, the incident likely impacted blue crab embryos. In order to assess the effect of oil on embryonic growth and development, we collected embryonated eggs from seven different female blue crabs from the GOM throughout the spawning season and exposed them to an oil concentration of 500 ppb (the approximate concentration of oil at the surface water near the site of the Deepwater Horizon oil rig). Exposure to oil at this concentration caused a significantly larger proportion of prezoeae vs. zoeae to hatch from embryonated eggs in experiments lasting longer than 4 days. Exposure to oil did not significantly affect overall survival or development rate. The prezoeal stage is a little-studied stage of blue crab development. Though it may or may not be a normal stage of development, this stage has been found to occur in suboptimal conditions and has lower survival than zoeal stages. The larger proportion of prezoeae following prolonged exposure to oil thus indicates that crude oil at concentrations likely to be experienced by crabs after the DWH spill negatively impacted the development of blue crab embryos. In addition to providing insight into the effects of the DWH, this study sheds light on embryonic development in blue crabs, a critical, but poorly investigated phase of this important species’ life cycle. [ABSTRACT FROM AUTHOR]

For seasonal migrants, non-breeding regions can play different roles in the ecology of their annual cycles: as stopover habitat, overwintering habitat, or as a combination in which some individuals stop-over and others over-winter. Such functional variations can lead to variation in occupancy dynamics and migration phenology to these different regions. In this study, we used data from archived Doppler weather surveillance radar to compare site-occupancy and movement dynamics of a migratory songbird (tree swallow Tachycineta bicolor) between two non-breeding areas: southeastern Louisiana and central peninsular Florida, USA. Specifically, in each area, we 1) quantified long-term (1996-2012) non-breeding season occupancy dynamics, 2) quantified variation in timing of autumn migration, and 3) tested which climate variables along their respective flyways were best correlated with variation in dates of arrival. Additionally, we cross-validated the dynamics from archived radar with data from eBird, a large-scale citizen science database that provides an independent measure of avian occupancy. We found strong and significant correlations between radar-estimated and eBird-estimated occupancy dynamics in both Louisiana and Florida. Long-term Louisiana occupancy dynamics conformed to our hypothesis that this region acts as a combined stopover and overwintering region whereas Florida occupancy dynamics were akin to a traditional winter region. Arrival to Louisiana during the study period was much earlier and took place over a much shorter arrival window than did arrival to Florida, which showed much more gradual arrival over the course of several months. At both sites, annual variation in mean arrival date was best explained by the amount of precipitation along the lower portions of their respective migration flyways. [ABSTRACT FROM AUTHOR]

The Blue Crab, Callinectes sapidus, is a commercially, culturally, and ecologically significant species in the Gulf of Mexico (GOM), whose offshore stages were likely impacted by the Deepwater Horizon oil spill (DWH). To test for DWH effects and to better understand the planktonic ecology of this species, we monitored Callinectes spp. megalopal settlement and condition at sites within and outside of the spill extent during and one year after the DWH. We tested for DWH effects by comparing 2010 settlement against baseline data available for two sites, and by testing for differences in settlement and condition inside and outside of the spill extent. We also developed time series models to better understand natural drivers of daily settlement variation (seasonal and lunar trends, hydrodynamics, wind) during 2010 and 2011. Overall, we found that neither megalopal settlement nor body weight were significantly reduced at oiled sites, but that high unexplained variation and low statistical power made detection of even large effects unlikely. Time series models revealed remarkably consistent and relatively strong seasonal and lunar trends within sites (explaining on average 28% and 9% of variation, respectively), while wind and hydrodynamic effects were weak (1–5% variation explained) and variable among sites. This study provides insights into DWH impacts as well as the natural drivers of Callinectes spp. megalopal settlement across the northern GOM. [ABSTRACT FROM AUTHOR]

One of the greatest feats of avian migration is the non-stop crossing of extensive areas of inhospitable habitat such as deserts and seas. Differences in spring and autumn migration routes have been reported in species that cross such barriers, and are thought to have evolved in response to seasonal variation in prevailing wind direction. We tested the hypothesis that migration routes vary seasonally with respect to the Gulf of Mexico in the tree swallow Tachycineta bicolor using solar geolocators attached and retrieved at 4 breeding sites in central North America. We found that 100 % of birds (n = 10) made a trans-Gulf flight of >850 km from Louisiana south to their wintering grounds in the Yucatan Peninsula in 12-36 hours, achieving minimum ground speeds as high as 32 m/s. Although most days during autumn migration were characterized by unfavorable headwinds blowing to the northwest, migration over the Gulf mostly occurred on days with strong winds blowing to the south. In contrast, in 8 of 9 (88 %) birds on spring migration returned from the wintering grounds towards Louisiana following a clockwise loop pattern flying over land to the west around the Gulf. During this spring period there were few days with prevailing winds from the south to assist northward migration. Results suggest that, despite being up to three times further (ca. 2,700 km), a coastal circum-Gulf spring migration represents the less risky route when wind conditions are not favorable. These findings also help to resolve a long-standing dispute in the literature concerning migration patterns between the US Gulf coast and Mexico, and provide insight into the factors shaping migration strategies of small songbirds migrating across large bodies of water [Current Zoology 60(5): 653-659, 2014]. [ABSTRACT FROM AUTHOR]

The 2010 Deepwater Horizon oil spill, the largest ever accidental release of oil into marine waters, affected hundreds of miles of US northern Gulf of Mexico coastline that is important habitat for migratory shorebirds. Shorebirds are particularly susceptible to oil contamination because of their subsurface probe-foraging behavior and reliance on intertidal habitat. More than one million migratory shorebirds representing 28 species were potentially exposed to Deepwater Horizon oil during their 2010-2011 nonbreeding season. Although only 8.6% of the shorebirds trapped from fall 2010 to spring 2011 showed visible signs of oiling, nonlethal effects and degradation of habitat can affect populations in ways that carry over into subsequent seasons. Here, we discuss how the spill could affect populations of migratory shorebirds through acute mortality, as well as through long-term and indirect pathways. We also discuss the potential impacts on ecosystems far from the spill, including prairie grasslands and the Arctic, where migratory shorebirds breed. [ABSTRACT FROM AUTHOR]

The 2010 Deepwater Horizon oil release posed the challenges of two types of spill: a familiar spill characterized by buoyant oil, fouling and killing organisms at the sea surface and eventually grounding on and damaging sensitive shoreline habitats, and a novel deepwater spill involving many unknowns. The subsurface retention of oil as finely dispersed droplets and emulsions, wellhead injection of dispersants, and deepwater retention of plumes of natural gas undergoing rapid microbial degradation were unprecedented and demanded the development of a new model for deep-water well blowouts that includes subsurface consequences. Existing governmental programs and policies had not anticipated this new theater of impacts, which thereby challenged decisionmaking on the spill response, on the assessment of natural resource damages, on the preparation for litigation to achieve compensation for public trust losses, and on restoration. Modification of laws and policies designed to protect and restore ocean resources is needed in order to accommodate oil drilling in the deep sea and other frontiers. [ABSTRACT FROM AUTHOR]

Conservation strategies for migratory animals are typically based on ad-hoc or simple ranking methods and focus on a single period of the annual cycle. We use a density-dependent population model to examine one-time land purchase strategies for a migratory population with a breeding and wintering grounds. Under equal rates of habitat loss, we show that it is optimal to invest more, but never solely, in the habitat with the higher density dependence to habitat cost ratio. When there are two habitats that vary in quality within a season, the best strategy is to invest only in one habitat. Whether to purchase high- or low-quality habitat depends on the general life history of the species and the ratio of habitat quality to habitat cost. When carry-over effects are incorporated, it is almost always optimal to invest in high-quality habitat during the season that produces the carry-over effect. We apply this model to a threatened warbler population and show the optimal strategy is to purchase more breeding than wintering habitat despite the fact that breeding habitat is over ten times more expensive. Our model provides a framework for developing year-round conservation strategies for migratory animals and has important implications for long-term planning and management. [ABSTRACT FROM AUTHOR]

Burrowing crabs of the genus Uca inhabit tidal mudflats and beaches. They feed actively during low tide and remain in their burrows when the tide is high. The timing of this activity has been shown to persist in the absence of external light and tidal cues, indicating the presence of an internal timing mechanism. Researchers report the persistence of several variations in locomotor activity under laboratory conditions that cannot be explained by a single circatidal clock. Previous studies supported two alternative hypotheses: the presence of either two circalunidian clocks, or a circadian and circatidal clock to regulate these activity rhythms. In this paper, we formulate mathematical models to describe and test these hypotheses. The models suggested by the literature contain some important differences beyond the frequency of proposed clocks, and these are reflected in the mathematical formulations and simulation results. One hypothesis suggests independent phase oscillators, while the other hypothesis suggests that they are coupled in anti-phase. Neither model is able to recover all of the variations in locomotor acitivity observed under laboratory conditions. However, we propose a new model that incorporates aspects of both existing hypotheses and is able to reproduce all laboratory observations. (Author correspondence: ) [ABSTRACT FROM AUTHOR]

Measures of animal behavior can be used in a variety of situations to make inferences about the environment and population status. Work by our research group shows that migratory shorebirds adjust their usage of, and behavior at, stopover sites in response to environmental conditions. Motivated by this, we built an individual-based model of migrating shorebirds moving through a sequence of alternating small and large stopover sites. Birds at larger sites are safer from predators, but we assumed that less food is available than at small sites. In the model, both predation risk and food intake are density-dependent, and the behavior of migrants is controlled by two rules: one that determines whether a bird will depart a stopover site, and one that controls the individual's foraging versus vigilance intensity. The optimal behavior is calculated by maximizing a payoff function that depends on arrival date and arrival energy stores at the final site. We used this model to predict mass gain, foraging intensity, and usage by migrants of small and large sites under various conditions. We examined the effects of a flyway-wide reduction in the amount of food, a flyway-wide increase in predation danger, and the effects of lowering the overall population size. The mass action of many individuals. each optimizing its migration timing and routing, leads to the emergence of distinctive patterns of behavior and site choice under these differing environmental conditions. When food availability is reduced throughout the flyway, our model predicts that foraging intensity increases at every stopover site, thereby forcing birds to accept greater danger to maintain the fitness benefit of a timely arrival to the breeding area. A flyway-wide increase in predation danger results in fewer migrants choosing (and/or migrants staying a shorter time at) small stopover sites, balanced by a higher usage of large sites. These effects contrast with what is observed under true population declines, when the usage of both small and large sites declines. [ABSTRACT FROM AUTHOR]

Understanding the dynamics of small populations is obviously important for declining or rare species but is also particularly important for invading species. The Allee effect, where fitness is reduced when conspecific density is low, can dramatically affect the dynamics of biological invasions. Here, we summarize the literature of Allee effects in biological invasions, revealing an extensive theory of the consequences of the Allee effect in invading species and some empirical support for the theory. Allee effects cause longer lag times, slower spread and decreased establishment likelihood of invasive species. Expected spatial ranges, distributions and patterns of species may be altered when an Allee effect is present. We examine how the theory can and has been used to detect Allee effects in invasive species and we discuss how the presence of an Allee effect and its successful or unsuccessful detection may affect management of invasives. The Allee effect has been shown to change optimal control decisions, costs of control and the estimation of the risk posed by potentially invasive species. Numerous ways in which the Allee effect can influence the efficacy of biological control are discussed. [ABSTRACT FROM AUTHOR]

Results from both a spatially explicit stochastic simulation model and a spatially implicit deterministic model show that a weak Allee effect can slow the spread of an invasive plant, Spartina alterniflora, in a Pacific Coast estuary. The mean rate of spread with the Allee effect is ∼ 19%; removing the Allee effect results in a mean rate of spread of ∼31%. Sensitivity analysis both with and without the Allee effect reveal that seedling establishment, inflorescence density, and outcrossed seed production are key factors determining invasion rate. When there is an Allee effect, the invasion rate is sensitive to variation in self-pollinated seed production. By structuring the population according to density classes instead of the more usual age or stage classes, the deterministic model demonstrates a novel way of representing density dependence and an Allee effect in population biology. This approach could be applied to model the population dynamics of any species that spreads from multiple foci and in which these foci later coalesce. [ABSTRACT FROM AUTHOR]

1. There are very few general guidelines available to improve the process of eradicating invasive species. We addressed the basic question of whether it is more efficient to prioritize the removal of outliers or core populations of an invasive grass,Spartina alterniflora.2. We used a structured model in which the population of the invasive species is partitioned into different classes based on local conspecific density in order to investigate density-based eradication strategies.3. TheSpartinapopulation at a Pacific coast estuary in Washington state, USA, is subject to an Allee effect: at low density plants produce fewer propagules than in high-density coalesced meadows. Plants at low density, however, are able to spread faster vegetatively. We used a genetic algorithm to find the optimal division of resources between removal of high-density and low-density plants. We explored the consequences of the Allee effect, contrasting financial budgets available for control operations and the inclusion of seedling control in addition to the control of mature plants.4. We found that the optimal strategy was dependent on the annual budget available for control. At low and medium budgets, it was necessary to remove the low-density plants first to achieve eradication, but if more money was available then the optimal strategy was to prioritize high-density areas.5. Without an Allee effect the optimal strategy would always be to prioritize the removal of fast-growing, low-density sub-populations. Seedling control did not change the optimal strategy but did, in some cases, reduce the cost of eradication.6. Synthesis and applications. Given the uncertainty in future budgets allocated for control of invasiveSpartina, we recommend a strategy that prioritizes the removal of low-density subpopulations ofS. alternifloraover high-density subpopulations. The Allee effect in this system is not sufficiently strong to outweigh the importance of the rapid vegetative spread of the plants at low density.Journal of Applied Ecology(2004)41, 1049 –1057 [ABSTRACT FROM AUTHOR]

It is well known that forest fragmentation reduces fecundity in several avian species, including wood thrush, Hylocichla mustelina, a migratory songbird that has been declining for several decades. However, I found that landscape-scale density in wood thrush was lower and population declines steeper in higher quality, less-fragmented landscapes (an inverse buffer effect) than in poor quality landscapes. These patterns suggest that wood thrush was not limited by availability of breeding habitat but that declines were primarily driven by non-breeding season events. A two-season model predicts that if this hypothesis is correct, breeding population trends will be negatively related to the strength of density dependence (b') in the breeding season. To test this, a site-dependence model was used to construct fecundity-density curves and showed that landscape fragmentation affected the shape of density dependence. In good quality landscapes, the onset of strong density dependence was much more abrupt than in poorer quality landscapes and the realized strength of density dependence, b', was lower in good quality landscapes. Population trends were negatively associated with b', providing support for the non-breeding limitation hypothesis. The combination of the negative associations of trends with b' and b' with landscape quality explain the inverse buffer effect.

Benthic infaunal communities are important components of coastal ecosystems. Understanding the relationships between the structure of these communities and characteristics of the habitat in which they live is becoming progressively more important as coastal systems face increasing stress from anthropogenic impacts and changes in climate. To examine how sediment characteristics and infaunal community composition were related along the northern Gulf of Mexico coast, we sampled intertidal infaunal communities at seven sites covering common habitat types at a regional scale. Across 69 samples, the communities clustered into four distinct groups on the basis of faunal composition. Nearly 70% of the variation in the composition of the communities was explained by salinity, median grain size, and total organic content. Our results suggest that at a regional level coarse habitat characteristics are able to explain a large amount of the variation among sites in infaunal community structure. By examining the relationships between infaunal communities and their sedimentary habitats, we take a necessary first step that will allow the exploration of how changes in habitat and community composition influence higher trophic levels and ecosystem scale processes.