Integrated population modelling reveals potential drivers of demography from partially aligned data: a case study of snowy plover declines under human stressors

Knowledge of demography is essential for understanding wildlife population dynamics and developing appropriate conservation plans. However, population survey and demographic data (e.g., capture-recapture) are not always aligned in space and time, hindering our ability to robustly estimate population size and demographic processes. Integrated population models (IPMs) can provide inference for population dynamics with poorly aligned but jointly analysed population and demographic data. In this study, we used an IPM to analyse partially aligned population and demographic data of a migratory shorebird species, the snowy plover (Charadrius nivosus). Snowy plover populations have declined dramatically during the last two decades, yet the demographic mechanisms and environmental drivers of these declines remain poorly understood, hindering development of appropriate conservation strategies. We analysed 21 years (1998–2018) of partially aligned population survey, nest survey, and capture-recapture-resight data in three snowy plover populations (i.e., Texas, New Mexico, Oklahoma) in the Southern Great Plains of the US. By using IPMs we aimed to achieve better precision while evaluating the effects of wetland habitat and climatic factors (minimum temperature, wind speed) on snowy plover demography. Our IPM provided reasonable precision for productivity measures even with missing data, but population and survival estimates had greater uncertainty in years without corresponding data. Our model also uncovered the complex relationships between wetland habitat, climate, and demography with reasonable precision. Wetland habitat had positive effects on snowy plover productivity (i.e., clutch size and clutch fate), indicating the importance of protecting wetland habitat under climate change and other human stressors for the conservation of this species. We also found a positive effect of minimum temperature on snowy plover productivity, indicating potential benefits of warmth during night on their population. Based on our results, we suggest prioritizing population and capture-recapture surveys for understanding population dynamics and underlying demographic processes when data collection is limited by time and/or financial resources. Our modelling approach can be used to allocate limited conservation resources for evidence-based decision-making.

Neoptile feathers contribute to outline concealment of precocial chicks

Camouflage is a widespread strategy to increase survival. The cryptic plumage colouration of precocial chicks improves camouflage often through disruptive colouration. Here, we examine whether and how fringed neoptile feathers conceal the outline of chicks. We first conducted a digital experiment to test two potential mechanisms for outline concealment through appendages: (1) reduction of edge intensity and (2) luminance transition. Local Edge Intensity Analysis showed that appendages decreased edge intensity whereas a mean luminance comparison revealed that the appendages created an intermediate transition zone to conceal the object’s outline. For edge intensity, the outline diffusion was strongest for a vision system with low spatial acuity, which is characteristic of many mammalian chick predators. We then analysed photographs of young snowy plover (Charadrius nivosus) chicks to examine whether feathers increase outline concealment in a natural setting. Consistent with better camouflage, the outline of digitally cropped chicks with protruding feathers showed lower edge intensities than the outline of chicks without those feathers. However, the observed mean luminance changes did not indicate better concealment. Taken together, our results suggest that thin skin appendages such as neoptile feathers improve camouflage. As skin appendages are widespread, this mechanism may apply to many organisms.

CEUTA snowy plover open access data - COMMENTARY

Eberhart-Phillips et al. (2020, Scientific Data 7: 149) recently published a data-paper CeutaOPEN. However, the publication has significant shortcomings: the article does not explain the history nor the context of the project, it did not give credit to the developers of field methodology and data structure, and fails to acknowledge key contributions to the project. We request correcting these shortcomings.

Detectability and Abundance of Snowy Plovers at Salt Plains National Wildlife Refuge, Oklahoma

In the past two decades, Salt Plains National Wildlife Refuge has been increasingly recognized as important habitat for both breeding and migratory shorebirds. North American snowy plovers Charadrius nivosus in particular rely on the nearly 5,000 ha salt flat at Salt Plains National Wildlife Refuge, which thousands use as breeding and stopover habitat. Elsewhere on the Southern Great Plains, decadal declines up to 75% within snowy plover subpopulations have been documented and attributed to vegetation encroachment, increased rates of nest predation, and decreased availability of fresh surface water. Despite many attempts to estimate this species’ abundance across the continent, to date, no known attempt at distance sampling of snowy plovers has occurred. To address this paucity of data, we assessed feasibility of distance sampling methods to accurately estimate snowy plover abundance and detectability. Distance sampling surveys (2017-2018) indicated high detection probability (P = 0.80) and the population abundance estimate across the salt flat extrapolated to 3,307 individuals. The distance sampling population abundance estimate is lower than population abundance estimates determined by two previous studies within the last decade but far greater than 2,105 estimated for a study in 2006. Overall, distance sampling snowy plovers at Salt Plains National Wildlife Refuge proved to be an effective addition to pre-established survey protocols but further investigation is needed to compare accuracy and precision of methods used in this study, annual surveys conducted by Salt Plains National Wildlife Refuge, and other potential snowy plover surveys.

Allelic diversity and patterns of selection at the major histocompatibility complex class I and II loci in a threatened shorebird, the Snowy Plover (Charadrius nivosus)

Background Understanding the structure and variability of adaptive loci such as the major histocompatibility complex (MHC) genes is a primary research goal for evolutionary and conservation genetics. Typically, classical MHC genes show high polymorphism and are under strong balancing selection, as their products trigger the adaptive immune response in vertebrates. Here, we assess the allelic diversity and patterns of selection for MHC class I and class II loci in a threatened shorebird with highly flexible mating and parental care behaviour, the Snowy Plover (Charadrius nivosus) across its broad geographic range. Results We determined the allelic and nucleotide diversity for MHC class I and class II genes using samples of 250 individuals from eight breeding population of Snowy Plovers. We found 40 alleles at MHC class I and six alleles at MHC class II, with individuals carrying two to seven different alleles (mean 3.70) at MHC class I and up to two alleles (mean 1.45) at MHC class II. Diversity was higher in the peptide-binding region, which suggests balancing selection. The MHC class I locus showed stronger signatures of both positive and negative selection than the MHC class II locus. Most alleles were present in more than one population. If present, private alleles generally occurred at very low frequencies in each population, except for the private alleles of MHC class I in one island population (Puerto Rico, lineage tenuirostris). Conclusion Snowy Plovers exhibited an intermediate level of diversity at the MHC, similar to that reported in other Charadriiformes. The differences found in the patterns of selection between the class I and II loci are consistent with the hypothesis that different mechanisms shape the sequence evolution of MHC class I and class II genes. The rarity of private alleles across populations is consistent with high natal and breeding dispersal and the low genetic structure previously observed at neutral genetic markers in this species.

Fluffy feathers: how neoptile feathers contribute to camouflage in precocial chicks

Camouflage is a widespread strategy to increase survival. The plumage of precocial chicks often contains elements of disruptive colouration and background matching to enhance concealment. Chick plumage also features fringed feathers as appendages that may contribute to camouflage. Here, we examine whether and how neoptile feathers conceal the outline of chicks. We first conducted a digital experiment to test two potential mechanisms for outline diffusion through appendages: 1) edge intensity reduction and 2) luminance transition. Local Edge Intensity Analysis (LEIA) showed that appendages decreased edge intensity and a mean luminance comparison revealed that the appendages created an intermediate transition zone to conceal the object's outline. The outline was most diffused through an intermediate number of interspersed thin appendages. Increased appendage thickness resulted in fewer appendages improving camouflage, whereas increased transparency required more appendages for best concealment. For edge intensity, the outline diffusion was strongest for a vision system with low spatial acuity, which is characteristic of many mammalian predators. We then analysed photographs of young snowy plover (Charadrius nivosus) chicks to examine whether neoptile feathers increase outline concealment in a natural setting. Consistent with better camouflage, the outline of digitally cropped chicks with protruding feathers showed lower edge intensities than the outline of chicks cropped without those feathers. However, the observed mean luminance changes were not consistent with better concealment. Taken together, our results suggest that thin skin appendages such as neoptile feathers improve camouflage. As skin appendages are widespread, this mechanism may apply to a large variety of organisms.

Assessing Accuracy of Sampling Schemes to Estimate Western Snowy Plover Reproductive Success

Like many wildlife species of management concern, the western snowy plover Charadrius nivosus nivosus is the subject of intensive population monitoring. However, intensive monitoring of reproductive success for this shorebird is time-consuming, financially costly, and potentially disruptive to the birds of interest. These constraints mean that intensive monitoring is not feasible throughout the range of the federally threatened Pacific Coast population. In this study, we used data collected from one intensively monitored subpopulation to assess how reductions in monitoring effort (number of chicks individually marked) would affect the accuracy of estimates of fledging success for western snowy plover chicks. We used monitoring data collected on chicks hatching at 1,845 nests from 2003 to 2012 as a theoretical subpopulation from which to draw random samples for this assessment. As expected, we found that accuracy (as measured by the inverse of percentage difference between sampled and actual fledge rates) increased with increasing percentage of the subpopulation monitored each year. We also found that the day of the week that chicks hatched and were banded had no effect on fledging success. Thus, reducing monitoring effort by banding chicks on specific days of the week is one suitable method for subpopulation sampling that has no embedded biases in the subsequent estimate of fledging success. The results of our analyses provide estimates of the accuracy of different sampling schemes, which should help managers of this threatened shorebird assess appropriate monitoring methods. We recommend use of our methods for others interested in assessing accuracy of sampling schemes for reproductive success of western snowy plover or other birds with similar life-history traits.