Biodiversity is declining at unprecedented rates worldwide. Yet cascading effects of biodiversity loss on other taxa are largely unknown because baseline data are often unavailable. We document the ...collapse of a Neotropical snake community after the invasive fungal pathogen
caused a chytridiomycosis epizootic leading to the catastrophic loss of amphibians, a food source for snakes. After mass mortality of amphibians, the snake community contained fewer species and was more homogeneous across the study site, with several species in poorer body condition, despite no other systematic changes in the environment. The demise of the snake community after amphibian loss demonstrates the repercussive and often unnoticed consequences of the biodiversity crisis and calls attention to the invisible declines of rare and data-deficient species.
There is increasing need for methods that integrate multiple data types into a single analytical framework as the spatial and temporal scale of ecological research expands. Current work on this topic ...primarily focuses on combining capture–recapture data from marked individuals with other data types into integrated population models. Yet, studies of species distributions and trends often rely on data from unmarked individuals across broad scales where local abundance and environmental variables may vary. We present a modeling framework for integrating detection–nondetection and count data into a single analysis to estimate population dynamics, abundance, and individual detection probabilities during sampling. Our dynamic population model assumes that site-specific abundance can change over time according to survival of individuals and gains through reproduction and immigration. The observation process for each data type is modeled by assuming that every individual present at a site has an equal probability of being detected during sampling processes. We examine our modeling approach through a series of simulations illustrating the relative value of count vs. detection-nondetection data under a variety of parameter values and survey configurations. We also provide an empirical example of the model by combining long-term detection-nondetection data (1995–2014) with newly collected count data (2015–2016) from a growing population of Barred Owl (Strix varia) in the Pacific Northwest to examine the factors influencing population abundance over time. Our model provides a foundation for incorporating unmarked data within a single framework, even in cases where sampling processes yield different detection probabilities. This approach will be useful for survey design and to researchers interested in incorporating historical or citizen science data into analyses focused on understanding how demographic rates drive population abundance.
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Human-induced ecological change in the open oceans appears to be accelerating. Fisheries, climate change and elevated nutrient inputs are variously blamed, at least in part, for altering oceanic ...ecosystems. Yet it is challenging to assess the extent of anthropogenic change in the open oceans, where historical records of ecological conditions are sparse, and the geographical scale is immense. We developed millennial-scale amino acid nitrogen isotope records preserved in ancient animal remains to understand changes in food web structure and nutrient regimes in the oceanic realm of the North Pacific Ocean (NPO). Our millennial-scale isotope records of amino acids in bone collagen in a wide-ranging oceanic seabird, the Hawaiian petrel (Pterodroma sandwichensis), showed that trophic level declined over time. The amino acid records do not support a broad-scale increase in nitrogen fixation in the North Pacific subtropical gyre, rejecting an earlier interpretation based on bulk and amino acid specific δ15N chronologies for Hawaiian deep-sea corals and bulk δ15N chronologies for the Hawaiian petrel. Rather, our work suggests that the food web structure in the NPO has shifted at a broad geographical scale, a phenomenon potentially related to industrial fishing.
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Occupancy modeling is a widely used analytical technique for assessing species distributions and range dynamics. However, occupancy analyses frequently ignore variation in abundance of occupied ...sites, even though site abundances affect many of the parameters being estimated (e.g., extinction, colonization, detection probability). We introduce a new model ("dynamic N-occupancy") capable of providing accurate estimates of local abundance, population gains (reproduction/immigration), and apparent survival probabilities while accounting for imperfect detection using only detection/nondetection data. Our model utilizes heterogeneity in detection based on variations in site abundances to estimate latent demographic rates via a dynamic N-mixture modeling framework. We validate our model using simulations across a wide range of values and examine the data requirements, including the number of years and survey sites needed, for unbiased and precise estimation of parameters. We apply our model to estimate spatiotemporal heterogeneity in abundances of barred owls (Strix varia) within a recently invaded region in Oregon (USA). Estimates of apparent survival and population gains are consistent with those from a nearby radio-tracking study and elucidate how barred owl abundances have increased dramatically over time. The dynamic N-occupancy model greatly improves inferences on individual-level population processes from occupancy data by explicitly modeling the latent population structure.
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A common challenge for studying wildlife populations occurs when different survey methods provide inconsistent or incomplete inference on the trend, dynamics, or viability of a population. A ...potential solution to the challenge of conflicting or piecemeal data relies on the integration of multiple data types into a unified modeling framework, such as integrated population models (IPMs). IPMs are a powerful approach for species that inhabit spatially and seasonally complex environments. We provide guidance on exploiting the capabilities of IPMs to address inferential discrepancies that stem from spatiotemporal data mismatches. We illustrate this issue with analysis of a migratory species, the American Woodcock (Scolopax minor), in which individual monitoring programs suggest differing population trends. To address this discrepancy, we synthesized several long-term data sets (1963–2015) within an IPM to estimate continental-scale population trends, and link dynamic drivers across the full annual cycle and complete extent of the woodcock’s geographic range in eastern North America. Our analysis reveals the limiting portions of the life cycle by identifying time periods and regions where vital rates are lowest and most variable, as well as which demographic parameters constitute the main drivers of population change. We conclude by providing recommendations for resolving conflicting population estimates within an integrated modeling approach, and discuss how strategies (e.g., data thinning, expert opinion elicitation) from other disciplines could be incorporated into ecological analyses when attempting to combine multiple, incongruent data types.
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Stable isotope analyses of archival specimens have revealed trophic declines over the past 150 yr in a growing number of predatory pelagic seabirds that breed in the Hawaiian Islands. However, they ...have not examined whether isotopic shifts occurred primarily during a specific phase of the annual cycle, which could allow us to better identify the causes of trophic declines and potential consequences for affected populations. We evaluated seasonal (breeding versus nonbreeding season) foraging habits of 2 ecologically distinct species, Newell’s shearwater Puffinus newelli and Laysan albatross Phoebastria immutabilis, and extended this analysis back 50 and 100 yr, respectively. Our assessment relied on amino acid δ15N proxies for nutrient regime use (δ15NPhe) and trophic position (Δδ15NGlu-Phe) from 2 tissues (feather and bone collagen) reflecting different time scales. Both study species exhibited season-specific isotopic shifts resulting in more pronounced seasonality in modern populations. We also identified inter-species differences in nutrient regime use, regardless of season. Laysan albatross experienced a trophic decline exclusive to the breeding season, while their nonbreeding season foraging ecology has remained constant over the past century. In contrast, the nutrient regime at the base of the food chain for Newell’s shearwaters during the nonbreeding season underwent a shift within the last 50 yr, and the trophic decline they experienced was heavily weighted toward the nonbreeding season. Efforts to mitigate potential fitness consequences of future trophic declines might benefit from focusing on fisheries management near the Hawaiian Islands, where susceptible seabirds forage during winter/spring, rather than the entire North Pacific.
Isotopic niche has typically been characterized through carbon and nitrogen ratios and most modeling approaches are limited to two dimensions. Yet, other stable isotopes can provide additional power ...to resolve questions associated with foraging, migration, dispersal and variations in resource use. The ellipse niche model was recently generalized to n‐dimensions. We present an analogous methodology which incorporates variation across three stable dimensions to estimate the significant features of a population's isotopic niche space including: 1) niche volume (referred to as standard ellipsoid volume, SEV), 2) relative centroid location (CL), 3) shape and 4) area of overlap between multiple ellipsoids and 5) distance between two CLs. We conducted a simulation study showing the accuracy and precision of three dimensional niche models across a range of values. Importantly, the model correctly identifies differences in SEV and CL among populations, even with small sample sizes and in cases where the absolute values cannot precisely be recovered. We use these results to provide guidelines for sample size in conducting multivariate isotopic niche modeling. We demonstrate the utility of our approach with a case study of three bottlenose dolphin populations which appear to possess largely overlapping niches when analyzed with only carbon and nitrogen isotopes. Upon inclusion of sulfur, we see that the three dolphin ecotypes are in fact segregated on the basis of salinity and find the stable isotope niche of inshore bottlenose dolphins significantly larger than coastal and offshore populations.
We present simulation study testing the use of multi‐dimensional Bayesian ellipsoids to quantify the the isotopic niche of a population and provide guidelines for their use. We then examine three parapatric populations of bottlenose dolphins off the West Central Coast of Florida and find isotopic niche size decreases from nearshore to offshore populations.
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We examine individual specialization in foraging habits (foraging habitat and trophic level) of female bottlenose dolphins (Tursiops truncatus) resident in Sarasota Bay, Florida, USA, by analyzing ...time series of stable isotope (δ¹⁵N and δ¹³C) values in sequential growth layer groups within teeth. The isotope data provide a chronology of foraging habits over the lifetime of the individual and allowed us to show that female bottlenose dolphins exhibit a high degree of individual specialization in both foraging habitat and trophic level. The foraging habits used by adult females are similar to those they used as calves and may be passed down from mother to calf through social learning. We also characterized the foraging habits and home range of each individual by constructing standard ellipses from isotope values and dolphin sightings data (latitude and longitude), respectively. These data show that Sarasota Bay bottlenose dolphins forage within a subset of the habitats in which they are observed. Moreover, females with similar observational standard ellipses often possessed different foraging specializations. Female bottlenose dolphins may demonstrate individual specialization in foraging habits because it reduces some of the cost of living in groups, such as competition for prey.
We investigated how foraging habits vary among three ecologically distinct wide-ranging seabirds. Using amino acid δ¹⁵N proxies for nutrient regime (δ¹⁵NPhe) and trophic position (Δδ¹⁵NGlu-Phe), we ...compared Newell’s shearwater (Puffinus newelli) and Laysan albatross (Phoebastria immutabilis) foraging habits over the past 50–100 years, respectively, to published records for the Hawaiian petrel (Pterodroma sandwichensis). Standard ellipses constructed from the isotope proxies show that inter-population and interspecific foraging segregation have persisted for several decades. We found no evidence of a shift in nutrient regime at the base of the food web for the three species. However, our data identify a trophic decline during the past century for Newell’s shearwater and Laysan albatross (probability ≥ 0.97), echoing a similar decline observed in the Hawaiian petrel. During this time, Newell’s shearwaters and Hawaiian petrels have experienced population declines and Laysan albatross has experienced range extension and apparent population stability. Counting other recent studies, a pattern of trophic decline over the past century has now been identified in eight species of pelagic seabirds that breed in the Hawaiian Islands. Because our study species forage broadly across the North Pacific Ocean and differ in morphological and behavioral traits and feeding methods, the identified trophic declines suggest a pervasive shift in food web architecture within the past century.
Human-induced ecological change in the open oceans appears to be accelerating. Fisheries, climate change and elevated nutrient inputs are variously blamed, at least in part, for altering oceanic ...ecosystems. Yet it is challenging to assess the extent of anthropogenic change in the open oceans, where historical records of ecological conditions are sparse, and the geographical scale is immense. We developed millennial-scale amino acid nitrogen isotope records preserved in ancient animal remains to understand changes in food web structure and nutrient regimes in the oceanic realm of the North Pacific Ocean (NPO). Our millennial-scale isotope records of amino acids in bone collagen in a wideranging oceanic seabird, the Hawaiian petrel (Pterodroma sandwichensis), showed that trophic level declined over time. The amino acid records do not support a broad-scale increase in nitrogen fixation in the North Pacific subtropical gyre, rejecting an earlier interpretation based on bulk and amino acid specific δ¹⁵N chronologies for Hawaiian deep-sea corals and bulk δ¹⁵N chronologies for the Hawaiian petrel. Rather, our work suggests that the food web structure in the NPO has shifted at a broad geographical scale, a phenomenon potentially related to industrial fishing.
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