Francisco V. Dénes

Estimating abundance of unmarked animal populations: accounting for imperfect detection and other sources of zero inflation

Summary 1. Inference and estimates of abundance are critical for quantifying population dynamics and impacts of environmental change. Yet imperfect detection and other phenomena that cause zero inflation can induce estimation error and obscure ecological patterns. 2. Recent statistical advances provide an increasingly diverse array of analytical approaches for estimating population size to address these phenomena. 3. We examine how detection error and zero inflation in count data inform the choice of analytical method for estimating population size of unmarked individuals that are not uniquely identified. We review two established (GLMs and distance sampling) and nine emerging methods that use N-mixture models (Royle–Nichols model, and basic, zero inflated, temporary emigration, beta-binomial, generalized open-population, spatially explicit, single visit and multispecies) to estimate abundance of unmarked populations, focusing on their requirements and how each method accounts for imperfect detection and zero inflation. 4. Eight of the emerging methods can account for both imperfect detection and additional variation in population size in the forms of non-occupancy, temporary emigration, correlated detection and population dynamics. 5. Methods differ in sampling design requirements (e.g. count vs. detection/non-detection data, single vs. multiple visits, covariate data), and their suitability for a particular study will depend on the characteristics of the study species, scale and objectives of the study, and financial and logistical considerations. 6. Most emerging methods were developed over the past decade, so their efficacy is still under study, and additional statistical advances are likely to occur.

Estimating adult sex ratios in nature

Adult sex ratio (ASR, the proportion of males in the adult population) is a central concept in population and evolutionary biology, and is also emerging as a major factor influencing mate choice, pair bonding and parental cooperation in both human and non-human societies. However, estimating ASR is fraught with difficulties stemming from the effects of spatial and temporal variation in the numbers of males and females, and detection/capture probabilities that differ between the sexes. Here, we critically evaluate methods for estimating ASR in wild animal populations, reviewing how recent statistical advances can be applied to handle some of these challenges. We review methods that directly account for detection differences between the sexes using counts of unmarked individuals (observed, trapped or killed) and counts of marked individuals using mark–recapture models. We review a third class of methods that do not directly sample the number of males and females, but instead estimate the sex ratio indirectly using relationships that emerge from demographic measures, such as survival, age structure, reproduction and assumed dynamics. We recommend that detection-based methods be used for estimating ASR in most situations, and point out that studies are needed that compare different ASR estimation methods and control for sex differences in dispersal. This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.

Parrots as key multilinkers in ecosystem structure and functioning

Abstract Mutually enhancing organisms can become reciprocal determinants of their distribution, abundance, and demography and thus influence ecosystem structure and dynamics. In addition to the prevailing view of parrots (Psittaciformes) as plant antagonists, we assessed whether they can act as plant mutualists in the dry tropical forest of the Bolivian inter‐Andean valleys, an ecosystem particularly poor in vertebrate frugivores other than parrots (nine species). We hypothesised that if interactions between parrots and their food plants evolved as primarily or facultatively mutualistic, selection should have acted to maximize the strength of their interactions by increasing the amount and variety of resources and services involved in particular pairwise and community–wide interaction contexts. Food plants showed different growth habits across a wide phylogenetic spectrum, implying that parrots behave as super‐generalists exploiting resources differing in phenology, type, biomass, and rewards from a high diversity of plants (113 species from 38 families). Through their feeding activities, parrots provided multiple services acting as genetic linkers, seed facilitators for secondary dispersers, and plant protectors, and therefore can be considered key mutualists with a pervasive impact on plant assemblages. The number of complementary and redundant mutualistic functions provided by parrots to each plant species was positively related to the number of different kinds of food extracted from them. These mutually enhancing interactions were reflected in species‐level properties (e.g., biomass or dominance) of both partners, as a likely consequence of the temporal convergence of eco‐(co)evolutionary dynamics shaping the ongoing structure and organization of the ecosystem. A full assessment of the, thus far largely overlooked, parrot–plant mutualisms and other ecological linkages could change the current perception of the role of parrots in the structure, organization, and functioning of ecosystems.

Seed dispersal by macaws shapes the landscape of an Amazonian ecosystem

Seed dispersal is one of the most studied plant–animal mutualisms. It has been proposed that the dispersal of many large-seeded plants from Neotropical forests was primarily conducted by extinct megafauna, and currently by livestock. Parrots can transport large fruits using their beaks, but have been overlooked as seed dispersers. We demonstrate that three macaws (Ara ararauna, A. glaucogularis and A. severus) are the main dispersers of the large-seeded motacú palm Attalea princeps, which is the biomass-dominant tree in the Bolivian Amazonian savannas. Macaws dispersed fruits at high rates (75–100% of fruits) to distant (up to 1200 m) perching trees, where they consumed the pulp and discarded entire seeds, contributing to forest regeneration and connectivity between distant forests islands. The spatial distribution of immature palms was positively associated to the proximity to macaws’ perching trees and negatively to the proximity to cattle paths. The disperser role of livestock, presumably a substitute for extinct megafauna, had little effect due to soil compaction, trampling and herbivory. Our results underscore the importance of macaws as legitimate, primary dispersers of large-seeded plants at long distances and, specifically, their key role in shaping the landscape structure and functioning of this Amazonian biome.

Endangered plant-parrot mutualisms: seed tolerance to predation makes parrots pervasive dispersers of the Parana pine

Parrots are largely considered plant antagonists as they usually destroy the seeds they feed on. However, there is evidence that parrots may also act as seed dispersers. We evaluated the dual role of parrots as predators and dispersers of the Critically Endangered Parana pine (Araucaria angustifolia). Eight of nine parrot species predated seeds from 48% of 526 Parana pines surveyed. Observations of the commonest parrot indicated that 22.5% of the picked seeds were dispersed by carrying them in their beaks. Another five parrot species dispersed seeds, at an estimated average distance of c. 250 m. Dispersal distances did not differ from those observed in jays, considered the main avian dispersers. Contrary to jays, parrots often dropped partially eaten seeds. Most of these seeds were handled by parrots, and the proportion of partially eaten seeds that germinated was higher than that of undamaged seeds. This may be explained by a predator satiation effect, suggesting that the large seeds of the Parana pine evolved to attract consumers for dispersal. This represents a thus far overlooked key plant-parrot mutualism, in which both components are threatened with extinction. The interaction is becoming locally extinct long before the global extinction of the species involved.

Revisiting methods for estimating parrot abundance and population size

ABSTRACT Estimating abundance and population size is essential for many ecological and conservation studies of parrots. Achieving these goals requires methods that yield reliable estimates, but parrot traits can make them difficult to detect, count, and capture. We review established and emergent sampling and analytical methods used to estimate parrot abundance and population size, focusing on their assumptions, requirements, and limitations. Roost surveys are cost-effective if all roost locations in a region are known and stable, which is uncommon. Capture–recapture methods incorporate detection probability, but capturing, marking and resighting parrots can be difficult. Distance sampling estimates detection probability and surveys multiple species simultaneously, but is sensitive to the spatial distribution of individuals and excludes birds in flight. Roadside transects can cover large areas and survey multiple species, but habitats near roads may differ from the surrounding areas, biasing abundance estimates. Occupancy surveys and hierarchical models usually require spatially and temporally replicated datasets. Both allow estimation of detection probability; the former dispenses with count data, while the latter is a versatile set of methods that can incorporate multiple processes influencing detection and abundance. Finally, passive acoustic surveys can sample multiple species simultaneously, but identification of vocalisations can be difficult and time-consuming.

THE WHITE-COLLARED KITE (LEPTODON FORBESI SWANN, 1922) AND A REVIEW OF THE TAXONOMY OF THE GREY-HEADED KITE (LEPTODON CAYANENSIS LATHAM, 1790)

Abstract The White-collared Kite (Leptodon forbesi Swann, 1922), previously known by the holotype and three specimens from northeastern Brazil from the late 1980s, is considered by many as a juvenile variant of the Grey-headed Kite (L. cayanensis Latham, 1790). We present new morphological evidence from museum specimens of both species, including a previously misidentified specimen of L. forbesi, and field study to support the validity of the White-collared Kite as a species, now seen as endemic and severely threatened in northeastern Brazil. This species occurs only in remnants of the Atlantic Forest in the states of Alagoas and Pernambuco. It is distinguished from its congener by its white hind-collar, underwing coverts, and leading edge of the wings. The under surface of the secondaries show reduced black barring. The number of white and black tail bands is variable, and not a good diagnostic character. We also review all taxa described for L. cayanensis and show the described subspecies are not valid.

Biome‐scale signatures of land‐use change on raptor abundance: insights from single‐visit detection‐based models

Summary 1.Declines in raptor populations often result from the transformation of natural habitats to anthropogenic land uses, but the rate of population change can vary greatly among species. Declines associated with land transformation have been linked to loss of foraging habitat, prey resources and nest sites due to expanding cultivation, overgrazing, and disturbance of nests and persecution by humans. 2.We combined extensive road-survey counts of raptors, large-scale GIS datasets, and a single-visit conditional likelihood N-mixture model to generate biome-scale projections of abundance as a function of environmental covariates while correcting for detection error and other forms of zero-inflation. This approach was employed to investigate how land-use transformations in the threatened Cerrado savannas and Pantanal wetlands in Brazil have affected the populations of raptors on a large scale (>300 000 km2). We predicted that predominance of land uses with fewer or less accessible prey and scarcer nesting sites would sustain smaller raptor populations. 3.Twelve species were encountered sufficiently to estimate abundance, while 20 others were encountered too infrequently to permit abundance estimation. Detection of all 12 species was influenced by time of day, with variable species-specific effects that followed expectations based on foraging and flight behaviour. 4.Abundance of most species was negatively influenced by conversion of natural habitats to pastures, an effect that held even for generalist species considered poor indicators of habitat quality, but was not universally impacted by urbanization and soybeans, sugarcane and Eucalyptus plantations, confirming the expectation that some species may tolerate these habitats. Spatial projections of abundance appeared realistic for most species. 5.Synthesis and applications. Protection of the remaining natural habitats is essential to prevent further decline of raptor populations in the Brazilian Cerrado and Pantanal, and restoration of unproductive pastures into natural habitat could prove an efficient strategy to recover diminished raptor populations. The conditional likelihood single-visit approach is a valid and useful tool for measuring population size and for making detection-corrected inferences of abundance over large geographical scales with sensible research budgets. Incorporating the approach into a multi-species framework would allow future studies to make important inferences for entire communities. This article is protected by copyright. All rights reserved.

Influence of habitat suitability and sex-related detectability on density and population size estimates of habitat-specialist warblers

Knowledge about the population size and trends of common bird species is crucial for setting conservation priorities and management actions. Multi-species large-scale monitoring schemes have often provided such estimates relying on extrapolation of relative abundances in particular habitats to large-scale areas. Here we show an alternative to inference-rich predictive models, proposing methods to deal with caveats of population size estimations in habitat-specialist species, reed warblers (Acrocephalus scirpaceus and Acrocephalus arundinaceus). Reed warblers were only found in pure reedbeds within riparian woodlands or in riparian vegetation scattered within or around reedbed patches, as expected according to their habitat specialization. The proportion of individuals located in reedbed associated with lotic and lentic waters differed between species, and no reed warbler was recorded in reedbed located along dry streams. This indicates that microhabitat features or their effects on reedbed structure and other factors made a proportion of the apparently available habitat unsuitable for both warbler species. Most warblers detected were males performing territorial singing (females seldom sing and do not perform elaborate territorial song, and are undistinguishable from males by plumage). The regional population sizes of the warbler species (~4000 individuals of A. scirpaceus and ~ 1000 individuals of A. arundinaceus) were much smaller than those estimated for the same area by transforming relative abundance obtained at a national scale to population size through extrapolation by habitat at a regional scale. These results highlight the importance of considering the habitat actually used and its suitability, the manner of sex-related detection, population sex-ratio and their interactions in population estimates. Ideally, the value of predictive methods to estimate population size of common species should be tested before conducting large-scale monitoring, rather than a posteriori. Although logistically challenging, this can be achieved by designing monitoring programs including an intensive sampling of abundance in ad hoc reference areas of variable size.