Individual identification in acoustic recordings

Recent advances in bioacoustics combined with acoustic individual identification (AIID) could open frontiers for ecological and evolutionary research because traditional methods of identifying individuals are invasive, expensive, labor-intensive, and potentially biased. Despite overwhelming evidence that most taxa have individual acoustic signatures, the application of AIID remains challenging and uncommon. Furthermore, the methods most commonly used for AIID are not compatible with many potential AIID applications. Deep learning in adjacent disciplines suggests opportunities to advance AIID, but such progress is limited by training data. We suggest that broadscale implementation of AIID is achievable, but researchers should prioritize methods that maximize the potential applications of AIID, and develop case studies with easy taxa at smaller spatiotemporal scales before progressing to more difficult scenarios.

Wind farm noise shifts vocalizations of a threatened shrub-steppe passerine

Wind energy has experienced a notable development during the last decades, driving new challenges for animal communities. Although bird collisions with wind turbines and spatial displacement due to disturbance have been widely described in the literature, other potential impacts remain unclear. In this study, we addressed the effect of turbine noise on the vocal behaviour of a threatened shrub-steppe passerine highly dependent on acoustic communication, the Dupont's lark Chersophilus duponti. Based on directional recordings of 49 calling and singing males exposed to a gradient of turbine noise level (from 15 up to 51 dBA), we tested for differences in signal diversity, redundancy, and complexity, as well as temporal and spectral characteristics of their vocalizations (particularly the characteristic whistle). Our results unveiled that Dupont's lark males varied the vocal structure when subject to turbine noise, by increasing the probability of emitting more complex whistles (with increased number of notes) and shifting the dominant note (emphasizing the longest and higher-pitched note). In addition, males increased duration and minimum frequency of specific notes of the whistle, while repertoire size and signal redundancy remain constant. To our knowledge, this is the first study reporting multiple and complex responses on the vocal repertoire of animals exposed to turbine noise and unveiling a shift of the dominant note in response to anthropogenic noise in general. These findings suggest that the Dupont's lark exhibits some level of phenotypic plasticity, which might enable the species to cope with noisy environments, although the vocal adjustments observed might have associated costs or alter the functionality of the signal. Future wind energy projects must include fine-scale noise assessments to quantify the consequences of chronic noise exposure.

Population viability analysis of the endangered Dupont's Lark Chersophilus duponti in Spain

Steppe lands in Europe are critically affected by habitat loss and fragmentation, and hold over 50% of IUCN Red List bird species in Europe. Dupont's Lark is a threatened steppe-specialist passerine whose European geographic range is restricted to Spain, with less than 2000 pairs and an annual population decline of - 3.9%. Its strongly fragmented habitat leads to a metapopulation structure in the Iberian Peninsula that includes 24 populations and 100 subpopulations. We present an updated Population Viability Analysis based on the latest scientific knowledge regarding distribution, population trends, breeding biology and connectivity. Our results predict metapopulation extinction in 2-3 decades, through a centripetal contraction process from the periphery to the core. The probability of extinction in 20 years was 84.2%, which supports its relisting to Endangered in Spain following IUCN criteria. We carried out a sensitivity analysis showing that some parameters, especially productivity and survival of adults and juveniles, help to increase metapopulation viability. Simulation of management scenarios showed that habitat restoration in a subset of key subpopulations had a positive effect on the overall metapopulation persistence. Translocations of a limited number of individuals from source to recipient locations may help to rescue the most endangered subpopulations without reducing the global time to extinction of the metapopulation. In addition, we identified the most critical areas for action, where local populations of the species are prone to extinction. This work suggests that the viability of the Dupont's Lark metapopulation could be improved and its risk of extinction reduced if urgent and localized conservation measures are applied. In the short-term, habitat loss and fragmentation due to ploughing, reforestation and infrastructures implementation in Dupont's Lark habitat must be avoided. Habitat restoration and translocations could help to avoid imminent extinction of critical subpopulations. Restoration of extensive grazing is recommended as the most effective way to achieve the long-term conservation of Dupont's Lark in Spain.

Connectivity in Spanish metapopulation of Dupont's lark may be maintained by dispersal over medium-distance range and stepping stones

Background

Dupont’s Lark is an endangered bird, whose fragmented distribution in Europe is entirely restricted to Spain. This lark, suffering pronounced population decline and range contraction, inhabits steppes that have long been used for grazing sheep and are now threatened by rural abandonment and land use changes. Thus, for conservation of the lark, increasing knowledge about the connectivity of the Spanish metapopulation and identifying the most important connectivity nodes are crucial.

Methods

The study was carried out in Spain, using over 16,000 Dupont’s Lark georeferenced observations. We used distance buffers to define populations and subpopulations, based on the available scientific information. We identified potential stepping stones using a MaxEnt probability of presence model. Connectivity was assessed using Conefor software, using the centroid of each subpopulation and stepping stone as nodes. Each node was assigned a quantitative attribute based on total habitat area, within-node habitat quality and internal fragmentation. We evaluated different connectivity scenarios by potential movement thresholds (5–20–100 km) and presence or absence of stepping stones in the network.

Results

Dupont’s Lark Iberian metapopulation comprises 24 populations and 100 subpopulations, plus 294 potential stepping stones. Movement thresholds and stepping stones had a strong influence in the potential network connectivity. The most important nodes are located in the core of the metapopulation, which shows connectivity among subpopulations in the different indices and scenarios evaluated. Peripheral populations are more isolated and require stepping stones or medium (20 km) or long (100 km) potential movement thresholds to join the network.

Discussion

Metapopulation connectivity may be greater than expected, thanks to stepping stones and potential medium-distance movements. Connectivity is crucial for conservation and can be increased by preserving or improving adequate habitat in the most important nodes. Given the current species decline, steppe habitat should be urgently protected from land use changes and agriculture intensification, at least in the critical subpopulations and stepping stones. Long-term conservation of steppe lands and Dupont’s Lark in Spain requires the recovery of traditional grazing and more research on juvenile dispersion. Meanwhile, the conservation of potentially critical stepping stones should be incorporated to management plans.

Survival of a long-lived single island endemic, the Raso lark Alauda razae, in relation to age, fluctuating population and rainfall

Estimating and understanding variation in survival rates is crucial for the management of threatened species, especially those with limited population sizes and/or restricted ranges. Using a capture-resighting dataset covering 2004–2017, we estimate adult survival in the Raso lark Alauda razae, a Critically Endangered single-island Cape Verdean endemic, whose population varied 25-fold during the study. Average annual adult survival was similar for males (0.813 ± 0.011) and females (0.826 ± 0.011) over the period. These values are high for a temperate passerine but not unusual for an insular tropical species like the lark. The oldest bird was recorded 13 years after first ringing. There was strong evidence that survival varied among years (between 0.57 and 0.95), being generally higher in wetter years. Survival, especially of males, was lower when the population was large, but only in drier years. Survival declined with age but there was no evidence that this decline was other than linear. High survival, even in the face of dry conditions, at least when the population is depressed, has probably contributed to the persistence of the species on its 7 km² island home over several centuries.

Hierarchical habitat-use by an endangered steppe bird in fragmented landscapes is associated with large connected patches and high food availability

Multidimensional approaches must be employed when addressing habitat use patterns. In this study, we aim to elucidate the hierarchical nature of space use by species inhabiting fragmented landscapes, using the threatened Dupont’s lark (Chersophilus duponti). The intensity of space use by Dupont’s lark was estimated using the Kernel Density Function on territory locations in 2015. We measured descriptors of habitat quality at metapopulation (connectivity and patch size), landscape (land-use types and anthropogenic disturbance) and microhabitat-scale (plant structure and composition, herbivore abundance and food availability) at 37 sampling stations. We fitted a Partial Least Squares Regression (PLSR) which yielded two components, accounting for 81% of total variance. Metapopulation-scale factors had the greatest explanatory power (32%), followed by microhabitat (17%) landscape (10%) and spatial predictors (3.6%). Connectivity and patch size were key factors explaining habitat use, and wind farms had a negative effect. At microhabitat-scale, space use was positively associated with Coleoptera, Orthoptera, Araneae and Diptera biomass, but negatively with Formicidae and Blattodea biomass, the cover of Stipa spp, Koeleria vallesiana and moss. This research highlights the hierarchical nature of habitat use in fragmented landscapes. Therefore, conservation measures should ensure connectivity, guarantee a minimum patch size, and improve habitat quality within patches.

Estimating unbiased phenological trends by adapting site-occupancy models

As a response to climate warming, many animals and plants have been found to shift phenologies, such as appearance in spring or timing of reproduction. However, traditional measures for shifts in phenology that are based on observational data likely are biased due to a large influence of population size, observational effort, starting date of a survey, or other causes that may affect the probability of detecting a species. Understanding phenological responses of species to climate change, however, requires a robust measure that could be compared among studies and study years. Here, we developed a new method for estimating arrival and departure dates based on site-occupancy models. Using simulated data, we show that our method provided virtually unbiased estimates of phenological events even if detection probability or the number of sites occupied by the species is changing over time. To illustrate the flexibility of our method, we analyzed spring arrival of two long-distance migrant songbirds and the length of the flight period of two butterfly species, using data from a long-term biodiversity monitoring program in Switzerland. In contrast to many birds that migrate short distances, the two long-distance migrant songbirds tended to postpone average spring arrival by -0.5 days per year between 1995 and 2012. Furthermore, the flight period of the short-distance-flying butterfly species apparently became even shorter over the study period, while the flight period of the longer-distance-flying butterfly species remained relatively stable. Our method could be applied to temporally and spatially extensive data from a wide range of monitoring programs and citizen science projects, to help unravel how species and communities respond to global warming.

Joint effects of population size and isolation on genetic erosion in fragmented populations: finding fragmentation thresholds for management

Size and isolation of local populations are main parameters of interest when assessing the genetic consequences of habitat fragmentation. However, their relative influence on the genetic erosion of local populations remains unclear. In this study, we first analysed how size and isolation of habitat patches influence the genetic variation of local populations of the Dupont's lark (Chersophilus duponti), an endangered songbird. An information-theoretic approach to model selection allowed us to address the importance of interactions between habitat variables, an aspect seldom considered in fragmentation studies, but which explained up to 65% of the variance in genetic parameters. Genetic diversity and inbreeding were influenced by the size of local populations depending on their degree of isolation, and genetic differentiation was positively related to isolation. We then identified a minimum local population of 19 male territories and a maximum distance of 30 km to the nearest population as thresholds from which genetic erosion becomes apparent. Our results alert on possibly misleading conclusions and suboptimal management recommendations when only additive effects are taken into account and encourage the use of most explanatory but easy-to-measure variables for the evaluation of genetic risks in conservation programmes.

Can synchronizing feather-based measures of corticosterone and stable isotopes help us better understand habitat-physiology relationships?

Physiological mechanisms link the environment with population dynamics, and glucocorticoid hormones are of particular interest because they respond adaptively to environmental change and can influence vertebrate reproduction and fitness. We tested a novel approach of synchronizing feather-based measures of corticosterone (the primary avian glucocorticoid; CORTf) and ratios of stable isotopes (SIs) of C (δ(13)C) and N (δ(15)N) to provide information about environmental conditions and an integrated physiological response to those conditions over the same period of feather synthesis. Using a fragmented metapopulation of Dupont's larks Chersophilus duponti, an endangered steppe songbird, we analyzed interrelationships among CORTf, δ(13)C, δ(15)N, and the physical environment, including measures of habitat loss and fragmentation. CORTf was not related to any habitat variable measured directly. However, we detected a significant spatial structure to CORTf values and food availability, with greater similarity in both at smaller spatial scales. Using SIs as proxies for the local environment, we found CORTf was negatively related to δ(13)C. Values of CORTf, δ(13)C, and the relationship between the two were likely driven by variation in agricultural land use surrounding lark habitat patches. Our feather-based approach revealed that individual physiology was sensitive to environmental conditions (e.g., an interaction of food availability and variation in habitat) at a local scale, but not patch or landscape scales. Combining CORTf and SIs may be a promising tool because it can provide individual-based information about habitat, physiology, and their relationship during the same time period.

Multilevel selection and neighbourhood effects from individual to metapopulation in a wild passerine

Multilevel selection has rarely been studied in the ecological context of animal populations, in which neighbourhood effects range from competition among territorial neighbours to source-sink effects among local populations. By studying a Dupont's lark Chersophilus duponti metapopulation, we analyze neighbourhood effects mediated by song repertoires on fitness components at the individual level (life-span) and population level (growth rate). As a sexual/aggressive signal with strong effects on fitness, birdsong creates an opportunity for group selection via neighbour interactions, but may also have population-wide effects by conveying information on habitat suitability to dispersing individuals. Within populations, we found a disruptive pattern of selection at the individual level and an opposite, stabilizing pattern at the group level. Males singing the most complex songs had the longest life-span, but individuals with the poorest repertoires lived longer than 'average' males, a finding that likely reflects two male strategies with respect to fitness and sexual trait expression. Individuals from groups with intermediate repertoires had the longest life-span, likely benefitting from conspecific signalling to attract females up to the detrimental spread of competitive interactions in groups with superior vocal skills. Within the metapopulation selection was directional but again followed opposite patterns at the two levels: Populations had the highest growth rate when inhabiting local patches with complex repertoires surrounded by patches with simple repertoires. Here the song may impact metapopulation dynamics by guiding prospecting individuals towards populations advertising habitat quality. Two fitness components linked to viability were therefore influenced by the properties of the group, and birdsong was the target of selection, contributing to linking social/sexual processes at the local scale with regional population dynamics.

An island paradigm on the mainland: host population fragmentation impairs the community of avian pathogens

Emergent infectious diseases represent a major threat for biodiversity in fragmented habitat networks, but their dynamics in host metapopulations remain largely unexplored. We studied a large community of pathogens (including 26 haematozoans, bacteria and viruses as determined through polymerase chain reaction assays) in a highly fragmented mainland bird metapopulation. Contrary to recent studies, which have established that the prevalence of pathogens increase with habitat fragmentation owing to crowding and habitat-edge effects, the analysed pathogen parameters were neither dependent on host densities nor related to the spatial structure of the metapopulation. We provide, to our knowledge, the first empirical evidence for a positive effect of host population size on pathogen prevalence, richness and diversity. These new insights into the interplay between habitat fragmentation and pathogens reveal properties of a host-pathogen system resembling island environments, suggesting that severe habitat loss and fragmentation could lower pathogen pressure in small populations.

Mimicry as a novel pathway linking biodiversity functions and individual behavioural performances

The feedback of biodiversity on individual trait variation is a poorly explored mechanistic pathway in ecological research. We analysed the relationship between biodiversity and individual performance by focusing on vocal mimicry, a widespread interaction that may serve in intra- and interspecific communication. We studied the songs of two lark species (genus Galerida) that increase the complexity of their song displays by mimicking other birds, and analysed the influence of bird species richness on individual song performance. The diversity of mimicked species and the prevalence of mimicry increased in areas characterized by great α and γ diversity (i.e. where larks experience more diverse encounters with community members, many of them being highly vocal owing to breeding). Conversely, the variability in species-specific song components peaked where larks were abundant, probably matching the complexity of conspecific social milieu. Some trade-offs existed between homo- and heterospecific complexity, suggesting that larks could change from population- to community-driven song variation by tracking the composition of the auditory environment. Mimicry, which serves communication with conspecifics or predators, may mediate interactions, ultimately cascading to aspects of ecological diversity other than those promoting its complexity.