Detection Rate of Bird Species and What It Depends on: Tips for Field Surveys

Bird counting inevitably suffers from imperfect detection, which varies across species, habitats, period of the day, and seasons. Although various modeling techniques have recently been developed to account for this phenomenon, the biological basis of natural variation in detection remains insufficiently known. This study examined the bird species’ detection rate throughout the day, considering their body mass and diet type, concerning the environment and weather characteristics. Species detection rates were significantly affected by the number of individuals of that species but were unrelated to body mass. Overall, species with the highest detection rate were Corn bunting, Blackbird, European robin, House sparrow and Common chiffchaff. Granivores-insectivores and insectivores showed significant differences in detection rates throughout the day among habitats, with higher detection rates in grasslands during the afternoon. Insectivores showed higher detection rates in farmland during midday (warmest time of the day). Granivores, omnivores and scavengers did not show changes in detection rates in different day periods. Such patterns in daily detection rates were significant even when considering abundance and total species richness in each community. Finally, cloudiness was unrelated to the overall detection rate of birds, while temperature and wind affected detection rates in some guilds. Our findings provide some advice for choosing a suitable ornithological sampling method by considering the avian communities composition in combination with the type of environment, the diet of bird species, and the period of the day.

Distribution of tiger salamanders in northern Sonora, Mexico: comparison of sampling methods and possible implications for an endangered subspecies

Many aquatic species in the arid USA-Mexico borderlands region are imperiled, but limited information on distributions and threats often hinders management. To provide information on the distribution of the Western Tiger Salamander (Ambystoma mavortium), including the USA-federally endangered Sonoran Tiger Salamander (Ambystoma mavortium stebbinsi), we used traditional (seines, dip-nets) and modern (environmental DNA [eDNA]) methods to sample 91 waterbodies in northern Sonora, Mexico, during 2015-2018. The endemic Sonoran Tiger Salamander is threatened by introgressive hybridization and potential replacement by another sub-species of the Western Tiger Salamander, the non-native Barred Tiger Salamander (A. m. mavortium). Based on occupancy models that accounted for imperfect detection, eDNA sampling provided a similar detection probability (0.82 [95% CI: 0.56-0.94]) as seining (0.83 [0.46-0.96]) and much higher detection than dip-netting (0.09 [0.02-0.23]). Volume of water filtered had little effect on detection, possibly because turbid sites had greater densities of salamanders. Salamanders were estimated to occur at 51 sites in 3 river drainages in Sonora. These results indicate tiger salamanders are much more widespread in northern Sonora than previously documented, perhaps aided by changes in land and water management practices. However, because the two subspecies of salamanders cannot be reliably distinguished based on morphology or eDNA methods that are based on mitochondrial DNA, we are uncertain if we detected only native genotypes or if we documented recent invasion of the area by the non-native sub-species. Thus, there is an urgent need for methods to reliably distinguish the subspecies so managers can identify appropriate interventions.

Habitat Occupancy by Spruce Grouse (Canachites canadensis) in the south of its range, Québec, Canada

Studying habitat occupancy at the margins of species’ distributions can be helpful in clarifying species’ requirements and planning management measures. Spruce grouse (Canachites canadensis Linnaeus, 1758), a bird species associated with northern short-needle coniferous forests in North America, has its southeastern range limit where coniferous forests are mixed with temperate deciduous forests and agricultural lands. Some isolated populations are found in these habitats. Using a single-season occupancy modelling approach, we investigated habitat use by spruce grouse, accounting for imperfect detection, in the lowlands of the St. Lawrence River in southern Québec, Canada. We conducted call-response spruce over three years at 279 sites (59 sites in 2007, 100 sites in 2008 and 120 sites in 2009). At the site level, the probability of occupancy was 21% (IC: 10.7% - 37.9%) and probability of detection was 54% (IC: 34.7% - 73.0%). Based on the covariates in the models, occurrence increased with higher cover of coniferous trees and low deciduous shrubs, and decreased with higher cover of deciduous trees. Finally, detection probability was highest at the beginning of the survey (50% in late April) and was influenced by year.

Contrasting responses of large carnivores to land use management across an Asian montane landscape in Iran

Land-use change has led to substantial range contractions for many species. Such contractions are particularly acute for wide-ranging large carnivores in Asia’s high altitude areas, which are marked by high spatiotemporal variability in resources. Current conservation planning for human-dominated landscapes often takes one of two main approaches: a “coexistence” (land sharing) approach or a “separation” (land sparing) approach. In this study, we evaluated the effects of land-use management on a guild of large carnivores in a montane ecosystem located in northeastern Iran. We used interview surveys to collect data on Persian leopard Panthera pardus saxicolor and grey wolf Canis lupus and modeled the areas occupied by these species in a Bayesian framework. After accounting for imperfect detection, we found that wolves had a higher probability of occupying the study area than leopards (82%; 95% CI 73–90% vs. 63%; 95% CI 53–73%). Importantly, each predator showed contrasting response to land-use management. National Parks (i.e. human-free areas) had a positive association with leopard occupancy (αNational Park = 2.56, 95% CI 0.22–5.77), in contrast to wolves, which displayed a negative association with National Parks (αNational Park = − 1.62, 95% CI − 2.29 to 0.31). An opposite pattern was observed for human-dominated areas (i.e. Protected Areas and Communal Lands), where occupancy was higher for wolves but lower for leopards. Our study suggests that to protect these large carnivores, a combination of land sharing and land sparing approaches is desirable within Iran montane landscapes. Any recovery program for big cats in Iranian mountains, and likely similar mountainous landscapes in west Asia, should take into account other sympatric carnivores and how they can affect adjacent human communities. For example, conflict mitigation and compensation efforts are required to include the guild of large carnivores, instead of solely targeting the charismatic big cats.

Survival analyses

Survival analyses are a key tool for demographers, ecologists, and evolutionary biologists. This chapter presents the most common methods and illustrates their use for species across the Tree of Life. It discusses the challenges associated with various types of survival data, how to model species with a complex life cycle, and includes the impact of environmental factors and individual heterogeneity. It covers the analysis of ‘known-fate’ data collected in lab conditions, using the Kaplan–Meier estimator and Cox’s proportional hazard regression analysis. Alternatively, survival data collected on free-ranging populations usually involve individuals missing at certain monitoring occasions and unknown time at death. The chapter provides an overview of capture–mark–recapture (CMR) models, from single-state to multi-state and multi-event models, and their use in animal and plant demography to estimate demographic parameters while correcting for imperfect detection of individuals. It discusses various inference frameworks available to implement CMR models using a frequentist or Bayesian approach. Only humans are an exception among free-ranging populations, with the existence of several consequent databases with perfect knowledge of age and cause of death for all individuals. The chapter presents an overview of the most common models used to describe mortality patterns over age and time using human mortality data. Throughout, focus is placed on eight case studies, which involve lab organisms, free-ranging animal populations, plant populations, and human populations. Each example includes data and codes, together with step-by-step guidance to run the survival analysis.

Longitudinal demographic data collection

Several long-term field studies are running worldwide on many taxa across the Tree of Life. These longitudinal studies involve several visits to the study population with repeated observations/measurements. Demographic data can be collected at the population level (e.g. time series of population counts) or at the individual level (e.g. monitoring of marked and/or georeferenced individuals throughout their life). These data are then used to estimate demographic parameters such as annual population abundances, survival, growth, and reproductive rates. This chapter introduces the reader to monitoring methods (including recent technologies) that can be implemented in the field to collect specific demographic data on mobile species (e.g. birds, mammals) at both the population and individual levels, while dealing with imperfect detection. It also presents the procedures and the type of demographic data that can be collected on sessile species (e.g. corals, plants) at both levels. Finally, the chapter concludes with new aspects, current biases, and arising challenges for future long-term field studies.

Why Are Species’ Traits Weak Predictors of Range Shifts?

We examine the evidence linking species’ traits to contemporary range shifts and find they are poor predictors of range shifts that have occurred over decades to a century. We then discuss reasons for the poor performance of traits for describing interspecific variation in range shifts from two perspectives: ( a) factors associated with species’ traits that degrade range-shift signals stemming from the measures used for species’ traits, traits that are typically not analyzed, and the influence of phylogeny on range-shift potential and ( b) issues in quantifying range shifts and relating them to species’ traits due to imperfect detection of species, differences in the responses of altitudinal and latitudinal ranges, and emphasis on testing linear relationships between traits and range shifts instead of nonlinear responses. Improving trait-based approaches requires a recognition that traits within individuals interact in unexpected ways and that different combinations of traits may be functionally equivalent. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.