Carnivora population dynamics are as slow and as fast as those of other mammals: implications for their conservation

PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets

In phylogenomics, incongruences between gene trees, resulting from both artifactual and biological reasons, can decrease the signal-to-noise ratio and complicate species tree inference. The amount of data handled today in classical phylogenomic analyses precludes manual error detection and removal. However, a simple and efficient way to automate the identification of outliers from a collection of gene trees is still missing. Here, we present PhylteR, a method that allows rapid and accurate detection of outlier sequences in phylogenomic datasets, i.e. species from individual gene trees that do not follow the general trend. PhylteR relies on DISTATIS, an extension of multidimensional scaling to 3 dimensions to compare multiple distance matrices at once. In PhylteR, these distance matrices extracted from individual gene phylogenies represent evolutionary distances between species according to each gene. On simulated datasets, we show that PhylteR identifies outliers with more sensitivity and precision than a comparable existing method. We also show that PhylteR is not sensitive to ILS-induced incongruences, which is a desirable feature. On a biological dataset of 14,463 genes for 53 species previously assembled for Carnivora phylogenomics, we show (i) that PhylteR identifies as outliers sequences that can be considered as such by other means, and (ii) that the removal of these sequences improves the concordance between the gene trees and the species tree. Thanks to the generation of numerous graphical outputs, PhylteR also allows for the rapid and easy visual characterization of the dataset at hand, thus aiding in the precise identification of errors. PhylteR is distributed as an R package on CRAN and as containerized versions (docker and singularity).

Estimating Wolf Population Size and Dynamics by Field Monitoring and Demographic Models: Implications for Management and Conservation

We estimated the current size and dynamics of the wolf population in Tuscany and investigated the trends and demographic drivers of population changes. Estimates were obtained by two different approaches: (i) mixed-technique field monitoring (from 2014 to 2016) that found the minimum observed pack number and estimated population size, and (ii) an individual-based model (run by Vortex software v. 10.3.8.0) with demographic inputs derived from a local intensive study area and historic data on population size. Field monitoring showed a minimum population size of 558 wolves (SE = 12.005) in 2016, with a density of 2.74 individuals/100 km2. The population model described an increasing trend with an average annual rate of increase λ = 1.075 (SE = 0.014), an estimated population size of about 882 individuals (SE = 9.397) in 2016, and a density of 4.29 wolves/100 km2. Previously published estimates of wolf population were as low as 56.2% compared to our field monitoring estimation and 34.6% in comparison to our model estimation. We conducted sensitivity tests to analyze the key parameters driving population changes based on juvenile and adult mortality rates, female breeding success, and litter size. Mortality rates played a major role in determining intrinsic growth rate changes, with adult mortality accounting for 62.5% of the total variance explained by the four parameters. Juvenile mortality was responsible for 35.8% of the variance, while female breeding success and litter size had weak or negligible effects. We concluded that reliable estimates of population abundance and a deeper understanding of the role of different demographic parameters in determining population dynamics are crucial to define and carry out appropriate conservation and management strategies to address human-wildlife conflicts.

The demographic causes of population change vary across four decades in a long-lived shorebird

Understanding which factors cause populations to decline begins with identifying which parts of the life cycle, and which vital rates, have changed over time. However, in a world where humans are altering the environment both rapidly and in different ways, the demographic causes of decline likely vary over time. Identifying temporal variation in demographic causes of decline is crucial to assure that conservation actions target current and not past threats. However, this has rarely been studied as it requires long time series. Here we investigate how the demography of a long‐lived shorebird (the Eurasian Oystercatcher Haematopus ostralegus) has changed in the past four decades, resulting in a shift from stable dynamics to strong declines (−9% per year), and recently back to a modest decline. Since individuals of this species are likely to respond differently to environmental change, we captured individual heterogeneity through three state variables: age, breeding status, and lay date (using integral projection models). Timing of egg‐laying explained significant levels of variation in reproduction, with a parabolic relationship of maximal productivity near the average lay date. Reproduction explained most variation in population growth rates, largely due to poor nest success and hatchling survival. However, the demographic causes of decline have also been in flux over the last three decades: hatchling survival was low in the 2000s but improved in the 2010s, while adult survival declined in the 2000s and remains low today. Overall, the joint action of several key demographic variables explain the decline of the oystercatcher, and improvements in a single vital rate cannot halt the decline. Conservations actions will thus need to address threats occurring at different stages of the oystercatcher's life cycle. The dynamic nature of the threat landscape is further supported by the finding that the average individual no longer has the highest performance in the population, and emphasizes how individual heterogeneity in vital rates can play an important role in modulating population growth rates. Our results indicate that understanding population decline in the current era requires disentangling demographic mechanisms, individual variability, and their changes over time.

Geographical variation in pace-of-life in a long-distance migratory bird: implications for population management

Life-history theory predicts that animals should develop adaptive trade-offs between survival and reproduction to maximize their fitness. This results in a continuum of life-history strategies among species, ranging from slow to fast paces-of-life. The optimal pace-of-life has been shown to vary within environmental gradients, with a commonly observed pattern of a slow-to-fast continuum from the tropics to the poles. Within species, pace-of-life variability has however received much less attention. In this study, we investigated whether or not the pace-of-life of populations within a species follows the expected slow-fast continuum associated with latitude. We analysed the variability of life-history strategies among populations of the European roller Coracias garrulus, a long-distance migratory species, comparing breeding parameters and adult survival between populations across a latitudinal gradient. The findings showed a negative correlation between survival and clutch size in roller populations, with a slower pace-of-life in the northern populations and a faster pace-of-life in the southern populations: a reverse gradient to what might be expected from inter-specific studies. These results suggest that northern populations would benefit from measures enhancing adult survival probability, such as reduction in harvesting rates, while southern populations would respond better to actions favouring reproductive success, such as nesting site provisioning. This study highlights that life-history traits can vary substantially between populations of a single species with a large latitudinal breeding range, and pinpoint how knowledge about this variability may be key in anticipating different populations' responses to threats as well as to conservation strategies.

Do Criminals Live Faster Than Soldiers and Firefighters? : A Comparison of Biodemographic and Psychosocial Dimensions of Life History Theory

A high risk of morbidity-mortality caused by a harsh and unpredictable environment is considered to be associated with a fast life history (LH) strategy, commonly linked with criminal behavior. However, offenders are not the only group with a high exposure to extrinsic morbidity-mortality. In the present study, we investigated the LH strategies employed by two groups of Polish men: incarcerated offenders (N = 84) as well as soldiers and firefighters (N = 117), whose professions involve an elevated risk of injury and premature death. The subjects were asked to complete the Mini-K (used as a psychosocial LH indicator) and a questionnaire which included a number of biodemographic LH variables. Although biodemographic and psychosocial LH indicators should be closely linked with each other, the actual connection between them is unclear. Thus, this study was driven by two aims: comparing LH strategies in two groups of men with a high risk of premature morbidity-mortality and investigating the relationship between the biodemographic and psychosocial LH dimensions. The study showed that incarcerated men employed faster LH strategies than soldiers and firefighters, but only in relation to biodemographic variables (e.g., number of siblings, age of sexual initiation, life expectancy). No intergroup differences emerged regarding psychosocial LH indicators. Moreover, the correlation analysis showed a weak association between biodemographic and psychosocial LH indicators. The results strengthen the legitimacy of incorporating biodemographic LH traits into research models and indicate the need for further research on the accuracy of the Mini-K. The possible explanations for the intergroup differences in LH strategies are discussed.

Pulsed food resources affect reproduction but not adult apparent survival in arctic foxes

As top or mesopredators, carnivores play a key role in food webs. Their survival and reproduction are usually thought to be influenced by prey availability. However, simultaneous monitoring of prey and predators is difficult, making it challenging to evaluate the impacts of prey on carnivores' demography. Using 13 years of field data on arctic foxes Vulpes lagopus in the Canadian High Arctic and a capture-recapture multi-event statistical approach, we investigated the hypothesis that increases in lemming abundance (a cyclic and unpredictable food source) and goose colony proximity (a stable but spatially and temporally limited food source) would be associated with increased apparent survival and reproduction probabilities of adults. Adult apparent survival varied greatly across years (0.13-1.00) but was neither affected by lemming nor goose variations in abundance. However, reproduction probabilities were strongly influenced by both lemming abundance and access to the goose colony. A fox breeding in the best conditions of food availability (year of high lemming density inside the goose colony) had a reproduction probability four times higher than one experiencing the worst conditions (year of low lemming density outside the goose colony). Breeding status of individuals also played a role, with breeders having a 10-20% higher probability of survival and 30% higher probability of reproduction the following year than non-breeders. As the Arctic ecosystem changes due to increased temperatures and species ranges, this study will allow better predictions of predator responses to management or environmental changes and a better understanding of ecosystem functioning.

The Importance of Reproduction for the Conservation of Slow-Growing Animal Populations

Both survival and reproduction are important fitness components, and thus critical to the viability of wildlife populations. Preventing one death (survival) or contributing one newborn (reproduction), has arguably the same effect on population dynamics-in each instance the population grows or is maintained by one additional member. However, for the conservation of slow-growing animal populations, the importance of reproduction is sometimes overlooked when evaluating wildlife management options. This has to do with the use of demographic sensitivity analyses, which quantify the relative contribution of vital rates to population growth. For slow-growing populations, the results of such analyses typically show that growth rates are more sensitive to changes in survival than to equal proportional changes in reproduction. Consequently, for slow-growing taxa, survival has been labelled a better fitness surrogate than reproduction. However, such a generalization, derived from conventional sensitivity analyses, is based on flawed approaches, such as omitting appropriate scaling of vital rates, and sometimes misinterpretations. In this chapter, I make the case that for the conservation of slow-growing species the role of reproduction is considerably greater than conventional sensitivity analyses would suggest. This is illustrated by case studies on wildlife populations that underscore the importance of reproduction for the conservation of slow-growing birds, ungulates, carnivores, and cetaceans.

Abundance, survival, recruitment and effectiveness of sterilization of free-roaming dogs: A capture and recapture study in Brazil

The existence of free-roaming dogs raises important issues in animal welfare and in public health. A proper understanding of these animals’ ecology is useful as a necessary input to plan strategies to control these populations. The present study addresses the population dynamics and the effectiveness of the sterilization of unrestricted dogs using capture and recapture procedures suitable for open animal populations. Every two months, over a period of 14 months, we captured, tagged, released and recaptured dogs in two regions in a city in the southeast region of Brazil. In one of these regions the animals were also sterilized. Both regions had similar social, environmental and demographic features. We estimated the presence of 148 females and 227 males during the period of study. The average dog:man ratio was 1 dog for each 42 and 51 human beings, in the areas without and with sterilization, respectively. The animal population size increased in both regions, due mainly to the abandonment of domestic dogs. Mortality rate decreased throughout the study period. Survival probabilities did not differ between genders, but males entered the population in higher numbers. There were no differences in abundance, survival and recruitment between the regions, indicating that sterilization did not affect the population dynamics. Our findings indicate that the observed animal dynamics were influenced by density-independent factors, and that sterilization might not be a viable and effective strategy in regions where availability of resources is low and animal abandonment rates are high. Furthermore, the high demographic turnover rates observed render the canine free-roaming population younger, thus more susceptible to diseases, especially to rabies and leishmaniasis. We conclude by stressing the importance of implementing educational programs to promote responsible animal ownership and effective strategies against abandonment practices.

Dynamics of a low-density tiger population in Southeast Asia in the context of improved law enforcement

Recovering small populations of threatened species is an important global conservation strategy. Monitoring the anticipated recovery, however, often relies on uncertain abundance indices rather than on rigorous demographic estimates. To counter the severe threat from poaching of wild tigers (Panthera tigris), the Government of Thailand established an intensive patrolling system in 2005 to protect and recover its largest source population in Huai Kha Khaeng Wildlife Sanctuary. Concurrently, we assessed the dynamics of this tiger population over the next 8 years with rigorous photographic capture-recapture methods. From 2006 to 2012, we sampled across 624-1026 km(2) with 137-200 camera traps. Cameras deployed for 21,359 trap days yielded photographic records of 90 distinct individuals. We used closed model Bayesian spatial capture-recapture methods to estimate tiger abundances annually. Abundance estimates were integrated with likelihood-based open model analyses to estimate rates of annual and overall rates of survival, recruitment, and changes in abundance. Estimates of demographic parameters fluctuated widely: annual density ranged from 1.25 to 2.01 tigers/100 km(2) , abundance from 35 to 58 tigers, survival from 79.6% to 95.5%, and annual recruitment from 0 to 25 tigers. The number of distinct individuals photographed demonstrates the value of photographic capture-recapture methods for assessments of population dynamics in rare and elusive species that are identifiable from natural markings. Possibly because of poaching pressure, overall tiger densities at Huai Kha Khaeng were 82-90% lower than in ecologically comparable sites in India. However, intensified patrolling after 2006 appeared to reduce poaching and was correlated with marginal improvement in tiger survival and recruitment. Our results suggest that population recovery of low-density tiger populations may be slower than anticipated by current global strategies aimed at doubling the number of wild tigers in a decade.

The relative importance of reproduction and survival for the conservation of two dolphin populations

It has been proposed that in slow‐growing vertebrate populations survival generally has a greater influence on population growth than reproduction. Despite many studies cautioning against such generalizations for conservation, wildlife management for slow‐growing populations still often focuses on perturbing survival without careful evaluation as to whether those changes are likely or feasible. Here, we evaluate the relative importance of reproduction and survival for the conservation of two bottlenose dolphin (Tursiops cf aduncus) populations: a large, apparently stable population and a smaller one that is forecast to decline. We also assessed the feasibility and effectiveness of wildlife management objectives aimed at boosting either reproduction or survival. Consistent with other analytically based elasticity studies, survival had the greatest effect on population trajectories when altering vital rates by equal proportions. However, the findings of our alternative analytical approaches are in stark contrast to commonly used proportional sensitivity analyses and suggest that reproduction is considerably more important. We show that

in the stable population reproductive output is higher, and adult survival is lower;

the difference in viability between the two populations is due to the difference in reproduction;

reproductive rates are variable, whereas survival rates are relatively constant over time;

perturbations on the basis of observed, temporal variation indicate that population dynamics are much more influenced by reproduction than by adult survival;

for the apparently declining population, raising reproductive rates would be an effective and feasible tool to reverse the forecast population decline; increasing survival would be ineffective.

Our findings highlight the importance of reproduction – even in slow‐growing populations – and the need to assess the effect of natural variation in vital rates on population viability. We echo others in cautioning against generalizations based on life‐history traits and recommend that population modeling for conservation should also take into account the magnitude of vital rate changes that could be attained under alternative management scenarios.

COMADRE: a global data base of animal demography

The open‐data scientific philosophy is being widely adopted and proving to promote considerable progress in ecology and evolution. Open‐data global data bases now exist on animal migration, species distribution, conservation status, etc. However, a gap exists for data on population dynamics spanning the rich diversity of the animal kingdom world‐wide. This information is fundamental to our understanding of the conditions that have shaped variation in animal life histories and their relationships with the environment, as well as the determinants of invasion and extinction.

Matrix population models (MPMs) are among the most widely used demographic tools by animal ecologists. MPMs project population dynamics based on the reproduction, survival and development of individuals in a population over their life cycle. The outputs from MPMs have direct biological interpretations, facilitating comparisons among animal species as different as Caenorhabditis elegans, Loxodonta africana and Homo sapiens.

Thousands of animal demographic records exist in the form of MPMs, but they are dispersed throughout the literature, rendering comparative analyses difficult. Here, we introduce the COMADRE Animal Matrix Database, an open‐data online repository, which in its version 1.0.0 contains data on 345 species world‐wide, from 402 studies with a total of 1625 population projection matrices. COMADRE also contains ancillary information (e.g. ecoregion, taxonomy, biogeography, etc.) that facilitates interpretation of the numerous demographic metrics that can be derived from its MPMs. We provide R code to some of these examples.

Synthesis: We introduce the COMADRE Animal Matrix Database, a resource for animal demography. Its open‐data nature, together with its ancillary information, will facilitate comparative analysis, as will the growing availability of databases focusing on other aspects of the rich animal diversity, and tools to query and combine them. Through future frequent updates of COMADRE, and its integration with other online resources, we encourage animal ecologists to tackle global ecological and evolutionary questions with unprecedented sample size.

Comparative life histories of fishes in the subgenus Limia (Pisces: Poeciliidae)

This study presents life-history descriptions for 12 species in the subgenus Limia, which are endemic to the Greater Antilles. All species in this study lack evidence of superfoetation, producing a single brood of offspring before developing subsequent broods. Interbrood intervals (number of days between parturition events) are also consistent with intervals of species that lack superfoetation. Maternal provisioning, characterized by matrotrophy index, is <1.0 for all species of Limia. This is consistent with species that provide little or no maternal provisioning to developing embryos after ovum fertilization (lecithotrophic). Four species exhibit potentially bi-modal size distributions of mature males. Work on other poeciliids suggests that such bimodal distributions can be caused by genetic polymorphisms in some species. Principle component analyses revealed an axis of interspecific variation in life histories that separated species with small size at maturity and the production of many, small offspring from those with large size at maturity and that produce few, large offspring. This pattern of life-history diversity occurs in many other groups of organisms.