Simultaneous-count models to estimate abundance from counts of unmarked individuals with imperfect detection

We developed a method to estimate population abundance from simultaneous counts of unmarked individuals over multiple sites. We considered that at each sampling occasion, individuals in a population could be detected at 1 of the survey sites or remain undetected and used either multinomial or binomial simultaneous-count models to estimate abundance, the latter being equivalent to an N-mixture model with one site. We tested model performance with simulations over a range of detection probabilities, population sizes, growth rates, number of years, sampling occasions, and sites. We then applied our method to 3 critically endangered vulture species in Cambodia to demonstrate the real-world applicability of the model and to provide the first abundance estimates for these species in Cambodia. Our new approach works best when existing methods are expected to perform poorly (i.e., few sites and large variation in abundance among sites) and if individuals may move among sites between sampling occasions. The approach performed better when there were >8 sampling occasions and net probability of detection was high (>0.5). We believe our approach will be useful in particular for simultaneous surveys at aggregation sites, such as roosts. The method complements existing approaches for estimating abundance of unmarked individuals and is the first method designed specifically for simultaneous counts.     

Importance of timely metadata curation to the global surveillance of genetic diversity

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.     

The double-edged sword of grant funding: a study of community-led climate change initiatives in remote rural Scotland

Community-led initiatives are commonly advocated as an effective way of encouraging individuals to adopt more sustainable lifestyles. Since 2008, the Scottish Government's climate challenge fund (CCF) has distributed over £50 million in grants to community-led, carbon-saving projects across the country. Drawing on participant observation within two CCF organisations in remote rural Scotland, this paper examines the assumption that the receipt of government funding is necessarily of overall benefit to community-led initiatives attempting to facilitate more sustainable communities in the long term. Observations indicate that funding can bring with it a number of significant complications to community-scale action as a result of: (i) misaligned output timeframes, (ii) administration demands, and (iii) local competition. It is concluded that the design of funding schemes can in fact hamper the full potential of grassroots initiatives to engender more sustainable lifestyles throughout the community.     

Causes and consequences of unequal seedling production in forest trees: a case study in red oaks

Inequality in reproductive success has important implications for ecological and evolutionary dynamics, but lifetime reproductive success is challenging to measure in long-lived species such as forest trees. While seed production is often used as a proxy for overall reproductive success, high mortality of seeds and the potential for trade-offs between seed number and quality draw this assumption into question. Parentage analyses of established seedlings can bring us one step closer to understanding the causes and consequences of variation in reproductive success. In this paper we demonstrate a new method for estimating individual seedling production and average percentage germination, using data from two mixed-species populations of red oaks (Quercus rubra, Q. velutina, Q. falcata, and Q. coccinea). We use these estimates to examine the distribution of female reproductive success and to test the relationship between seedling number and individual seed production, age, and growth rate. We show that both seed and seedling production are highly skewed, roughly conforming to zero-inflated lognormal distributions, rather than to the Poisson or negative-binomial distributions often assumed by population genetics analyses. While the number of established offspring is positively associated with mean annual seed production, a lower proportion of seeds from highly fecund individuals become seedlings. Our red oak populations also show evidence of trade-offs between growth rate and reproductive success. The high degree of inequality in seedling production shown here for red oaks, and by previous studies in other species, suggests that many trees may be more vulnerable to genetic drift than previously thought, if immigration in limited by fragmentation or other environmental changes.     

Why breed communally? Factors affecting fecundity in a communal breeding mammal: the banded mongoose (<Emphasis Type="Italic">Mungos mungo</Emphasis>)

Fecundity is an important component of fitness. In cooperatively breeding species, studies aimed at understanding the factors that affect fecundity have largely been restricted to species that exhibit high reproductive skew, where reproduction is monopolised by a few individuals. In such species, dominant suppression and inbreeding avoidance are the principal explanations for low fecundity in subordinate females. In this paper, we evaluate the relative effects of individual, social, and environmental factors on female fecundity in a low skew cooperative breeding mammal: the banded mongoose (Mungos mungo). Most females (80%) conceived in each breeding event, and most pregnant females (93%) carried their litter to term. The principal determinants of a females fecundity were intrinsic qualities, particularly age and body size. However, there was no evidence of dominant suppression of subordinate reproduction or inbreeding avoidance. Similarly, there was little indication that social or environmental factors influence fecundity. We suggest that in the banded mongoose, the apparent lack of costs to inbreeding, and the absence of dominant female suppression of reproduction in other females result in low reproductive skew. Indeed, in banded mongooses, like lions (Felis leo), multiple breeding may be a consequence of benefits to rearing young communally.Communicated by F. Trillmich     

A better rationale for wetland management

The present US Federal wetland management strategy under Section 404 of the Clean Water Act does not account for the differences in the natural values of wetlands and their different vulnerability to development pressure. The strategy, aimed at reducing the regulatory burden, provides for different levels of wetland protection, primarily by designating certain activities in or affecting wetlands as essentially harmless, having only minor impacts even when considered for their cumulative effects. Such activities are authorized under general permits precluding any evaluation of project impacts. A sounder, yet practical, rationale for wetland management and regulatory relief should be linked to the scarcity of certain wetland habitats, the habitat diversity or carrying capacity, the degree of degradation from past development, and the incremental losses already incurred within the same wetland ecosystem. The regulatory effort should be concentrated where these characteristics indicate high-value wetlands.Wetland impacts appear to fit into five basic orders of magnitude; these pertain to the relative cost and difficulty of impact mitigation. Up to 13 ecological and public-interest variables can modify the seriousness of the basic impact. Together, the basic orders of impact and modifying variables describe the theoretical framework for wetland management. However, a practical rationale for better wetland management must be constrained to factors not requiring a field investigation in advance of project planning for construction and development.This article was produced in part from work funded by the Office of Technology Assessment (OTA) of the United States Congress for use in its study, Wetlands: Their Use and Regulation. The views expressed do not necessarily represent those of OTA.