Six‐year demographic study reveals threat of stochastic extinction for remnant populations of a threatened amphibian

Sustained demographic studies are essential for early detection of species decline in time for effective management response. A paucity of such background data hindered the potential for successful conservation during the global amphibian decline and remains problematic today. The current study analysed 6 years of mark‐recapture data to determine the vital demographic rates in three habitat precincts of the threatened frog, Litoria aurea (Hylidae) and to understand the underlying causes of variability in population size. Variability in population size of L. aurea was similar to many pond‐breeding species; however this level of fluctuation is rare among threatened amphibians. Highly variable populations are at greater risk of local extinction and the low level of connectivity between L. aurea populations means they are at a greater risk of further decline due to stochastic extinction events and incapacity to recolonize distant habitat. We recommend that management of this species should encourage recolonization through creation of habitat corridors and reintroduction of L. aurea to areas where stochastic extinction events are suspected.     

Diversification in a biodiversity hot spot: landscape correlates of phylogeographic patterns in the African spotted reed frog

The Eastern Afromontane Biodiversity Hotspot is known for microendemism and exceptional population genetic structure. The region's landscape heterogeneity is thought to limit gene flow between fragmented populations and create opportunities for regional adaptation, but the processes involved are poorly understood. Using a combination of phylogeographic analyses and circuit theory, I investigate how characteristics of landscape heterogeneity including regional distributions of slope, rivers and streams, habitat and hydrological basins (drainages) impact genetic distance among populations of the endemic spotted reed frog (Hyperolius substriatus), identifying corridors of connectivity as well as barriers to dispersal. Results show that genetic distance among populations is most strongly correlated to regional and local hydrologic structure and the distribution of suitable habitat corridors, not isolation by distance. Contrary to expectations, phylogeographic structure is not coincident with the two montane systems, but instead corresponds to the split between the region's two major hydrological basins (Zambezi and East Central Coastal). This results in a paraphyletic relationship for the Malawian Highlands populations with respect to the Eastern Arc Mountains and implies that the northern Malawian Highlands are the diversity centre for H. substriatus. Although the Malawian Highlands collectively hold the greatest genetic diversity, individual populations have lower diversity than their Eastern Arc counterparts, with an overall pattern of decreasing population diversity from north to south. Through the study of intraspecific differentiation across a mosaic of ecosystem and geographic heterogeneity, we gain insight into the processes of diversification and a broader understanding of the role of landscape in evolution.     

Big cats at large: Density,structure, and spatio-temporal patterns of a leopard population free of anthropogenic mortality

Human impact is near pervasive across the planet and studies of wildlife populations free of anthropogenic mortality are increasingly scarce. This is particularly true for large carnivores that often compete with and, in turn, are killed by humans. Accordingly, the densities at which carnivore populations occur naturally, and their role in shaping and/or being shaped by natural processes, are frequently unknown. We undertook a camera-trap survey in the Sabi Sand Game Reserve (SSGR), South Africa, to examine the density, structure and spatio-temporal patterns of a leopard Panthera pardus population largely unaffected by anthropogenic mortality. Estimated population density based on spatial capture–recapture models was 11.8 ± 2.6 leopards/100 km². This is likely close to the upper density limit attainable by leopards, and can be attributed to high levels of protection (particularly, an absence of detrimental edge effects) and optimal habitat (in terms of prey availability and cover for hunting) within the SSGR. Although our spatio-temporal analyses indicated that leopard space use was modulated primarily by “bottom-up” forces, the population appeared to be self-regulating and at a threshold that is unlikely to change, irrespective of increases in prey abundance. Our study provides unique insight into a naturally-functioning carnivore population at its ecological carrying capacity. Such insight can potentially be used to assess the health of other leopard populations, inform conservation targets, and anticipate the outcomes of population recovery attempts.     

Using occupancy analysis to validate the use of footprint tunnels as a method for monitoring the hedgehog Erinaceus europaeus

Indirect survey methods are often used in studies of mammals but are susceptible to biases caused by failure to detect species where they are present. Occupancy analysis is an analytical technique which enables non‐detection rates to be estimated and which can be used to develop and refine novel survey methods. In this study, we investigated the use of footprint tunnels by volunteers as a method for surveying occupancy of sites by hedgehogs Erinaceus europaeus. The survey protocol led to a very low non‐detection rate and could reasonably be used to detect occupancy changes of 25% with statistical power of 0.95 in a national survey.     

Using citizen‐based survey data to determine densities of large mammals: a case study from Mana Pools National Park,Zimbabwe

Since 1993, members of the national wildlife society have undertaken annual surveys of large mammals in the Zambezi alluvial woodlands of Mana Pools National Park, Zimbabwe. Data are collected along 36 systematically‐arranged transects. We provide the first thorough assessment of the data from any survey within this long‐term project. The transect data from 2011 were analysed with DISTANCE software to assess if the data were suitable for determining the densities of large mammals using distance sampling techniques. Successful application of distance sampling depended on observers using printed, large‐scale, georeferenced satellite images onto which they mapped the location of animal groups detected. The assumptions of the distance sampling were well met and thus the 2011 survey provided reliable estimates of the densities of nine species of common large mammals on the Zambezi alluvium during the late dry season. Estimated density in this dry‐season concentration area varied from 3.6 km^?2 for kudu, to 204 km^?2 for impala. The precision of the estimates ranged from a coefficient of variation of 7.9% for elephant, to 25.5% for buffalo. For elephant, warthog and baboon, the morning and afternoon densities differed significantly.     

Using community photography to investigate phenology: A case study of coat molt in the mountain goat (Oreamnos americanus) with missing data

Participatory approaches, such as community photography, can engage the public in questions of societal and scientific interest while helping advance understanding of ecological patterns and processes. We combined data extracted from community‐sourced, spatially explicit photographs with research findings from 2018 fieldwork in the Yukon, Canada, to evaluate winter coat molt patterns and phenology in mountain goats (Oreamnos americanus), a cold‐adapted, alpine mammal. Leveraging the community science portals iNaturalist and CitSci, in less than a year we amassed a database of almost seven hundred unique photographs spanning some 4,500 km between latitudes 37.6°N and 61.1°N from 0 to 4,333 m elevation. Using statistical methods accounting for incomplete data, a common issue in community science datasets, we identified the effects of intrinsic (sex and presence of offspring) and broad environmental (latitude and elevation) factors on molt onset and rate and compared our findings with published data. Shedding occurred over a 3‐month period between 29 May and 6 September. Effects of sex and offspring on the timing of molt were consistent between the community‐sourced and our Yukon data and with findings on wild mountain goats at a long‐term research site in west‐central Alberta, Canada. Males molted first, followed by females without offspring (4.4 days later in the coarse‐grained, geographically wide community science sample; 29.2 days later in our fine‐grained Yukon sample) and lastly females with new kids (6.2; 21.2 days later, respectively). Shedding was later at higher elevations and faster at northern latitudes. Our findings establish a basis for employing community photography to examine broad‐scale questions about the timing of ecological events, as well as sex differences in response to possible climate drivers. In addition, community photography can help inspire public participation in environmental and outdoor activities specifically with reference to iconic wildlife.     

Grass Gazers: Using citizen science as a tool to facilitate practical and online science learning for secondary school students during the COVID‐19 lockdown

The coronavirus disease of 2019 (COVID‐19) pandemic has impacted educational systems worldwide during 2020, including primary and secondary schooling. To enable students of a local secondary school in Brisbane, Queensland, to continue with their practical agricultural science learning and facilitate online learning, a “Grass Gazers” citizen science scoping project was designed and rapidly implemented as a collaboration between the school and a multidisciplinary university research group focused on pollen allergy. Here, we reflect on the process of developing and implementing this project from the perspective of the school and the university. A learning package including modules on pollen identification, tracking grass species, measuring field greenness, using a citizen science data entry platform, forensic palynology, as well as video guides, risk assessment and feedback forms were generated. Junior agriculture science students participated in the learning via online lessons and independent data collection in their own local neighborhood and/or school grounds situated within urban environments. The university research group and school coordinator, operating in their own distributed work environments, had to develop, source, adopt, and/or adapt material rapidly to meet the unique requirements of the project. The experience allowed two‐way knowledge exchange between the secondary and tertiary education sectors. Participating students were introduced to real‐world research and were able to engage in outdoor learning during a time when online, indoor, desk‐based learning dominated their studies. The unique context of restrictions imposed by the social isolation policies, as well as government Public Health and Department of Education directives, allowed the team to respond by adapting teaching and research activity to develop and trial learning modules and citizen science tools. The project provided a focus to motivate and connect teachers, academic staff, and school students during a difficult circumstance. Extension of this citizen project for the purposes of research and secondary school learning has the potential to offer ongoing benefits for grassland ecology data acquisition and student exposure to real‐world science.     

Using n-alkanes to estimate diet composition of herbivores: a novel mathematical approach

N-alkanes are long-chain saturated hydrocarbons occurring in plant cuticles that can be used as chemical markers for estimating the diet composition of herbivores. An important constraint of using n-alkanes to estimate diet composition with currently employed mathematical procedures is that the number of markers must be equal or larger than the number of diet components. This is a considerable limitation when dealing with free-ranging herbivores feeding on complex plant communities. We present a novel approach for the estimation of diet composition using n-alkanes which applies equally to cases where the number of markers is lower, equal or greater than the number of plant species in the diet. The model uses linear programming to estimate the minimum and maximum proportions of each plant in the diet, and avoids the need for grouping species in order to reduce the number of estimated dietary components. We illustrate the model with two data sets of n-alkane content of plants and faeces obtained from a sheep grazing experiment conducted in Australia and a red deer study in Portugal. Our results are consistent with previous studies on those data sets and provide additional information on the proportions of individual species in the diet. Results show that sheep included in the diet high proportions of white clover (from 0.25 to 0.37), and relatively high proportions of grasses (e.g. brome from 0.14 to 0.26) but tended to avoid Lotus spp. (always less than 0.04 of the diet). For red deer we found high proportions of legumes (e.g. Trifolium angustifolium and Vicia sativa reaching maximum proportions of 0.42 and 0.30 of the diet, respectively) with grasses being less important and Cistus ladanifer, a browse, also having relevance (from 0.21 to 0.42 of the diet).     

Generalists are the most urban‐tolerant of birds: a phylogenetically controlled analysis of ecological and life history traits using a novel continuous measure of bird responses to urbanization

Identifying which ecological and life history traits influence a species’ tolerance to urbanization is critical to understanding the trajectory of biodiversity in an increasingly urbanizing world. There is evidence for a wide array of contrasting patterns for single trait associations with urbanization. In a continental‐scale analysis, incorporating 477 species and >5 000 000 bird observations, we developed a novel and scalable methodology that evaluated the ecological and life history traits which most influence a species’ adaptability to persist in urban environments. Specifically, we assigned species‐specific scores based on continuous measures of response to urbanization, using VIIRS night‐time light values (i.e. radiance) as a proxy for urbanization. We identified generalized, phylogenetically controlled patterns: bird species which are generalists (i.e. large niche breadth), with large clutch size, and large residual brain size are among the most urban‐tolerant bird species. Conversely, specialized feeding strategies (i.e. insectivores and granivores) were negatively associated with urbanization. Enhancement and persistence of avian biodiversity in urban environments probably relies on protecting, maintaining and restoring diverse habitats serving a range of life history strategies.     

Teaching an experiential field course via online participatory science projects: A COVID‐19 case study of a UC California Naturalist course

Experience and training in field work are critical components of undergraduate education in ecology, and many university courses incorporate field‐based or experiential components into the curriculum in order to provide students hands‐on experience. Due to the onset of the COVID‐19 pandemic and the sudden shift to remote instruction in the spring of 2020, many instructors of such courses found themselves struggling to identify strategies for developing rigorous field activities that could be completed online, solo, and from a student''s backyard. This case study illustrates the process by which one field‐based course, a UC California Naturalist certification course offered at the University of California, Davis, transitioned to fully remote instruction. The transition relied on established, publicly available, online participatory science platforms (e.g., iNaturalist) to which the students contributed data and field observations remotely. Student feedback on the course and voluntary‐continued engagement with the participatory science platforms indicates that the student perspective of the experience was on par with previous traditional offerings of the course. This case study also includes topics and participatory science resources for consideration by faculty facing a similar transition from group field activities to remote, individual field‐based experiences.     

Resistance to RHD virus in wild Australian rabbits: Comparison of susceptible and resistant individuals using a genomewide approach

Deciphering the genes involved in disease resistance is essential if we are to understand host–pathogen coevolutionary processes. The rabbit haemorrhagic disease virus (RHDV) was imported into Australia in 1995 as a biocontrol agent to manage one of the most successful and devastating invasive species, the European rabbit (Oryctolagus cuniculus). During the first outbreaks of the disease, RHDV caused mortality rates of up to 97%. Recently, however, increased genetic resistance to RHDV has been reported. Here, we have aimed to identify genomic differences between rabbits that survived a natural infection with RHDV and those that died in the field using a genomewide next‐generation sequencing (NGS) approach. We detected 72 SNPs corresponding to 133 genes associated with survival of a RHD infection. Most of the identified genes have known functions in virus infections and replication, immune responses or apoptosis, or have previously been found to be regulated during RHD. Some of the genes identified in experimental studies, however, did not seem to play a role under natural selection regimes, highlighting the importance of field studies to complement the genomic background of wildlife diseases. Our study provides a set of candidate markers as a tool for the future scanning of wild rabbits for their resistance to RHDV. This is important both for wild rabbit populations in southern Europe where RHD is regarded as a serious problem decimating the prey of endangered predator species and for assessing the success of currently planned RHDV variant biocontrol releases in Australia.     

Variation in thermal niche of a declining river‐breeding frog: From counter‐gradient responses to population distribution patterns

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Using genotyping data to assign markers to their chromosome type and to infer the sex of individuals: a Bayesian model‐based classifier

The recent democratization of next‐generation‐sequencing‐based approaches towards nonmodel species has made it cost‐effective to produce large genotyping data sets for a wider range of species. However, when no detailed genome assembly is available, poor knowledge about the organization of the markers within the genome might hamper the optimal use of this abundant information. At the most basic level of genomic organization, the type of chromosome (autosomes, sex chromosomes, mitochondria or chloroplast in plants) may remain unknown for most markers which might be limiting or even misleading in some applications, particularly in population genetics. Conversely, the characterization of sex‐linked markers allows molecular sexing of the individuals. In this study, we propose a Bayesian model‐based classifier named detsex, to assign markers to their chromosome type and/or to perform sexing of individuals based on genotyping data. The performance of detsex is further evaluated by a comprehensive simulation study and by the analysis of real data sets from various origins (microsatellite and SNP data derived from genotyping assay designs and NGS experiments). Irrespective of the origin of the markers or the size of the data set, detsex was proved efficient (i) to identify the sex‐linked markers, (ii) to perform molecular sexing of the individuals and (iii) to perform basic quality check of the genotyping data sets. The underlying structure of the model also allows to consider each of these potential applications either separately or jointly.     

The power of potential natural vegetation (and of spatial‐temporal scale): a response to Carrión & Fernández (2009)

A commentary by Carrión & Fernández (Journal of Biogeography, 2009, 36 , 2202–2203) compared Holocene pollen records with models of potential natural vegetation (PNV) proposed in the phytosociological literature and concluded that the predicted PNV resulted from anthropogenic disturbance. However, the authors misinterpreted PNV, leading to two serious flaws in their assumptions: (1) PNV is not defined as a pre‐anthropic or climax plant community; and (2) PNV is not a concept restricted to the phytosociological method. Therefore we criticize the conclusions expressed in the commentary, and we stress the need for an interdisciplinary approach based on multi‐temporal and multi‐spatial scales to achieve a modern framework for the study of plant communities.     

Using extant patterns of dental variation to identify species in the primate fossil record: a case study of middle Eocene <Emphasis Type="Italic">Omomys</Emphasis> from the Bridger Basin,southwestern Wyoming

Patterns of extant primate dental variation provide important data for interpreting taxonomic boundaries in fossil forms. Here I use dental data from several well-known living primates (as well as data from selected Eocene forms) to evaluate dental variation in Middle Eocene Omomys, the first North American fossil primate identified by paleontologists. Measurements were collected from a sample of 148 omomyid dental specimens recovered from Bridger B localities in the Bridger Basin, Wyoming. Most of these specimens have not previously been described. Nonmetric traits were also scored for this sample. Lower molar coefficients of variation range from 4.01 for M₂ length (n = 80) to 6.73 for M₃ talonid width (n = 57). All of the nonmetric traits scored exhibit less than 100% presence in the overall sample, including traits previously described as representative of Omomys (e.g., P₄ metaconids present in 91%, n = 55; M² pericones present in 80%, n = 15). Dental traits also vary in a set of spatially restricted localities from the same fossil horizon and in a separate, single fossil locality (DMNH 868, P₄ metaconids present in 67%, n = 6). An increasing frequency in several premolar traits across time in these more restricted samples suggests an anagenetic change in Bridger B Omomys. However, this degree of morphological variability is consistent with that seen in extant primate species from single locations. Metric variation in this sample is comparable to that seen in other Eocene primates, such as new data presented here for the omomyid Arapahovius gazini from the Washakie Basin, southern Wyoming. Omomys metric variation is also comparable to that found in several samples of well-known extant primates from single localities (e.g., ring-tailed lemurs and gray–brown mouse lemurs). These metric data also correspond to the patterns of variability described in previously published studies of Omomys carteri. In sum, a single species interpretation (O. carteri) for this new Bridger B Omomys sample from southern Wyoming is affirmed, and this study illustrates the usefulness of dental data from extant primates for evaluating primate fossil samples.