An Opportunistic Assessment of the Impact of Squirrelpox Disease Outbreaks upon a Red Squirrel Population Sympatric with Grey Squirrels in Wales

Native red squirrels (Sciurus vulgaris) persisted in the coastal mainland woodlands of northern Gwynedd whilst sympatric with an invasive grey squirrel (Sciurus carolinensis) population suppressed by culling. Squirrelpox disease in the red squirrel population was recorded in 2017 and 2020/21. An autumn 2020 outbreak was associated with only 17.4% of animals caught and marked in the preceding June known to be present in March 2021. Despite an opportunistic data collection lacking the rigour of empirical experimental design, we observed low local survival rates similar to previously published accounts reported during major squirrelpox outbreaks. The use of a conservation dog to detect red squirrel carcasses resulted in positive detection and confirmation of a temporal and spatial expansion of one disease outbreak. The study is the first in Wales to use conservation dogs and the findings reinforce the vital strategic importance of geographical isolation reducing sympatry of red with grey squirrels in European regions where the introduced congener is a source of the squirrelpox infection.

Characterization of Triatomine Bloodmeal Sources Using Direct Sanger Sequencing and Amplicon Deep Sequencing Methods

Knowledge of host associations of blood-feeding vectors may afford insights into managing disease systems and protecting public health. However, the ability of methods to distinguish bloodmeal sources varies widely. We used two methods—Sanger sequencing and amplicon deep sequencing—to target a 228 bp region of the vertebrate CYTB gene and determine hosts fed upon by triatomines (n = 115) collected primarily in Texas, USA. Direct sanger sequencing of PCR amplicons was successful for 36 samples (31%). Sanger sequencing revealed 15 distinct host species, which included humans, domestic animals (Canis lupus familiaris, Ovis aries, Gallus gallus, Bos taurus, Felis catus, and Capra hircus), wildlife (Rattus rattus, Bufo nebulifer, Sciurus carolinensis, Sciurus niger, Odocoileus virginianus), and captive animals (Panthera tigris, Colobus spp., Chelonoidis carbonarius). Samples sequenced by the Sanger method were also subjected to Illumina MiSeq amplicon deep sequencing. The amplicon deep sequencing results (average of 302,080 usable reads per sample) replicated the host community revealed using Sanger sequencing, and detected additional hosts in five triatomines (13.9%), including two additional blood sources (Procyon lotor, Bassariscus astutus). Up to four bloodmeal sources were detected in a single triatomine (Bufo nebulifer, Homo sapiens, Canis lupus familiaris, and Sciurus carolinensis). Enhanced understanding of vector-host-parasite networks may allow for integrated vector management programs focusing on highly-utilized and highly-infected host species.

Parallel evolution of urban-rural clines

Urbanization is the dominant trend of global land use change. The replicated nature of environmental change associated with urbanization should drive parallel evolution, yet insight into the repeatability of evolutionary processes in urban areas has been limited by a lack of multi-city studies. Here we leverage community science data on coat color in >60,000 eastern gray squirrels (Sciurus carolinensis) across 43 North American cities to test for parallel clines in melanism, a genetically based trait associated with thermoregulation and crypsis in gray squirrels. We show the prevalence of melanism in these mammals was positively associated with urbanization. Urban-rural clines in melanism were strongest in the largest cities with extensive forest cover and weakest or absent in cities with warm winter temperature, where thermal selection likely limits the prevalence of melanism. Our results demonstrate that novel traits can evolve in a highly repeatable manner among urban areas, modified by factors intrinsic to individual cities, including size, land cover, and climate.

Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal

Background Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization (across three cities) on the microbiome of eastern grey squirrels (Sciurus carolinensis). Grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate). Results Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built-environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations. Conclusions Squirrel microbiomes differed between city and rural environments, but differences of comparable magnitude were observed between land classes at a within-city scale. We did not observe strong evidence that inter-environmental differences were the result of disparate selective pressures. Rather, our results suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. However, these processes were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.

Natural strongholds for red squirrel conservation in Scotland

The Eurasian Red Squirrel (Sciurus vulgaris) is under threat from the invasive North American eastern Grey Squirrel (Sciurus carolinensis) with 80% of the remaining red squirrel populations in the British Isles found in Scotland. In this study we develop a spatially explicit mathematical model of the red and grey squirrel system and use it to assess the population viability of red squirrels across Scotland. In particular, we aim to identify existing forests – natural strongholds for red squirrels – that can successfully support red squirrels under UK Forestry Standard management and protect them from potential disease-mediated competition from grey squirrels. Our model results indicate that if current levels of grey squirrel control, which restrict or reduce the distribution of grey squirrels, are continued then there will be large expanses of forests in northern Scotland that support viable red squirrel populations. Model results that represent (hypothetical) scenarios where grey squirrel control no longer occurred indicated that grey squirrel range expansion and the process of red squirrel replacement would be slow. Model results for an assumed worst-case scenario where grey squirrels have expanded to all regions in Scotland identified forest regions – denoted natural strongholds – that could currently support red squirrels under UK Forestry Standard management practice. The results will be used to inform forest management policy and support a strategic review of red squirrel management by land management agencies and other stakeholders.

Shades of Grey: Host Phenotype Dependent Effect of Urbanization on the Bacterial Microbiome of a Wild Mammal

Background Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization on the microbiome of eastern grey squirrels (Sciurus carolinensis). Eastern grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate). Results Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations. Conclusions Habitat heterogeneity at fine spatial scales affects host-associated microbiomes, however, we found little evidence that this pattern was the result of similar selective pressures acting on the microbiome within environments. Further, this result, those of phylogeny-independent analyses, and patterns of beta-dispersion lead us to suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. These patterns were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.

Novel combination of CRISPR-based gene drives eliminates resistance and localises spread

Invasive species are among the major driving forces behind biodiversity loss. Gene drive technology may offer a humane, efficient and cost-effective method of control. For safe and effective deployment it is vital that a gene drive is both self-limiting and can overcome evolutionary resistance. We present HD-ClvR in this modelling study, a novel combination of CRISPR-based gene drives that eliminates resistance and localises spread. As a case study, we model HD-ClvR in the grey squirrel (Sciurus carolinensis), which is an invasive pest in the UK and responsible for both biodiversity and economic losses. HD-ClvR combats resistance allele formation by combining a homing gene drive with a cleave-and-rescue gene drive. The inclusion of a self-limiting daisyfield gene drive allows for controllable localisation based on animal supplementation. We use both randomly mating and spatial models to simulate this strategy. Our findings show that HD-ClvR could effectively control a targeted grey squirrel population, with little risk to other populations. HD-ClvR offers an efficient, self-limiting and controllable gene drive for managing invasive pests.

Cognitive Performance of Wild Eastern Gray Squirrels (Sciurus carolinensis) in Rural and Urban, Native, and Non-native Environments

Enhanced cognitive ability has been shown to impart fitness advantages to some species by facilitating establishment in new environments. However, the cause of such enhancement remains enigmatic. Enhanced cognitive ability may be an adaptation occurring during the establishment process in response to new environments or, alternatively, such ‘enhancement’ may merely reflect a species’ characteristic. Based on previous findings that have shown ‘enhanced’ cognitive ability (i.e., higher success rate in solving novel food-extraction problems or, ‘innovation’) in Eastern gray squirrels (Sciurus carolinensis), a successful mammalian invader and urban dweller, we used an intraspecific comparative paradigm to examine the cause of their ‘enhanced’ cognitive ability. We conducted a field study to compare cognitive performance of free-ranging squirrels residing in rural and urban habitats in native (United States) and non-native environments (United Kingdom). By using established tasks, we examined squirrels’ performance in easy and difficult, novel food-extraction problems (innovation), a motor memory recall test of the difficult problem, and a spatial learning task. We found that the four groups of squirrels showed comparable performance in most measures. However, we also found that the native urban squirrels showed: (1) higher success rate on the first visit for the difficult problem than the non-native urban squirrels; (2) some evidence for higher recall latency for the difficult problem after an extended period than the non-native rural squirrels; and (3) learning when encountering the same difficult problem. These results suggest that the previously reported ‘enhanced’ performance is likely to be a general characteristic and thus, a pre-adaptive phenotypic trait that brings fitness advantages to this species in a new environment. Despite this, some cognitive abilities in gray squirrels such as solving novel problems has undergone mild variation during the adaptive process in new environments.