Counting calories in cormorants : dynamic body acceleration predicts daily energy expenditure measured in pelagic cormorants

The doubly-labelled water assays and accelerometers were paid for by the authors. Funding to reach Middleton Island was supported through the Animal Behaviour Society Research Grant and the Northern Scientific Training Program of Indigenous and Northern Affairs Canada.Peer reviewedPublisher PD

Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses

Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013–2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally

The ecology and fitness consequences of gut microbiome variation in Sable Island feral horses (Equus caballus)

Gut microbiomes are understood to be integral to the ecology and evolution of animal life, but until very recently, the scientific literature has lacked robust empirical characterization of the host genetic basis and fitness consequences of microbiome variation within wild animal populations. As a closed population of free-living but exhaustively surveyed fate-known individuals which are obligately reliant on their gut microbiomes, the feral horses of Sable Island (Nova Scotia) provide a tractable study system in which to study the ecology, host-to-host transmission, and fitness consequences of microbiome variation in the wild. In this thesis, I begin by characterizing the ecological determinants of the Sable Island horse hindgut microbiome (Chapter 2) and validate the use of shallow shotgun metagenomic sequencing methods for characterizing diverse microbial communities in the horse hindgut (Chapter 3). In applying a shallow shotgun metagenomic sequencing method to a dataset of 2394 fecal samples from 794 individuals spanning 7 years of collection, I find evidence that variation the gut microbiome is visible to host-level selection (Chapter 4). Further quantitative genetic analyses of these data reveal that microbiome features are weakly heritable on average (Chapter 5), suggesting a limited capacity for the microbiome to rapidly respond to selection; but animal model and eco-phylogenetic null model results independently provide evidence that the social dispersal of microbes between horses is an important determinant of microbiome structure. Furthermore, the microbiota which show the strongest evidence for social structuring are those which are most consequential for horse survival. These findings support hypotheses that non-genetic inheritance mechanisms (microbe dispersal) could critically underlie the ability for microbiomes to adaptively respond to selection on ecologically-relevant timescales. However, host inbreeding may constrain the capacity for microbiome variation to adaptively respond to host-level selection, since microbe responses to inbreeding were negatively associated with the estimated effects of those same microbiota on horse survival (Chapter 6). The proximate environmental and host genetic mechanisms underpinning microbiome variation, patterns of context-specific selection, and strain-level transmission remain to be characterized in detail. Nonetheless, this thesis contains tentative but important empirical milestones in describing the eco-evolutionary significance of host-associated microbiomes in the wild

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

Abstract 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

Seasonal dynamics in the mammalian microbiome between disparate environments

Abstract Host‐associated bacterial microbiomes can facilitate host acclimation to seasonal environmental change and are hypothesized to help hosts cope with recent anthropogenic environmental perturbations (e.g., landscape modification). However, it is unclear how recurrent and recent forms of environmental change interact to shape variation in the microbiome. The majority of wildlife microbiome research occurs within a single seasonal context. Meanwhile, the few studies of seasonal variation in the microbiome often restrict focus to a single environmental context. By sampling urban and exurban eastern grey squirrel populations in the spring, summer, autumn, and winter, we explored whether seasonal rhythms in the grey squirrel gut microbiome differed across environments using a 16S amplicon sequencing approach. Differences in the microbiome between urban and exurban squirrels persisted across most of the year, which we hypothesize is linked to anthropogenic food consumption, but we also observed similarities in the urban and exurban grey squirrel microbiome during the autumn, which we attribute to engrained seed caching instincts in preparation for the winter. Host behaviour and diet selection may therefore be capable of maintaining similarities in microbiome structure between disparate environments. However, the depletion of an obligate host mucin glycan specialist (Akkermansia) during the winter in both urban and exurban squirrels was among the strongest differential abundance patterns we observed. In summary, urban grey squirrels showed different seasonal patterns in their microbiome than squirrels from exurban forests; however, in some instances, host behaviour and physiological responses might be capable of maintaining similar microbiome responses across seasons

Data from: Stress and the microbiome: linking glucocorticoids to bacterial community dynamics in wild red squirrels

Bacterial diversity within animals is emerging as an essential component of health, but it is unknown how stress may influence the microbiome. We quantify a proximate link between the oral microbiome and hypothalamic–pituitary–adrenal (HPA) axis activity using faecal glucocorticoid metabolites (FGM) in wild red squirrels (Tamiasciurus hudsonicus). Not only was bacterial diversity lower at higher levels of FGM, but also between capture periods a change in bacterial relative abundance was related to an increase in FGM. These linkages between the HPA axis and microbiome communities represent a powerful capacity for stress to have multi-dimensional effects on health

SRA #SRP064395

Oral microbiome sequence dat

Squirrel FGM concentrations

Fecal glucocorticoid metabolite concentration

Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel (Sciurus carolinensis)

Urbanization is a persistent and widespread driver of global environmental change, potentially shaping evolutionary processes due to genetic drift and reduced gene flow in cities induced by habitat fragmentation and small population sizes. We tested this prediction for the eastern grey squirrel (Sciurus carolinensis), a common and conspicuous forest-dwelling rodent, by obtaining 44K SNPs using reduced representation sequencing (ddRAD) for 403 individuals sampled across the species' native range in eastern North America. We observed moderate levels of genetic diversity, low levels of inbreeding, and only a modest signal of isolation-by-distance. Clustering and migration analyses show that estimated levels of migration and genetic connectivity were higher than expected across cities and forested areas, specifically within the eastern portion of the species' range dominated by urbanization, and genetic connectivity was less than expected within the western range where the landscape is fragmented by agriculture. Landscape genetic methods revealed greater gene flow among individual squirrels in forested regions, which likely provide abundant food and shelter for squirrels. Although gene flow appears to be higher in areas with more tree cover, only slight discontinuities in gene flow suggest eastern grey squirrels have maintained connected populations across urban areas in all but the most heavily fragmented agricultural landscapes. Our results suggest urbanization shapes biological evolution in wildlife species depending strongly on the composition and habitability of the landscape matrix surrounding urban areas