Widespread genetic connectivity of feral pigeons across the Northeastern megacity

Carlen, Elizabeth J.; Munshi‐South, Jason

doi:10.1111/eva.12972

Cited by 33 publications

(30 citation statements)

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“…We used K-means clustering of principal components for K = 1 to K = 5 and Bayesian Information Criteria (BICs) to assess the optimal number of genetic clusters. The value of K with the lowest BIC value was considered optimal 66 . DAPC was applied using the Adegenet package 2.1.1 in R (52).…”

Section: Methodsmentioning

confidence: 99%

Extreme philopatry and genetic diversification at unprecedented scales in a seabird

Danckwerts

Humeau

Pinet

et al. 2021

Sci Rep

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Effective conservation requires maintenance of the processes underlying species divergence, as well as understanding species’ responses to episodic disturbances and long-term change. We explored genetic population structure at a previously unrecognized spatial scale in seabirds, focusing on fine-scale isolation between colonies, and identified two distinct genetic clusters of Barau’s Petrels (Pterodroma baraui) on Réunion Island (Indian Ocean) corresponding to the sampled breeding colonies separated by 5 km. This unexpected result was supported by long-term banding and was clearly linked to the species’ extreme philopatric tendencies, emphasizing the importance of philopatry as an intrinsic barrier to gene flow. This implies that loss of a single colony could result in the loss of genetic variation, impairing the species’ ability to adapt to threats in the long term. We anticipate that these findings will have a pivotal influence on seabird research and population management, focusing attention below the species level of taxonomic organization.

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Section: Methodsmentioning

confidence: 99%

Extreme philopatry and genetic diversification at unprecedented scales in a seabird

Danckwerts

Humeau

Pinet

et al. 2021

Sci Rep

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“…For example, the phyllosphere microbiota of trees-with which squirrels closely associate-are themselves affected by urbanization [28]. Finally, the near-constant exchange of people and resources between cities facilitates gene ow and prevent the genetic isolation of urban wildlife populations [110,111]. A similar mechanism might allow for greater bacterial dispersal between cities than between isolated rural forest fragments.…”

Section: Discussionmentioning

confidence: 99%

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

Stothart

Newman

2021

Preprint

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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.

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“…For example, the phyllosphere microbiota of trees-with which squirrels closely associate-are themselves affected by urbanization [28]. Finally, the near-constant exchange of people and resources between cities facilitates gene flow and prevent the genetic isolation of urban wildlife populations [110,111]. A similar mechanism might allow for greater bacterial dispersal between cities than between isolated rural forest fragments.…”

Section: Discussionmentioning

confidence: 99%

Shades of grey: Coat-colour dependent effect of urbanization on the bacterial microbiome of a wild mammal

Stothart

Newman

2021

Preprint

View full text Add to dashboard Cite

Background: Host-associated microbiota can be fundamental to the ecology of their host and may even help wildlife species colonize novel niches or 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 both 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). Many of the bacterial genera identified as characterizing the microbiomes of built-environment squirrels are though 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 phylogenetic 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, and therefore putatively, host physiology. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide an ideal free-living system with which to study how host genetics mediate environment x microbiome interactions.

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Widespread genetic connectivity of feral pigeons across the Northeastern megacity

Cited by 33 publications

References 100 publications

Extreme philopatry and genetic diversification at unprecedented scales in a seabird

Extreme philopatry and genetic diversification at unprecedented scales in a seabird

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

Shades of grey: Coat-colour dependent effect of urbanization on the bacterial microbiome of a wild mammal

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