Widespread genetic connectivity of feral pigeons across the Northeastern megacity

Environmental and social correlates of the plumage color polymorphism in an urban dweller, feral pigeon (Columba livia f. domestica)

We examined how urban environments affect the abundance, proportion, and diversity of plumage color morphs in feral pigeons. Five major plumage color morphs (black, blue, white, red, and mixed) were counted in sixty 25-ha plots in Poznań City (Poland). Generalized additive models were used to study the correlations among abundance, proportion of morphs, and environmental factors. Anthropogenic food sources were positively correlated with the abundance of black morphs and the proportions of black and red morphs. The blue morph abundance peaked at a moderate percentage of tall building cover, but its proportion decreased. A similar decrease was observed in the mixed plumage morphs. The abundance of blue morphs decreased, whereas the abundance of white morphs and the proportion of red morphs increased as the distance from the city center increased. The plumage color morph diversity (Simpson) index was positively correlated with food sources and hedgerow density but negatively correlated with street density. Color morph diversity in the study area may be sustained by differential responses of morphs to the environmental features of the urban environment. However, the positive correlation between the abundance of morphs indicates social attraction rather than social isolation among plumage color morphs.

Does urbanisation lead to parallel demographic shifts across the world in a cosmopolitan plant?

Urbanisation is occurring globally, leading to dramatic environmental changes that are altering the ecology and evolution of species. In particular, the expansion of human infrastructure and the loss and fragmentation of natural habitats in cities is predicted to increase genetic drift and reduce gene flow by reducing the size and connectivity of populations. Alternatively, the 'urban facilitation model' suggests that some species will have greater gene flow into and within cities leading to higher diversity and lower differentiation in urban populations. These alternative hypotheses have not been contrasted across multiple cities. Here, we used the genomic data from the GLobal Urban Evolution project (GLUE), to study the effects of urbanisation on non-adaptive evolutionary processes of white clover (Trifolium repens) at a global scale. We found that white clover populations presented high genetic diversity and no evidence of reduced Ne linked to urbanisation. On the contrary, we found that urban populations were less likely to experience a recent decrease in effective population size than rural ones. In addition, we found little genetic structure among populations both globally and between urban and rural populations, which showed extensive gene flow between habitats. Interestingly, white clover displayed overall higher gene flow within urban areas than within rural habitats. Our study provides the largest comprehensive test of the demographic effects of urbanisation. Our results contrast with the common perception that heavily altered and fragmented urban environments will reduce the effective population size and genetic diversity of populations and contribute to their isolation.

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.

Population structure and hybridisation in a population of Hawaiian feral chickens

Chickens are believed to have inhabited the Hawaiian island of Kauai since the first human migrations around 1200AD, but numbers have peaked since the tropical storms Iniki and Iwa in the 1980s and 1990s that destroyed almost all the chicken coops on the island and released large numbers of domestic chickens into the wild. Previous studies have shown these now feral chickens are an admixed population between Red Junglefowl (RJF) and domestic chickens. Here, using genetic haplotypic data, we estimate the time of the admixture event between the feral population on the island and the RJF to 1981 (1976-1995), coinciding with the timings of storm Iwa and Iniki. Analysis of genetic structure reveals a greater similarity between individuals inhabiting the northern and western part of the island to RJF than individuals from the eastern part of the island. These results point to the possibility of introgression events between feral chickens and the wild chickens in areas surrounding the Koke'e State Park and the Alaka'i plateau, posited as two of the major RJF reservoirs in the island. Furthermore, we have inferred haplotype blocks from pooled data to determine the most plausible source of the feral population. We identify a clear contribution from RJF and layer chickens of the White Leghorn (WL) breed. This work provides independent confirmation of the traditional hypothesis surrounding the origin of the feral populations and draws attention to the possibility of introgression of domestic alleles into the wild reservoir.

Going Wild in the City-Animal Feralization and Its Impacts on Biodiversity in Urban Environments

Domestication describes a range of changes to wild species as they are increasingly brought under human selection and husbandry. Feralization is the process whereby a species leaves the human sphere and undergoes increasing natural selection in a wild context, which may or may not be geographically adjacent to where the originator wild species evolved prior to domestication. Distinguishing between domestic, feral, and wild species can be difficult, since some populations of so-called "wild species" are at least partly descended from domesticated "populations" (e.g., junglefowl, European wild sheep) and because transitions in both directions are gradual rather than abrupt. In urban settings, prior selection for coexistence with humans provides particular benefit for a domestic organism that undergoes feralization. One risk is that such taxa can become invasive not just at the site of release/escape but far away. As humanity becomes increasingly urban and pristine environments rapidly diminish, we believe that feralized populations also hold conservation value.

Moving past the challenges and misconceptions in urban adaptation research

Although the field of urban evolutionary ecology has recently expanded, much progress has been made in identifying adaptations that arise as a result of selective pressures within these unique environments. However, as studies within urban environments have rapidly increased, researchers have recognized that there are challenges and opportunities in characterizing urban adaptation. Some of these challenges are a consequence of increased direct and indirect human influence, which compounds long-recognized issues with research on adaptive evolution more generally. In this perspective, we discuss several common research challenges to urban adaptation related to (1) methodological approaches, (2) trait-environment relationships and the natural history of organisms, (3) agents and targets of selection, and (4) habitat heterogeneity. Ignoring these challenges may lead to misconceptions and further impede our ability to draw conclusions regarding evolutionary and ecological processes in urban environments. Our goal is to first shed light on the conceptual challenges of conducting urban adaptation research to help avoid the propagation of these misconceptions. We further summarize potential strategies to move forward productively to construct a more comprehensive picture of urban adaptation, and discuss how urban environments also offer unique opportunities and applications for adaptation research.

Genetic Structure of Racing Pigeons (Columba livia) Kept in Poland Based on Microsatellite Markers

Pigeons played a major role in communication before the invention of the telephone and the telegraph, as well as in wars, where they were used to carry information and orders over long distances. Currently, numerous sports competitions and races are held with their participation, and their breeding is demanding not only for breeders, but also for the birds themselves. Therefore, an analysis of the genetic structure of racing pigeons kept in Poland was undertaken on the basis of 16 microsatellite markers, as well as the evaluation of the microsatellite panel recommended by ISAG. For this purpose, Bayesian clustering, a dendrogram, and Principal Coordinate Analysis were conducted. In addition, statistical analysis was performed. Based on this research, it was observed that racing pigeons are genetically mixed, regardless of their place of origin. Moreover, genetic diversity was estimated at a relatively satisfactory level (Ho = 0.623, He = 0.684), and no alarmingly high inbreeding coefficient was observed (F = 0.088). Moreover, it was found that the panel recommended by ISAG can be successfully used in Poland for individual identification and parentage testing (PIC = 0.639, CE-1P = 0.9987233, CE-2P = 0.9999872, CE-PP = 0.99999999).

A Theory of City Biogeography and the Origin of Urban Species

Many of the choices humans make with regard to infrastructure, urban planning and other phenomena have impacts that will last thousands of years. This can readily be seen in modern cities in which contemporary streets run along street grids that were laid out thousands of years prior or even in which ancient viaducts still play a role. However, rarely do evolutionary biologists explicitly consider the future of life likely to be associated with the decisions we are making today. Here, we consider the evolutionary future of species in cities with a focus on the origin of lineages and species. We do so by adjusting evolutionary predictions from the theory of island biogeography so as to correspond to the unique features of cities as islands. Specifically, the species endemic to cities tend to be associated with the gray habitats in cities. Those habitats tend to be dominated by human bodies, pet bodies and stored food. It is among such species where the origin of new lineages is most likely, although most research on evolution in cities has focused on green habitats. We conclude by considering a range of scenarios for the far future and their implications for the origin of lineages and species.

Population Genomics Analysis with RAD, Reprised: Stacks 2

Restriction enzymes have been one of the primary tools in the population genetics toolkit for 50 years, being coupled with each new generation of technology to provide a more detailed view into the genetics of natural populations. Restriction site-Associated DNA protocols, which joined enzymes with short-read sequencing technology, have democratized the field of population genomics, providing a means to assay the underlying alleles in scores of populations. More than 10 years on, the technique has been widely applied across the tree of life and served as the basis for many different analysis techniques. Here, we provide a detailed protocol to conduct a RAD analysis from experimental design to de novo analysis-including parameter optimization-as well as reference-based analysis, all in Stacks version 2, which is designed to work with paired-end reads to assemble RAD loci up to 1000 nucleotides in length. The protocol focuses on major points of friction in the molecular approaches and downstream analysis, with special attention given to validating experimental analyses. Finally, the protocol provides several points of departure for further analysis.

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.

The Genetic Diversity and Structure of the European Turtle Dove Streptopelia turtur

Simple Summary

The European Turtle Dove, Streptopelia turtur, is a widespread Palearctic species. Due to a long-term population decline, it is listed as vulnerable by the IUCN. Population genetics studies are important to the management of threatened species. Previous research based on mitochondrial DNA cytochrome-b of European Turtle Doves sampled in Western and Southern Europe showed a lack of genetic structure of this species. The present study aimed to identify the possible genetic divergence in the European Turtle Dove. A total of 258 birds collected from Spain, Ukraine, and Morocco were examined using mitochondrial DNA cytochrome-b and D-loop sequence analysis. The high genetic diversity was evaluated in both loci analysed. Various population genetic analyses displayed genetic differences between Turtle Doves from Morocco and Ukraine, and certain Spanish samples. The results of this study will be vital for effective conservation and sustainable management of this vulnerable species.

Abstract

The European Turtle Dove, Streptopelia turtur, a long-distance migrant wintering in Africa, is a widespread Palearctic species. This species is classified as vulnerable and is undergoing a long-term demographic decline. The results of the previous study (based on mitochondrial (mtDNA) cytochrome-b (cytb) sequences of birds from Western and Southern Europe) indicated that the species was not genetically structured. We analysed the mtDNA cytb and D-loop of 258 birds collected from Morocco, Spain, and Ukraine. High genetic variability, expressed by haplotype diversity and nucleotide diversity, was revealed in both cytb (Hd = 0.905 ± 0.009, π = 0.00628 ± 0.00014) and the D-loop (Hd = 0.937 ± 0.009, π = 0.01502 ± 0.00034). SAMOVA and principal coordinates analysis revealed the birds belonged to two genetically distinct groups. One group included birds collected in Spain, while birds sampled in Morocco and Ukraine formed another group. Furthermore, significant genetic differentiation was identified between Turtle Doves from Morocco and Ukraine, and certain Spanish samples. The present results indicate that specific management and conservation plans relevant for the species in various regions should be applied. However, further nuclear DNA research and new studies (particularly in Eastern Europe) are necessary for the decisive results on genetic structure of this species.

Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity

The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.

Extreme philopatry and genetic diversification at unprecedented scales in a seabird

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.

Dispersal ability predicts spatial genetic structure in native mammals persisting across an urbanization gradient

As the rate of urbanization continues to increase globally, a growing body of research is emerging that investigates how urbanization shapes the movement-and consequent gene flow-of species in cities. Of particular interest are native species that persist in cities, either as small relict populations or as larger populations of synanthropic species that thrive alongside humans in new urban environments. In this study, we used genomic sequence data (SNPs) and spatially explicit individual-based analyses to directly compare the genetic structure and patterns of gene flow in two small mammals with different dispersal abilities that occupy the same urbanized landscape to evaluate how mobility impacts genetic connectivity. We collected 215 white-footed mice (Peromyscus leucopus) and 380 big brown bats (Eptesicus fuscus) across an urban-to-rural gradient within the Providence, Rhode Island (U.S.A.) metropolitan area (population =1,600,000 people). We found that mice and bats exhibit clear differences in their spatial genetic structure that are consistent with their dispersal abilities, with urbanization having a stronger effect on Peromyscus mice. There were sharp breaks in the genetic structure of mice within the Providence urban core, as well as reduced rates of migration and an increase in inbreeding with more urbanization. In contrast, bats showed very weak genetic structuring across the entire study area, suggesting a near-panmictic gene pool likely due to the ability to disperse by flight. Genetic diversity remained stable for both species across the study region. Mice also exhibited a stronger reduction in gene flow between island and mainland populations than bats. This study represents one of the first to directly compare multiple species within the same urban-to-rural landscape gradient, an important gap to fill for urban ecology and evolution. Moreover, here we document the impacts of dispersal capacity on connectivity for native species that have persisted as the urban landscape matrix expands.

Urban evolution comes into its own: Emerging themes and future directions of a burgeoning field

Urbanization has recently emerged as an exciting new direction for evolutionary research founded on our growing understanding of rapid evolution paired with the expansion of novel urban habitats. Urbanization can influence adaptive and nonadaptive evolution in urban-dwelling species, but generalized patterns and the predictability of urban evolutionary responses within populations remain unclear. This editorial introduces the special feature "Evolution in Urban Environments" and addresses four major emerging themes, which include: (a) adaptive evolution and phenotypic plasticity via physiological responses to urban climate, (b) adaptive evolution via phenotype-environment relationships in urban habitats, (c) population connectivity and genetic drift in urban landscapes, and (d) human-wildlife interactions in urban spaces. Here, we present the 16 articles (12 empirical, 3 review, 1 capstone) within this issue and how they represent each of these four emerging themes in urban evolutionary biology. Finally, we discuss how these articles address previous questions and have now raised new ones, highlighting important new directions for the field.

Feral pigeon populations: their gene pool and links with local domestic breeds

Columba livia is a wild bird whose domestication has led to a large number of pigeon breeds. The occasional loss or straying of domestic birds determined the origin of feral pigeons, which are now widespread all around the world. In this study, we assumed that the main contribution to feral populations is provided by domestic breeds reared in the same areas. We tested this hypothesis by analysing the variability of 12 microsatellite loci in nine Italian feral populations sampled in areas with different intensities of breeding and selecting domestic breeds. We included in the analysis samples belonging to ten domestic lineages commonly bred in Italy. The pattern of geographic differentiation of feral populations turned out to be rather complex and only partially explained by the geographic distance between populations. This pattern can be understood only when the domestic breeds were included in the analysis. In particular, feral populations located in regions with a long-lasting tradition of pigeon breeding showed a high level of admixture with domestic breeds, in particular with Racing Homer and Piacentino. Ferals from Bolzano, Venice and Sassari were characterized by unique genetic components, mostly not shared by other feral populations and by the considered domestic breeds. Our results further emphasize the complex genetic structure of feral populations whose origin can be properly investigated by taking into account the pool of domestic pigeons bred in the considered area.