Gentrification drives patterns of alpha and beta diversity in cities.

While there is increasing recognition that social processes in cities like gentrification have ecological consequences, we lack nuanced understanding of the ways gentrification affects urban biodiversity. We analyzed a large camera trap dataset of mammals (>500 g) to evaluate how gentrification impacts species richness and community composition across 23 US cities. After controlling for the negative effect of impervious cover, gentrified parts of cities had the highest mammal species richness. Change in community composition was associated with gentrification in a few cities, which were mostly located along the West Coast. At the species level, roughly half (11 of 21 mammals) had higher occupancy in gentrified parts of a city, especially when impervious cover was low. Our results indicate that the impacts of gentrification extend to nonhuman animals, which provides further evidence that some aspects of nature in cities, such as wildlife, are chronically inaccessible to marginalized human populations.

Urbanization, climate and species traits shape mammal communities from local to continental scales.

Human-driven environmental changes shape ecological communities from local to global scales. Within cities, landscape-scale patterns and processes and species characteristics generally drive local-scale wildlife diversity. However, cities differ in their structure, species pools, geographies and histories, calling into question the extent to which these drivers of wildlife diversity are predictive at continental scales. In partnership with the Urban Wildlife Information Network, we used occurrence data from 725 sites located across 20 North American cities and a multi-city, multi-species occupancy modelling approach to evaluate the effects of ecoregional characteristics and mammal species traits on the urbanization-diversity relationship. Among 37 native terrestrial mammal species, regional environmental characteristics and species traits influenced within-city effects of urbanization on species occupancy and community composition. Species occupancy and diversity were most negatively related to urbanization in the warmer, less vegetated cities. Additionally, larger-bodied species were most negatively impacted by urbanization across North America. Our results suggest that shifting climate conditions could worsen the effects of urbanization on native wildlife communities, such that conservation strategies should seek to mitigate the combined effects of a warming and urbanizing world.

Wealth and urbanization shape medium and large terrestrial mammal communities.

Urban biodiversity provides critical ecosystem services and is a key component to environmentally and socially sustainable cities. However, biodiversity varies greatly within and among cities, leading to human communities with changing and unequal experiences with nature. The "luxury effect," a hypothesis that predicts a positive correlation between wealth, typically measured by per capita income, and species richness may be one indication of these inequities. While the luxury effect is well studied for some taxa, it has rarely been investigated for mammals, which provide unique ecosystem services (e.g., biological pest control) and exhibit significant potential for negative human-wildlife interactions (e.g., nuisances or conflicts). We analyzed a large dataset of mammal detections across 20 North American cities to test whether the luxury effect is consistent for medium- to large-sized terrestrial mammals across diverse urban contexts. Overall, support for the luxury effect, as indicated by per capita income, was inconsistent; we found evidence of a luxury effect in approximately half of our study cities. Species richness was, however, highly and negatively correlated with urban intensity in most cities. We thus suggest that economic factors play an important role in shaping urban mammal communities for some cities and species, but that the strongest driver of urban mammal diversity is urban intensity. To better understand the complexity of urban ecosystems, ecologists and social scientists must consider the social and political factors that drive inequitable human experiences with nature in cities.

Landscape-scale differences among cities alter common species' responses to urbanization.

Understanding how biodiversity responds to urbanization is challenging, due in part to the single-city focus of most urban ecological research. Here, we delineate continent-scale patterns in urban species assemblages by leveraging data from a multi-city camera trap survey and quantify how differences in greenspace availability and average housing density among 10 North American cities relate to the distribution of eight widespread North American mammals. To do so, we deployed camera traps at 569 sites across these ten cities between 18 June and 14 August. Most data came from 2017, though some cities contributed 2016 or 2018 data if it was available. We found that the magnitude and direction of most species' responses to urbanization within a city were associated with landscape-scale differences among cities. For example, eastern gray squirrel (Sciurus carolinensis), fox squirrel (Sciurus niger), and red fox (Vulpes vulpes) responses to urbanization changed from negative to positive once the proportion of green space within a city was >~20%. Likewise, raccoon (Procyon lotor) and Virginia opossum (Didelphis virginiana) responses to urbanization changed from positive to negative once the average housing density of a city exceeded about 700 housing units/km2 . We also found that local species richness within cities consistently declined with urbanization in only the more densely developed cities (>~700 housing units/km2 ). Given our results, it may therefore be possible to design cities to better support biodiversity and reduce the negative influence of urbanization on wildlife by, for example, increasing the amount of green space within a city. Additionally, it may be most important for densely populated cities to find innovative solutions to bolster wildlife resilience because they were the most likely to observe diversity losses of common urban species.

What can we learn from wildlife sightings during the COVID-19 global shutdown?

During the worldwide shutdown in response to the COVID-19 pandemic, many reports emerged of urban wildlife sightings. While these images garnered public interest and declarations of wildlife reclaiming cities, it is unclear whether wildlife truly reoccupied urban areas or whether there were simply increased detections of urban wildlife during this time. Here, we detail key questions and needs for monitoring wildlife during the COVID-19 shutdown and then link these with future needs and actions with the intent of improving conservation within urban ecosystems. We discuss the tools ecologists and conservation scientists can use to safely and effectively study urban wildlife during the shutdown. With a coordinated, multicity effort, researchers and community scientists can rigorously investigate the responses of wildlife to changes in human activities, which can help us address long-standing questions in urban ecology, inspire conservation of wildlife, and inform the design of sustainable cities.

Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird.

The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA) while controlling for population structure. Analysis of genome-wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (a) drift in geographic isolation, (b) differentiation along continuous selective gradients and (c) isolation-by-adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci.

Microgeographic morphological variation across larval wood frog populations associated with environment despite gene flow.

Gene flow has historically been thought to constrain local adaptation; yet, recent research suggests that populations can diverge despite exchanging genes. Here I use a common garden experiment to assess the combined effects of gene flow and natural selection on morphological variation of 16 wood frog (Rana sylvatica) populations, a species known to experience divergent selection pressures in open- and closed-canopy ponds across relatively small geographic scales. Wood frog tadpoles from different ponds showed significant morphological variation associated with canopy type with a trade-off between tail length and body depth consistent with previous research. In contrast, neutral genetic differentiation of nine microsatellite loci as measured by Jost's D was not associated with canopy type, indicating no pattern of isolation by environment. Genetic structure analyses indicated some substructure across the 16 ponds (K = 4); however, three out of four assigned clusters included both open- and closed-canopy ponds. Together, these results suggest that morphological divergence among these wood frog populations is occurring despite gene flow and that selection within these environments is strong. Furthermore, morphological variation among ponds differed across two sampling periods during larval development, demonstrating the importance of evaluating phenotypic divergence over multiple time periods and at a time relevant to the processes being studied.

The specific and exclusive microbiome of the deep-sea bone-eating snail, Rubyspira osteovora.

Rubyspira osteovora is an unusual deep-sea snail from Monterey Canyon, California. This group has only been found on decomposing whales and is thought to use bone as a novel source of nutrition. This study characterized the gut microbiome of R. osteovora, compared to the surrounding environment, as well as to other deep-sea snails with more typical diets. Analysis of 16S rRNA gene sequences revealed that R. osteovora digestive tissues host a much lower bacterial diversity (average Shannon index of 1.9; n = 12), compared to environmental samples (average Shannon index of 4.4; n = 2) and are dominated by two bacterial genera: Mycoplasma and Psychromonas (comprising up to 56% and 42% average total recovered sequences, respectively). These two bacteria, along with Psychrilyobacter sp. (∼16% average recovered sequences), accounted for between 43% and 92% of the total recovered sequences in individual snail digestive systems, with other OTUs present at much lower proportions. The relative abundance of these three groups remained similar over 6 years of sampling (collection date was not shown to be a significant predictor of community structure), suggesting a long-term association. Furthermore, these bacterial genera were either not present (Mycoplasma and Psychromonas) or at very low abundance (<0.04% for Psychrilyobacter), in environmental samples and other deep-sea gastropods, supporting the uniqueness of the R. osteovora gut microbiome.

Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province.

The California Floristic Province (CFP) in western North America is a globally significant biodiversity hotspot. Elucidating patterns of endemism and the historical drivers of this diversity has been an important challenge of comparative phylogeography for over two decades. We generated phylogenomic data using ddRADseq to examine genetic structure in Uroctonus forest scorpions, an ecologically restricted and dispersal-limited organism widely distributed across the CFP north to the Columbia River. We coupled our genetic data with species distribution models (SDMs) to determine climatically suitable areas for Uroctonus both now and during the Last Glacial Maximum. Based on our analyses, Uroctonus is composed of two major genetic groups that likely diverged over 2 million years ago. Each of these groups itself contains numerous genetic groups that reveal a pattern of vicariance and microendemism across the CFP. Migration rates among these populations are low. SDMs suggest forest scorpion habitat has remained relatively stable over the last 21 000 years, consistent with the genetic data. Our results suggest tectonic plate rafting, mountain uplift, river drainage formation and climate-induced habitat fragmentation have all likely played a role in the diversification of Uroctonus. The intricate pattern of genetic fragmentation revealed across a temporal continuum highlights the potential of low-dispersing species to shed light on small-scale patterns of biodiversity and the underlying processes that have generated this diversity in biodiversity hotspots.

Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system.

Understanding if the members of an ecological community have co-diversified is a central concern of evolutionary biology, as co-diversification suggests prolonged association and possible coevolution. By sampling associated species from an ecosystem, researchers can better understand how abiotic and biotic factors influence diversification in a region. In particular, studies of co-distributed species that interact ecologically can allow us to disentangle the effect of how historical processes have helped shape community level structure and interactions. Here we investigate the Sarracenia alata pitcher plant system, an ecological community where many species from disparate taxonomic groups live inside the fluid-filled pitcher leaves. Direct sequencing of the eukaryotes present in the pitcher plant fluid enables us to better understand how a host plant can shape and contribute to the genetic structure of its associated inquilines, and to ask whether genetic variation in the taxa are structured in a similar manner to the host plant. We used 454 amplicon-based metagenomics to demonstrate that the pattern of genetic diversity in many, but not all, of the eukaryotic community is similar to that of S. alata, providing evidence that associated eukaryotes share an evolutionary history with the host pitcher plant. Our work provides further evidence that a host plant can influence the evolution of its associated commensals.

Historical Species Distribution Models Predict Species Limits in Western Plethodon Salamanders.

Allopatry is commonly used to predict boundaries in species delimitation investigations under the assumption that currently allopatric distributions are indicative of reproductive isolation; however, species ranges are known to change over time. Incorporating a temporal perspective of geographic distributions should improve species delimitation; to explore this, we investigate three species of western Plethodon salamanders that have shifted their ranges since the end of the Pleistocene. We generate species distribution models (SDM) of the current range, hindcast these models onto a climatic model 21 Ka, and use three molecular approaches to delimit species in an integrated fashion. In contrast to expectations based on the current distribution, we detect no independent lineages in species with allopatric and patchy distributions (Plethodon vandykei and Plethodon larselli). The SDMs indicate that probable habitat is more expansive than their current range, especially during the last glacial maximum (LGM) (21 Ka). However, with a contiguous distribution, two independent lineages were detected in Plethodon idahoensis, possibly due to isolation in multiple glacial refugia. Results indicate that historical SDMs are a better predictor of species boundaries than current distributions, and strongly imply that researchers should incorporate SDM and hindcasting into their investigations and the development of species hypotheses.

Applications of next-generation sequencing to phylogeography and phylogenetics.

This is a time of unprecedented transition in DNA sequencing technologies. Next-generation sequencing (NGS) clearly holds promise for fast and cost-effective generation of multilocus sequence data for phylogeography and phylogenetics. However, the focus on non-model organisms, in addition to uncertainty about which sample preparation methods and analyses are appropriate for different research questions and evolutionary timescales, have contributed to a lag in the application of NGS to these fields. Here, we outline some of the major obstacles specific to the application of NGS to phylogeography and phylogenetics, including the focus on non-model organisms, the necessity of obtaining orthologous loci in a cost-effective manner, and the predominate use of gene trees in these fields. We describe the most promising methods of sample preparation that address these challenges. Methods that reduce the genome by restriction digest and manual size selection are most appropriate for studies at the intraspecific level, whereas methods that target specific genomic regions (i.e., target enrichment or sequence capture) have wider applicability from the population level to deep-level phylogenomics. Additionally, we give an overview of how to analyze NGS data to arrive at data sets applicable to the standard toolkit of phylogeography and phylogenetics, including initial data processing to alignment and genotype calling (both SNPs and loci involving many SNPs). Even though whole-genome sequencing is likely to become affordable rather soon, because phylogeography and phylogenetics rely on analysis of hundreds of individuals in many cases, methods that reduce the genome to a subset of loci should remain more cost-effective for some time to come.

Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata.

We collected ~29 kb of sequence data using Roche 454 pyrosequencing in order to estimate the timing and pattern of diversification in the carnivorous pitcher plant Sarracenia alata. Utilizing modified protocols for reduced representation library construction, we generated sequence data from 86 individuals across 10 populations from throughout the range of the species. We identified 76 high-quality and high-coverage loci (containing over 500 SNPs) using the bioinformatics pipeline PRGmatic. Results from a Bayesian clustering analysis indicate that populations are highly structured, and are similar in pattern to the topology of a population tree estimated using *BEAST. The pattern of diversification within Sarracenia alata implies that riverine barriers are the primary factor promoting population diversification, with divergence across the Mississippi River occurring more than 60,000 generations before present. Further, significant patterns of niche divergence and the identification of several outlier loci suggest that selection may contribute to population divergence. Our results demonstrate the feasibility of using next-generation sequencing to investigate intraspecific genetic variation in nonmodel species.

Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation? Insights from tests with niche models.

The role of ecology in the origin of species has been the subject of long-standing interest to evolutionary biologists. New sources of spatially explicit ecological data allow for large-scale tests of whether speciation is associated with niche divergence or whether closely related species tend to be similar ecologically (niche conservatism). Because of the confounding effects of spatial autocorrelation of environmental variables, we generate null expectations for niche divergence for both an ecological-niche modeling and a multivariate approach to address the question: do allopatrically distributed taxa occupy similar niches? In a classic system for the study of niche evolution--the Aphelocoma jays--we show that there is little evidence for niche divergence among Mexican Jay (A. ultramarina) lineages in the process of speciation, contrary to previous results. In contrast, Aphelocoma species that exist in partial sympatry in some regions show evidence for niche divergence. Our approach is widely applicable to the many cases of allopatric lineages in the beginning stages of speciation. These results do not support an ecological speciation model for Mexican Jay lineages because, in most cases, the allopatric environments they occupy are not significantly more divergent than expected under a null model.