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1. Urbanization alters small rodent community composition but not abundance

   https://doi.org/10.7717/peerj.4885  

   Alvarez Guevara, Jessica N. ; Ball, Becky A. ( January 2018 , PeerJ)

   Desert ecosystems are one of the fastest urbanizing areas on the planet. This rapid shift has the potential to alter the abundances and species richness of herbivore and plant communities. Herbivores, for example, are expected to be more abundant within urban desert remnant parks located within cities due to anthropogenic activities that concentrate food resources and reduce native predator populations. Despite this assumption, previous research conducted around Phoenix, AZ, USA has shown that top-down herbivory led to equally reduced plant biomass in both urban and outlying locations. It is unclear if this insignificant difference in herbivory at urban and outlying sites is due to unaltered desert herbivore populations or altered activity levels that counteract abundance differences. Small rodent herbivore/granivore populations were surveyed at four sites inside and four sites outside of the core of Phoenix during fall 2014 and spring 2015 in order to determine whether abundances and richness differ significantly between urban and rural sites. In order to survey species composition and abundance at these sites, 100 Sherman traps and eight larger wire traps that are designed to attract and capture small vertebrates such as mice, rats, and squirrels were set at each site for two consecutive trap nights.more »Results suggest that the commonly assumed effect of urbanization on herbivore abundances does not apply to small rodent populations in a desert city, as overall small rodent abundances were statistically similar regardless of location. Though a significant difference was not found for species richness, a significant difference between small rodent genus richness at these sites was observed, with altered community composition. The compositional differences likely reflect the altered vegetative community and may impact ecological interactions at these sites.« less
2. An urban diet differentially alters the gut microbiome and metabolomic profiles compared with a seed diet in mourning doves

   https://doi.org/10.1152/ajpregu.00323.2021  

   Mohr, Alex E. ; Basile, Anthony J. ; Sweazea, Karen L. ( October 2022 , American Journal of Physiology-Regulatory, Integrative and Comparative Physiology)

   Urbanization influences food quality and availability for many avian species, with increased access to human refuse and food subsidies in built environments. In relation to such nutritional intakes and their presumed impact on microbes harbored in the intestinal tract and metabolic profiles of host physiological systems, our overall knowledge of the role of gut microbiome (GM) and metabolomic expression in the avian host lags far behind our understanding of mammals. Therefore, the objective of this investigation was to examine the potential differential effect of an urban modeled versus control (i.e., bird seed) diet on the GM, the metabolic profiles of plasma, liver, adipose, kidney, and muscle tissues, and circulating endotoxin and inflammatory factors in urban-caught mourning doves ( Zenaida macroura). We hypothesized that the urban diet would differently impact the profiles of the GM and tissue metabolomes and increase plasma lipopolysaccharide (LPS) and proinflammatory factors compared with animals fed a seed diet. After a 4-wk-diet period, contents of the large intestine were sequenced to profile the microbiome, metabolomic analyses were performed on plasma and tissue homogenates, and circulating LPS and inflammatory markers were assessed. The composition of the GM was significantly dissimilar between diets, with greater abundance of Erysipelatoclostridiaceae, Sanguibacteraceae,more »Oribacterium, and Sanguibacter and decreased circulating LPS in the urban-fed birds. These differences were largely not reflected in the surveyed metabolomes and plasma inflammatory markers. This research supports the notion that the microbial composition in urban doves is impacted by diet, though may only weakly associate with host physiology.« less
3. Variation in Hematological Indices, Oxidative Stress, and Immune Function Among Male Song Sparrows From Rural and Low-Density Urban Habitats

   https://doi.org/10.3389/fevo.2022.817864  

   Goodchild, Christopher G. ; VanDiest, Isaac ; Lane, Samuel J. ; Beck, Michelle ; Ewbank, Hallum ; Sewall, Kendra B. ( February 2022 , Frontiers in Ecology and Evolution)

   A central theme in the field of ecology is understanding how environmental variables influence a species’ distribution. In the last 20 years, there has been particular attention given to understanding adaptive physiological traits that allow some species to persist in urban environments. However, there is no clear consensus on how urbanization influences physiology, and it is unclear whether physiological differences in urban birds are directly linked to adverse outcomes or are representative of urban birds adaptively responding to novel environmental variables. Moreover, though low-density suburban development is the fastest advancing form of urbanization, most studies have focused on animals inhabiting high intensity urban habitats. In this study, we measured a suite of physiological variables that reflect condition and immune function in male song sparrows ( Melospiza melodia ) from rural and suburban habitats. Specifically, we measured hematological indices [packed cell volume (PCV), hemoglobin concentration, mean corpuscular hemoglobin concentration (MCHC)], circulating glutathione (total, reduced, and oxidized), oxidative damage (d-ROM concentration), antioxidant capacity, and components of the innate immune system [bacteria killing ability (BKA), white blood cell counts]. We also measured whole-animal indices of health, including body condition (scaled mass index length) and furcular fat. Song sparrows inhabiting suburban environments exhibited lowermore »hemoglobin and MCHC, but higher body condition and furcular fat scores. Additionally, suburban birds had higher heterophil counts and lower lymphocyte counts, but there were no differences in heterophil:lymphocyte ratio or BKA between suburban and rural birds. PCV, glutathione concentrations, and oxidative damage did not differ between suburban and rural sparrows. Overall, suburban birds did not exhibit physiological responses suggestive of adverse outcomes. Rather, there is some evidence that sparrows from rural and suburban habitats exhibit phenotypic differences in energy storage and metabolic demand, which may be related to behavioral differences previously observed in sparrows from these populations. Furthermore, this study highlights the need for measuring multiple markers of physiology across different types of urban development to accurately assess the effects of urbanization on wildlife.« less
4. The precautionary principle and dietary DNA metabarcoding: commonly used abundance thresholds change ecological interpretation

   https://doi.org/10.5061/dryad.kwh70rz4s  

   Littleford-Colquhoun, Bethan ; Freeman, Patrick ; Sackett, Violet ; Tulloss, Camille ; McGarvey, Lauren ; Geremia, Chris ; Kartzinel, Tyler ( January 2021 )

   Abstract

   Dietary DNA metabarcoding enables researchers to identify and characterize trophic interactions with a high degree of taxonomic precision. It is also sensitive to sources of bias and contamination in the field and lab. One of the earliest and most common strategies for dealing with such sensitivities has been to filter resulting sequence data to remove low-abundance sequences before conducting ecological analyses based on the presence or absence of food taxa. Although this step is now often perceived to be both necessary and sufficient for cleaning up datasets, evidence to support this perception is lacking and more attention needs to be paid to the related risk of introducing other undesirable errors. Using computer simulations, we demonstrate that common strategies to remove low-abundance sequences can erroneously eliminate true dietary sequences in ways that impact downstream dietary inferences. Using real data from well-studied wildlife populations in Yellowstone National Park, we further show how these strategies can markedly alter the composition of individual dietary profiles in ways that scale-up to obscure ecological interpretations about dietary generalism, specialism, and niche partitioning. Although the practice of removing low-abundance sequences may continue to be a useful strategy to address a subset of research questions that focus on a subset of relatively abundant food resources, its continued widespread use risks generating misleading perceptions about the structure of trophic networks. Researchers working with dietary DNA metabarcoding data—or similar data such as environmental DNA, microbiomes, or pathobiomes—should be aware of potential drawbacks and consider alternative bioinformatic, experimental, and statistical solutions.
   

   Methods

   We used fecal DNA metabarcoding to characterize the diets of bison and bighorn sheep in winter and summer. Our analyses are based on 35 samples (median per species per season = 10) analyzed using the P6 loop of the chloroplast trnL(UAA) intron together with publicly available plant reference data (Illumina sequence read data are available at NCBI (BioProject: PRJNA780500)). Obicut was used to trim reads with a minimum quality threshold of 30, and primers were removed from forward and reverse reads using cutadapt. All further sequence identifications were performed using obitools; forward and reverse sequences were aligned using the illuminapairedend command using a minimum alignment score of 40, and only joined sequences retained. We used the obiuniq command to group identical sequences and tally them within samples, enabling us to quantify the relative read abundance (RRA) of each sequence. Sequences that occurred ≤2 times overall or that were ≤8 bp were discarded. Sequences were considered to be likely PCR artifacts if they were highly similar to another sequence (1 bp difference) and had a much lower abundance (0.05%) in the majority of samples in which they occurred; we discarded these sequences using the obiclean command. Overall, we characterized 357 plant sequences and a subset of 355 sequences were retained in the dataset after rarefying samples to equal sequencing depth. We then applied relative read abundance thresholds from 0% to 5% to the fecal samples. We compared differences in the inferred dietary richness within and between species based on individual samples, based on average richness across samples, and based on the total richness of each population after accounting for differences in sample size.
   

   Other

   The readme file contains an explanation of each of the variables in the dataset. Information on the methodology can be found in the associated manuscript referenced above. 
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5. Urban colonization through multiple genetic lenses: The city‐fox phenomenon revisited

   https://doi.org/10.1002/ece3.4898  

   DeCandia, Alexandra L. ; Brzeski, Kristin E. ; Heppenheimer, Elizabeth ; Caro, Catherine V. ; Camenisch, Glauco ; Wandeler, Peter ; Driscoll, Carlos ; vonHoldt, Bridgett M. ( January 2019 , Ecology and Evolution)

   Urbanization is driving environmental change on a global scale, creating novel environments for wildlife to colonize. Through a combination of stochastic and selective processes, urbanization is also driving evolutionary change. For instance, difficulty in traversing human‐modified landscapes may isolate newly established populations from rural sources, while novel selective pressures, such as altered disease risk, toxicant exposure, and light pollution, may further diverge populations through local adaptation. Assessing the evolutionary consequences of urban colonization and the processes underlying them is a principle aim of urban evolutionary ecology. In the present study, we revisited the genetic effects of urbanization on red foxes (Vulpes vulpes) that colonized Zurich, Switzerland. Through use of genome‐wide single nucleotide polymorphisms and microsatellite markers linked to the major histocompatibility complex (MHC), we expanded upon a previous neutral microsatellite study to assess population structure, characterize patterns of genetic diversity, and detect outliers associated with urbanization. Our results indicated the presence of one large evolutionary cluster, with substructure evident between geographic sampling areas. In urban foxes, we observed patterns of neutral and functional diversity consistent with founder events and reported increased differentiation between populations separated by natural and anthropogenic barriers. We additionally reported evidence of selection acting on MHC‐linkedmore »markers and identified outlier loci with putative gene functions related to energy metabolism, behavior, and immunity. We concluded that demographic processes primarily drove patterns of diversity, with outlier tests providing preliminary evidence of possible urban adaptation. This study contributes to our overall understanding of urban colonization ecology and emphasizes the value of combining datasets when examining evolutionary change in an increasingly urban world.

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