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Continent-wide effects of urbanization on bird and mammal genetic diversity
Schmidt, Chloé; Domaratzki, Michael; Kinnunen, Riikka; Bowman, Jeff; Garroway, Colin — 2020-01-20 <p>Urbanization and associated<b> </b>environmental changes are causing global declines in vertebrate populations. In general, population declines of the magnitudes now detected should lead to reduced effective population sizes for animals living in proximity to humans and disturbed lands. This is cause for concern because effective population sizes set the rate of genetic diversity loss due to genetic drift, the rate of increase in inbreeding, and the efficiency with which selection can act on beneficial alleles. We predicted that the effects of urbanization should decrease effective population size and genetic diversity, and increase population-level genetic differentiation. To test for such patterns, we repurposed and reanalyzed publicly archived genetic data sets for North American birds and mammals. After filtering, we had usable raw genotype data from 85 studies and 41,023 individuals, sampled from 1,008 locations spanning 41 mammal and 25 bird species. We used census-based urban-rural designations, human population density, and the Human Footprint Index as measures of urbanization and habitat disturbance. As predicted, mammals sampled in more disturbed environments had lower effective population sizes and genetic diversity, and were more genetically differentiated from those in more natural environments. There were no consistent relationships detectable for birds. This suggests that, in general, mammal populations living near humans may have less capacity to respond adaptively to further environmental changes, and be more likely to suffer from effects of inbreeding.</p>
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The population genetics of urban and rural amphibians in North America
Dryad
Schmidt, Chloé; Garroway, Colin — 2021-06-04 <p>Human land transformation is one of the leading causes of vertebrate population declines. These declines are thought to be partly due to decreased connectivity and habitat loss reducing animal population sizes in disturbed habitats. With time, this can lead to declines in effective population size and genetic diversity which restricts the ability of wildlife to efficiently cope with environmental change through genetic adaptation. However, it is not well understood whether these effects generally hold across taxa. We address this question by repurposing and synthesizing raw microsatellite data from online repositories for 19 amphibian species sampled at 554 georeferenced sites in North America. For each site, we estimated gene diversity, allelic richness, effective population size, and population differentiation. Using binary urban-rural census designations, and continuous measures of human population density, the Human Footprint Index, and impervious surface cover, we tested for generalizable effects of human land use on amphibian genetic diversity. We found minimal evidence, either positive or negative, for relationships between genetic metrics and urbanization in our repurposed data. Together with previous work on focal species that also found varying effects of urbanization on genetic composition, it seems likely that the consequences of urbanization are not easily generalizable within or across amphibian species. Questions about the genetic consequences of urbanization for amphibians should be addressed on a case-by-case basis. This contrasts with general negative effects of urbanization in mammals and consistent, but species-specific, positive and negative effects in birds.</p>
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Structural and socioeconomic features of cities predict migratory bird species richness
Dryad
Kinnunen, Riikka; Fraser, Kevin; Schmidt, Chloé; Garroway, Colin — 2023-12-10 <p>Cities are aggregates of human activities where our decisions shape the environment creating heterogeneity across urban centers that can have significant ecological effects on wildlife. Many bird species are found in cities during the breeding season, which implies they find sufficient resources in cities to support them during this energetically costly time. As populations of many migratory bird species are declining, knowledge of how they are affected by urbanization is needed. Yet, we know little about how the species richness of migratory birds varies across different types of cities. Here we ask if cities' structural and socioeconomic features can predict the species richness of migratory birds that generally select different breeding habitats during the breeding season. We used eBird data from census-designated urban areas in the United States to model the relationship between features of cities (housing density, median income, city age, and commuting time), environmental disturbance (measured by the human footprint index) and species richness by fitting generalized linear models to data. We show that commuting time was the most important factor determining species richness across cities and the rest of the city features were weakly associated with species richness. Overall species were responding to city variation in similar ways.  While we expected that cities with more disturbance would have lower species richness, our results indicate that some species are able to tolerate even highly disturbed cities and that cities in certain regions may act as a refuge to birds. This knowledge is important for our general understanding of cities as habitat for birds and how migratory birds respond to across-city variation during the breeding season.</p>
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Evidence for an extreme founding effect in a highly successful invasive species: data and R code
Dryad
Waterman, Jane; Kratzer, Kateryna; van der Marel, Annemarie; Garroway, Colin; López-Darias, Marta; Petersen, Stephen — 2020-08-15 <p>The adaptive potential of invasive species is  thought to decrease during founding events due to reduced genetic diversity, limiting the new population’s ability to colonize novel habitats. Barbary ground squirrels (<i>Atlantoxerus getulus</i>) were purportedly introduced as a single breeding pair to the island of Fuerteventura but have expanded to over a million individuals spread across the island in just over 50 years. We estimated the number of founders and measured the level of genetic diversity in this population using the mitochondrial displacement loop and microsatellite markers. Island samples (<i>n</i> = 19) showed no variation in the d-loop, suggesting a single founding female, while Moroccan samples (<i>n</i> = 6) each had unique mitochondrial haplotypes. The microsatellite data of the island population (<i>n</i> = 256 individuals) revealed a small effective population size, low levels of heterozygosity, and high levels of inbreeding, supporting a founding population size of two to three individuals. Our results suggest that <i>A. getulus</i> has undergone an intense genetic bottleneck during their colonization of the island. They are one of the few species where introduction effort does not explain invasion success, although further investigation may explain how they have avoided the worst expected effects following an extreme genetic bottleneck.</p>
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Canadian Arctic narwhal and bowhead whale genomic variants
Zenodo
de Greef, Evelien; Müller, Claudio; Thorstensen, Matt; Ferguson, Steven; Watt, Cortney; Marcoux, Marianne; Petersen, Stephen; Garroway, Colin — 2024-09-20 This dataset contains resequencing data used in our Arctic whale genomics research exaiming population structure and demographic history in bowhead whales and narwhal, including unfiltered genomic variants and filtered SNPs. Source code for genomic analyses is available at github.com/edegreef/arctic-whales-resequencing. Data uploaded here contain: bowhead_sample_info.csv - metadata for bowhead whale samples bowhead_RWmap_allvariants.vcf.gz - all variant calls in bowhead whales, including indels and SNPs (n = 21) bowhead_RWmap_snps.filtered.autosomes.vcf.gz - bowhead whale SNPs filtered for quality, bi-allelic sites, and autosomes (n = 21) bowhead_RWmap_snps.filtered.autosomes.hwe_maf_LDprunedr08_n20.vcf.gz - bowhead whale SNPs filtered for quality, bi-allelic sites, out of HWE, MAF > 0.05, LD-pruned, removal of close kin (n = 20). narwhal_sample_info.csv - metadata for narwhal samples narwhal_allvariants.vcf.gz - all variant calls in narwhals, including indels and SNPs for bowhead whales (n = 62*) narwhal_snps.filtered.autosomes.vcf.gz - narwhal SNPs filtered for quality, bi-allelic sites, and autosomes (n = 62*) narwhal_snps.filtered.autosomes.hwe_maf_LDprunedr08_n57.vcf.gz - narwhal SNPs filtered for quality, bi-allelic sites, out of HWE, MAF > 0.05, LD-pruned, removal of duplicates, close kin, and samples with high missingness (n = 57) The asterisk* is to note this includes 2 duplicate samples that were removed from the analyses and respective manuscript. https://creativecommons.org/licenses/by/4.0/legalcode

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(Author: Garroway, Colin)

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