DOI: 10.5061/dryad.c0282c8
title: Data from: Genetics of urban colonization: neutral and adaptive variation in coyotes (Canis latrans) inhabiting the New York metropolitan area

description: Theory predicts that range expansion results in genetic diversity loss in
 colonizing populations. Rapid reduction of population size exacerbates
 negative effects of genetic drift, while sustained isolation decreases
 neutral variation. Amid this demographic change, natural selection can act
 to maintain functional diversity. Thus, characterizing neutral and
 functional variation is critical for disentangling the evolutionary forces
 that shape genetic variation in newly established populations. Coyotes
 (Canis latrans) provide an ideal study system for examining the genetic
 effects of urban colonization. Capable of thriving in environments ranging
 from natural to highly urbanized, this mobile carnivore recently
 established a breeding population in New York City (NYC), one of the most
 densely populated areas in the United States. In the present study, we
 characterized neutral and functionally linked genetic diversity on a
 regional scale, traversing NYC and its surrounding counties in the New
 York metropolitan area. We report decreased variation and significant
 genotypic differentiation in NYC coyotes following recent colonization of
 this super-urban environment. In accordance with our hypotheses, we
 observed evidence for a recent population bottleneck as coyotes entered
 NYC. Counter to our expectations, we found only minimal support for
 selection maintaining diversity at immune-linked loci. These findings
 suggest that stochastic processes, such as genetic drift, are more likely
 driving patterns of decreased variation in super-urban coyotes. This work
 not only improves our understanding of NYC’s newest inhabitants, but also
 contributes to the growing body of knowledge surrounding urban
 colonization ecology. It highlights the importance of examining both
 neutral and functional variation when assessing the roles of drift and
 selection in newly established populations. When combined with similar
 studies across diverse systems, these insights can aid wildlife management
 and green design to better facilitate gene flow and maintain healthy
 populations of wildlife in an increasingly urban world.
description: MHC-linked
 microsatellite genotypesThis data file contains
 genotypes for 14 microsatellite markers linked to major histocompatibility
 complex (MHC) genes that were genotyped in 105 coyotes (Canis latrans)
 sampled in New York, New Jersey, and Connecticut. Metadata includes sample
 identification number and urbanization subgroup. The two subgroups include
 coyotes sampled within New York City (NYC) and outside of NYC (non-NYC).
 Please see the map provided in Figure 1 to better visualize sampling
 locations. Missing genotype data is indicated with
 zeros.tristate_coyote_MHC_msat_genotypes_2019.01.22.xlsxNeutral microsatellite genotypesThis data file contains genotypes for nine neutral microsatellite markers that were genotyped in 105 coyotes (Canis latrans) sampled in New York, New Jersey, and Connecticut. Metadata includes sample identification number and urbanization subgroup. The two subgroups include coyotes sampled within New York City (NYC) and outside of NYC (non-NYC). Please see the map provided in Figure 1 to better visualize sampling locations. Missing genotype data is indicated with zeros.tristate_coyote_neutral_msat_genotypes_2019.01.22.xlsx