City life alters the gut microbiome and stable isotope profiling of the eastern water dragon ( Intellagama lesueurii )

Urbanisation is one of the most significant threats to biodiversity, due to the rapid and large-scale environmental alterations it imposes on the natural landscape. It is, therefore, imperative that we understand the consequences of and mechanisms by which, species can respond to it. In recent years, research has shown that plasticity of the gut microbiome may be an important mechanism by which animals can adapt to environmental change, yet empirical evidence of this in wild non-model species remains sparse. Using an empirical replicated study system, we show that city life alters the gut microbiome and stable isotope profiling of a wild native non-model species - the eastern water dragon (Intellagama lesueurii) in Queensland, Australia. City dragons exhibit a more diverse gut microbiome than their native habitat counterparts and show gut microbial signatures of a high fat and plant rich diet. Additionally, we also show that city dragons have elevated levels of the Nitrogen-15 isotope in their blood suggesting that a city diet, which incorporates novel anthropogenic food sources, may also be richer in protein. These results highlight the role that gut microbial plasticity plays in an animals' response to human-altered landscapes

Data from: Fresh Is best: accurate SNP genotyping from koala scats

Maintaining genetic diversity is a crucial component in conserving threatened species. For the iconic Australian koala, there is little genetic information on wild populations that is not either skewed by biased sampling methods (e.g. sampling effort skewed towards urban areas) or of limited usefulness due to low numbers of microsatellites used. The ability to genotype DNA extracted from koala scats using next-generation sequencing technology will not only help resolve location sample bias but also improve the accuracy and scope of genetic analyses (e.g. neutral versus adaptive genetic diversity, inbreeding, and effective population size). Here we present the successful SNP genotyping (1272 SNP loci) of koala DNA extracted from scat, using a proprietary DArTseq™ protocol. We compare genotype results from two day old scat DNA and 14 day old scat DNA to a blood DNA template, to test accuracy of scat genotyping. We find that DNA from fresher scat results in fewer loci with missing information than DNA from older scat, however, 14 day old scat can still provide useful genetic information, depending on the research question. We also find that a subset of 209 conserved loci can accurately identify individual koalas, even from older scat samples. In addition, we find that DNA sequences identified from scat samples through the DArTseq™ process can provide genetic identification of koala diet species, bacterial and viral pathogens, and parasitic organisms

Enviro_data_master

File includes environmental variables for Eastern Water Dragon nests and randomly sampled points at Roma Street Parklands. Data is displayed as follows: Nest (1 = presence, 0 = absence), ID of nest or random point, latitude, longitude, compass aspect of the point or nest sampled, slope in degrees, canopy cover, soil compactness (kg/cm), soil type of the nest, top soil, mother of the nest (if known), and season the nest was collected

Data from: Archipelagos of the Anthropocene: rapid and extensive differentiation of native terrestrial vertebrates in a single metropolis

Some of the best evidence for rapid evolutionary change comes from studies of archipelagos and oceanic islands. City parks are analogous systems as they create geographically isolated green spaces that differ in size, structure, and complexity. Very little, however, is known about whether city parks in single urban centres drive selection and result in the diversification of native species. Here, we provide evidence for the rapid genetic and morphological differentiation of a native lizard (Intellagama lesueurii) at four geographically close yet unconnected parks within one city. Year of establishment of each city park varied from 1855 (oldest) to 2001 (youngest) equating to a generation time range of 32 to three generations. Genetic divergence among city park populations was large despite the small pairwise geographic distances (< 5km) and found to be two to three times higher for microsatellites and three to 33 times higher for mtDNA relative to non-urban populations. Patterns of morphological differentiation were also found to be most extensive among the four city park populations. In contrast to non-urban populations, city park populations showed significant differentiation in relative body size, relative head and limb morphology and relative forelimb and hindlimb length. Crucially, we show that these patterns of differentiation are unlikely to have been caused by founder events and/or drift alone. Our results suggest that city park ‘archipelagos’ could represent theatres for rapid evolution that may, in time, favour adaptive diversification

Genotypes_13 markers

Genotypes for four city parks (CP1, CP2 and CP3), three isolated non-urban (INU1, INU2 and INU3) and three connected non-urban populations (CNU1, CNU2 and CNU3) of eastern water dragons (Intellagama lesueurii). 13 microsatellite markers are included (taken from Frere et al., 2012) in the file, File is in the format accepted for GeneALEx

nest depth

Includes nest depth measurements for Eastern Water Dragons at Roma street Parklands over 2016-2017 nesting seasons

Clutch size

Nesting data from 2016-2017 from Eastern Water Dragons at Roma Street Parklands. File includes Nest (1 presence), name of the nest, latitude, longitude, slope measured in degrees, canopy cover, soil compactness (kg/cm), soil type, top soil type, clutch size, mother of the clutch (if known), and season nest was found

Maternal_excursions

File includes data for maternal excursions for Eastern Water Dragons at Roma Street Parklands. Data is as follows: ID of nest, maternal ID, total area of mothers 95% KUD (home range), proportion of sand in that home range, proportion of loam in that home range, number of points sampled in home range, number of loam points sampled in home range, number of sand points sampled in home range, nest soil type, excursion behaviour of mother (1 = nesting excursion, 0 = no excursion), length of the excursion, log transformed length of excursion, and log10 transformed length

Data from: Maternal nesting behaviour in city dragons: a species with temperature-dependent sex determination

Urban environments present some of the greatest challenges to species survival. This is particularly true for species that exhibit thermally sensitive traits, such as temperature-dependent sex determination (TSD). This is because urban environments not only present species with entirely novel ecosystems, but species will also experience increased temperatures. These temperature increases may result not only in offspring mortality, but also skewed population sex ratios. To persist in cities, urban dwellers with TSD will therefore need to adjust the temperature of the nesting environment, either through phenotypic plasticity or rapid evolution through natural selection. Here, we investigate the nesting ecology of a long-lived, urban dwelling reptile, the eastern water dragon (Intellagama lesueurii), to understand how a TSD species may respond to urban environments. Based on data collected from 72 nests over 2 nesting seasons, we show that city dragons not only dug significantly deeper nests than previously observed across their natural riparian habitat, but also nested in novel substrates. Furthermore, we observed a behaviour not previously described in this species, where mothers travel outside of their core home range to nest. This excursion behaviour potentially represents a greater maternal investment and is linked to the selection of specific microhabitats