The Rufous-collared Sparrow (Zonotrichia capensis) shows phenotypic and behavioural variation throughout its continental distribution. In particular, the Patagonian subspecies Z. c. australis is strikingly distinct from other subspecies, lacking the black crown stripes that characterize the species, with a uniformly grey head or one with only subtle traces of black, and overall paler plumage. We sequenced whole genomes of 18 individuals (nine Z. c. australis and nine from other subspecies from northern Argentina) to explore the genomic basis of these colour differences and to investigate how they may have evolved. We detected a single ~465-kb divergence peak on chromosome 5 that contrasted with a background of low genomic differentiation and contains the ST5 gene. ST5 regulates RAB9A, which is required for melanosome biogenesis and melanocyte pigmentation in mammals, making it a strong candidate gene for the melanic plumage polymorphism within Z. capensis. This genomic island of differentiation may have emerged because of selection acting on allopatric populations. Concordantly, mitochondrial DNA indicated that Z. c. australis diverged from other subspecies ~400,000 years ago, probably as a consequence of Pleistocene glaciations. Phenotypic differences are consistent with Gloger’s rule, which predicts lighter coloured individuals in colder and drier climates like that of Patagonia. Future studies should focus on a contact zone in northern Patagonia where individuals show intermediate colour patterning, most likely as a result of gene flow between subspecies, to test whether colour differences are promoting the early speciation of Z. c. australis through assortative mating.

Genetic monitoring using non-invasive samples provides a complement or alternative to traditional population monitoring methods. However, Next Generation Sequencing approaches to monitoring typically require high quality DNA and the use of non-invasive samples (e.g. scat) is often challenged by poor DNA quality and contamination by non-target species. One promising solution is a highly multiplexed sequencing approach called Genotyping-in-thousands by sequencing (GT-seq), which can enable cost-efficient genomics-based monitoring for populations based on non-invasively collected samples. Here, we develop and validate a GT-seq panel of 324 single nucleotide polymorphisms (SNPs) optimized for genotyping of polar bears based on DNA from non-invasively collected fecal samples. We demonstrate 1) successful GT-seq genotyping of DNA from a range of sample sources, including successful genotyping of 85.7% of non-invasively collected fecal samples determined to contain polar bear DNA, and 2) that we can reliably differentiate individuals, ascertain sex, assess relatedness, and resolve population structure of Canadian polar bear subpopulations based on a GT-seq panel of 324 SNPs. Our GT-seq data reveal similar spatial-genetic patterns as previous polar bear studies but at lesser cost per sample and using non-invasively collected samples, indicating the potential of this approach for population monitoring. This GT-seq panel provides the foundation for a non-invasive toolkit for polar bear monitoring and contribute to community-based programs – a framework which may serve as a model for wildlife management and contribute to conservation and policy for species worldwide.