Signatures of genetic adaptation to extremely varied Australian environments in introduced European house sparrows

Abstract

Due to its history of multiple introductions to novel environments worldwide, the house sparrow has been used as a model species to study local adaption in invasive avian species. New genomic resources such as a custom 200K SNP array and a house sparrow reference genome provide great prospects for studying rapid local adaptation in this invasive species. Here, we analyse high-density genomewide genetic data collected across an extensive range of temperate, arid and tropical climates, in Australian populations that were introduced from Europe 150 years ago. We used two population differentiation (PD) and two ecological association (EA) methods to identify putative loci subject to selection across these varied climates. A majority of the outlier SNPs were identified through the use of the latent factor mixed models (LFMM) EA method, but the BayeScEnv EA method had the strongest overlap with the outliers from the two PD methods. Out of all the 971 outliers identified across the different methods, 38.3% were physically linked (within 20 kbps) to 575 known protein-coding regions in the house sparrow reference genome. Interestingly, some outlier genes had been previously identified in genome scan studies of broadly distributed species or had strong links to traits that are expected to be important to local adaptation, for example, heat-shock proteins, immune response and HOX genes. However, many outliers still have unknown relevance and some outliers can be false positives. Our results identify an opportunity to use the house sparrow model to further study local adaptation in an invasive species.

Contrasting patterns of local adaptation along climatic gradients between a sympatric parasitic and autotrophic tree species

“…(2013) to select candidate SNPs using a consensus approach, allowing for robust identification of adaptive loci independent from assumptions (and limitations) of a single model (Rellstab et al., 2015). In our study, numbers of loci identified with signals of selection varied by species, climatic variable and method; this has also been observed in other genomics studies (e.g., Ahrens, Byrne, & Rymer, 2019; Andrew, Jensen, Hagen, Lundregan, & Griffith, 2018; Hopley & Byrne, 2019). Furthermore, the overall proportion of SNPs identified as putatively adaptive in this study were similar to those observed in plant (e.g., Ahrens et al., 2019; Hopley & Byrne, 2019; Shryock et al., 2017) and other landscape genomic studies (e.g., Dudaniec, Yong, Lancaster, Svensson, & Hansson, 2018).…”

Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis

“…Given the unique advantages and disadvantages of each approach, unique combinations of PD and EA may help to reduce the number of false negatives and promote uncovering potential genomic footprints of selection [ 20 ]. For example, both PD and EA methods have been employed for the successful detection of putatively adaptive loci and assessment of environmental parameter influence on genetic variation within and among populations [ 7 , 10 , 20 , 24 ].…”

Resistance to gapeworm parasite has both additive and dominant genetic components in house sparrows, with evolutionary consequences for ability to respond to parasite challenge

“…The house sparrow ( Passer domesticus ) is a ubiquitous passerine bird that has been used as an ecological model species in previous genetic architecture studies (Andrew, Jensen, Hagen, Lundregan, & Griffith, 2018; Andrew et al., 2019; Lundregan et al., 2018; Silva et al., 2017). In Helgeland, northern Norway, a natural metapopulation of house sparrows has been studied at an individual level since 1993 and has a large sample archive with records of morphological and life history data, alongside individual genetic and pedigree information (Jensen et al., 2003, 2004; Pärn, Jensen, Ringsby, & Sæther, 2009).…”