Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow

Abstract

Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant ‘islands’. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which ‘islands’ of habitat are most in need of management and protection.

Quantifying the impacts of an invasive weed on habitat quality and prey availability for tiger snakes (Notechis scutatus) in urban wetlands

“…We examined western tiger snake habitats at two wetlands dominated by kikuyu and two wetlands dominated by native vegetation, all within 50 km of the Perth CBD, in south-west Western Australia (Fig 1). Western tiger snake populations have been previously documented as occurring at these wetlands (Lettoof et al 2021c). At Herdsman Lake (HL; 31.92°S, 115.80°E) and Kogolup Lake (KL; 32.12°S, 115.83°E) kikuyu was the dominant ground cover vegetation while at Loch McNess in Yanchep National Park (Y; 31.54°S, 115.68°E) and Black Swan Lake (BS; 32.47°S, 115.77°E) native vegetation predominated.…”

“…We examined western tiger snake habitats at two wetlands dominated by kikuyu and two wetlands dominated by native vegetation, all within 50 km of the Perth CBD, in south-west Western Australia (Fig 1). Western tiger snake populations have been previously documented as occurring at these wetlands (Lettoof et al 2021c). At Herdsman Lake (HL; 31.92°S, 115.80°E) and Kogolup Lake (KL;32.12°S,115.83°E)…”

“…In the south-west of the continent, western tiger snakes (N. s. occidentalis) are a top predator of wetland ecosystems (Aubret 2005), with their presence and abundance sensitive to an intact food web and habitat availability (Sergio et al 2008). Western tiger snakes persist in a subset of urban wetlands within the urban sprawl of Perth city (Lettoof et al 2021c) where they are considered bio-indicators of wetland health (Lettoof et al 2021b) and prey predominantly on frogs (Shine 1998, Lettoof et al 2020. Some of the urban wetlands inhabited by western tiger snakes are dominated by introduced kikuyu grass (Cenchrus clandestinus), a globally recognised invasive species, particularly in wetlands (Bird et al 2013, Boon andTesfamichael 2017).…”

“…A broadly inhospitable matrix of urban area likely restricts tiger snakes in Perth to the wetlands they inhabit (Lettoof et al 2021c), with little opportunity for individuals to move between habitat patches. Consequently, the quality of these wetlands and availability of prey are factors crucial for maintenance of viable population sizes.…”

Snake life history traits and their association with urban habitat use in a tropical city

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natural ecosystem change, native wildlife can (1) be extirpated, (2) persist in 'islands' of remnant habitat, or (3) adapt to the novel conditions (Lettoof et al 2021;McDonnell and Hahs 2015;Theng et al 2020). In response to global biodiversity declines, alongside an increase in human-wildlife conflict and zoonotic diseases, understanding the roles that physiological, behavioural and phylogenetic traits play in the persistence of species in urban environments is a focal area of research (Evans et al 2011;Liu et al 2021;Perrier et al 2018;Santini et al 2019).The success of wildlife in urban spaces has often been attributed to taxa that express behavioural and phenotypic plasticity (Dykstra 2018;Lowry et al 2013), and to species naturally occupying broader niches (i.e., generalists), rather than species that are adapted to a narrow range of environmental conditions (i.e., specialists) (

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