Abstract
Although edge-tolerant species are known to benefit from habitat fragmentation, less is known about the population genetic impacts fragmentation may exert on edge-tolerant species. We examined the landscape genomic structure of an edge-tolerant forest-dependent bird species, the Striped Tit-Babbler Mixornis gularis, in the heavily urbanized island of Singapore to determine if two centuries of fragmentation have led to signs of isolation and loss of population-genetic diversity in different parts of the island. We obtained a high-quality complete reference genome with 78x coverage. Using almost 4000 SNPs from double-digest RAD-Sequencing across 46 individuals, we found that the population has likely experienced a recent contraction in effective population size and presently exhibits low population genetic diversity. Using empirical and simulation-based landscape genomic analyses, we also found that the subtle population genetic structure observed in the Striped Tit-Babbler population in Singapore is likely driven by isolation by distance resulting from limited dispersal. Our results demonstrate that population genetic impoverishment and subdivision can accumulate at relatively rapid rates in edge-tolerant bird species such as the Striped Tit-Babbler as a result of fragmentation, and that subtle spatial genetic structure can be detected over fine spatial and temporal scales using relatively few multilocus genomic SNPs.
Highlights
Anthropogenic habitat fragmentation is a key driver of biodiversity loss worldwide[1,2,3]
Based on the first genome assembly of the Striped Tit-Babbler Mixornis gularis, combined with population-genomic analyses and landscape genetic simulations from 46 individuals across Singapore, we detected a pattern of reduced Ne and subtle but noticeable isolation by distance (IBD)-driven population subdivision along Singapore’s North-South axis
That these patterns were detected at fine spatial and temporal scales illustrates the utility of genome-wide multilocus SNPs in illuminating the genetic impacts of habitat fragmentation prior to the manifestation of deleterious physical effects
Summary
Anthropogenic habitat fragmentation is a key driver of biodiversity loss worldwide[1,2,3]. As one of the few woodland-dependent songbird species to have maintained healthy population levels in Singapore (4,000 to 10,000 individuals, mean estimated population density of 0.94 individuals ha−1 forest[26] (Fig. S19, Supplementary Information)) in spite of extensive habitat loss and fragmentation, the Striped Tit-Babbler has likely benefited from the forest edges and secondary forests created by early fragmentation. It is not known whether the Striped Tit-Babbler population in Singapore constitutes multiple isolated subpopulations or a single metapopulation
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