Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis

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.

A spatial genomic approach identifies time lags and historical barriers to gene flow in a rapidly fragmenting Appalachian landscape

“…Our study adds to a growing list highlighting the potential for genomic data sets to detect weak, recent or otherwise subtle spatial genetic patterns (González-Serna, Cordero, & Ortego, 2018;McCartney-Melstad et al, 2018;Murphy, Jones, Price, & Weisrock, 2018;Tan et al, 2018). Considering the problems time lags present for conservation planning, the use of SNP data sets and spatially informed analyses of genetic diversity will probably become increasingly important for placing patterns of population structuring in their proper genomic, temporal and geographical contexts.…”

Fine‐scale barriers to connectivity across a fragmented South‐East Asian landscape in six songbird species

“…Additionally, we find that even edge-tolerant and seemingly wellconnected species, such as M. gularis, are likely impacted by fragmentation in the longer term (see also Tan et al, 2018). The great resolution provided by genomic analysis, even at extremely small spatial scales, can help understand population dynamics within protected areas, identify immediate threats and inform conservation at larger scales.…”

“…Additionally, if Singapore's small-island status played a large role, we would expect comparable declines in genetic diversity in the more generalist species of our panel, at least one of which (M. gularis) was shown to be a relatively poor disperser ( Figures S7 and S9; also see Tan et al, 2018). Therefore, while Singapore's island status may have contributed marginally to lower genetic diversity, it cannot explain the magnitude of diversity loss in Singapore.…”

Historic DNA reveals Anthropocene threat to a tropical urban fruit bat

“…We hypothesized that this bat has remained largely insensitive to urbanization and deforestation on this island. However, Singapore's urban matrix has affected population demography even in edge species accustomed to disturbed habitats [6], raising the possibility of declining population genetic diversity during the last century. We directly tested this hypothesis using a temporal sampling approach.…”