The Power to Detect Recent Fragmentation Events Using Genetic Differentiation Methods

Abstract

Habitat loss and fragmentation are imminent threats to biological diversity worldwide and thus are fundamental issues in conservation biology. Increased isolation alone has been implicated as a driver of negative impacts in populations associated with fragmented landscapes. Genetic monitoring and the use of measures of genetic divergence have been proposed as means to detect changes in landscape connectivity. Our goal was to evaluate the sensitivity of Wright’s F st, Hedrick’ G’st, Sherwin’s MI, and Jost’s D to recent fragmentation events across a range of population sizes and sampling regimes. We constructed an individual-based model, which used a factorial design to compare effects of varying population size, presence or absence of overlapping generations, and presence or absence of population sub-structuring. Increases in population size, overlapping generations, and population sub-structuring each reduced F st, G’st, MI, and D. The signal of fragmentation was detected within two generations for all metrics. However, the magnitude of the change in each was small in all cases, and when N e was >100 individuals it was extremely small. Multi-generational sampling and population estimates are required to differentiate the signal of background divergence from changes in Fst, G’st, MI, and D associated with fragmentation. Finally, the window during which rapid change in Fst, G’st, MI, and D between generations occurs can be small, and if missed would lead to inconclusive results. For these reasons, use of F st, G’st, MI, or D for detecting and monitoring changes in connectivity is likely to prove difficult in real-world scenarios. We advocate use of genetic monitoring only in conjunction with estimates of actual movement among patches such that one could compare current movement with the genetic signature of past movement to determine there has been a change.

The influence of contemporary and historic landscape features on the genetic structure of the sand dune endemic, Cirsium pitcheri (Asteraceae)

“…A similar pattern was found in 20-year-old restorations where populations o500 m apart showed no evidence of introgression (Fant et al, 2013). Although this high divergence may be exacerbated by recent (4150 years) increases in fragmentation because of development in the area, the magnitude of difference is greater than can be expected, given the size of populations and generation time (Lloyd et al, 2013), suggesting that the divergence is in part an historic legacy. The relatively small genetic distance between populations at the southern edge of range to those in Sleeping Bear Dunes National Lakeshore, and given the southern populations only contain a subset of known alleles, would suggest that these populations are the result of sporadic founding events from the range center, rather than the result of a genetic bottleneck at the retreating edge (Hewitt, 2000;Petit et al, 2003Petit et al, , 2008Hu et al, 2009).…”

Three Molecular Markers Show No Evidence of Population Genetic Structure in the Gouldian Finch (Erythrura gouldiae)

“…However, modelling has shown a complete cessation of gene-flow can be statistically detectable within two generations using equilibrium estimators (e.g. F ST ) for microsatellite sampling schemes equivalent to ours and census population sizes of less than 500 individuals [19]. To our knowledge, there is no equivalent modelling done on high-throughput technology SNP data, but studies suggest that the number of SNPs employed here ought to be sufficient to distinguish very low levels of differentiation (e.g F ST <0.05) [19,84–86].…”

“…F ST ) for microsatellite sampling schemes equivalent to ours and census population sizes of less than 500 individuals [19]. To our knowledge, there is no equivalent modelling done on high-throughput technology SNP data, but studies suggest that the number of SNPs employed here ought to be sufficient to distinguish very low levels of differentiation (e.g F ST <0.05) [19,84–86]. Compared with previous attempts to measure population structure in the Gouldian finch [16,17], we are confident of our finding of the absence of genetic structure across the western range of the Gouldian finch because we included more sampling localities, analyses with different underlying assumptions, and more powerful genetic markers (SNPs) for detecting subtle differentiation [1,19,84,86].…”

“…More recently, data from six microsatellite loci and mitochondrial control region sequences from samples collected at two geographically distant localities (one in Western Australia and one in Northern Territory) indicated no evidence of structure [17]. It is possible that structure may not have been detected in this study due to poor geographic coverage of the species’ distribution [18], and the relatively small number, and characteristics of the loci employed may have lacked sufficient power to detect weak differentiation [19]. Additionally, while this study explored historical gene-flow, it is of greater use to management to compare these estimates to those from methods capable of assessing current gene-flow [17].…”

An overview of the utility of population simulation software in molecular ecology

“…However, this may be a poor model for studying genetic dynamics of real populations (Strand & Niehaus ; Lloyd et al . ). New simulators feature various mating systems (e.g.…”