3.1 Population bottlenecks as a timestamp in the genome
Population bottlenecks, detected using demographic inference methods, can help to infer the number and timing of independent colonization events. For example, there was a clear signature of population bottleneck in the invasive fall webworm (Hyphantria cunea ), although this predated introduction to China in 1979 (Wu et al., 2019). In contrast, there was no signal of a population bottleneck in invasive North American populations of the common carp, which instead shared a similar demographic history to putative ancestral populations in Europe (Yuan et al., 2018). A criticism of these studies is that they both used a sequentially Markovian coalescent (SMC), which is most appropriate for inferring demography in deep time (McVean & Cardin, 2005; Patton et al., 2019). Methods that use the site frequency spectrum, on the other hand, tend to perform better when inferring recent demographic change (Patton et al., 2019). A further complexity is that invasions often involve sequential introductions and admixture among differentiated source populations or even species, making their origins much harder to identify. Nonetheless, the timing and magnitude of admixture can be inferred by analysing the size distribution of haplotypes (Harris & Nielsen, 2013; see Box 3). In particular, Bayesian estimates of complex demographic parameters can be improved with the use of whole-genome sequence data compared to reduced-representation sequencing, largely due to the information added by haplotype statistics (Smith & Flaxman, 2020).
Whole genome sequence data should, in general, give more accurate demographic inference. This is because demographic inference in the recent past relies on the shallow coalescence times of low-frequency alleles. Assuming that sequencing is conducted at sufficient depth to accurately call low-frequency alleles (see Box 1), whole genome sequence data are therefore more likely to capture rare alleles required to time recent bottlenecks (Hahn, 2019). For example, Puckett et al.(2020) set out to test the hypothesis that a 1768 shipwreck introduced the brown rat (Rattus norvegicus ) to the Faroe Islands using reduced representation sequencing. Although three introduction events could be inferred, the authors were unable to estimate the timing of each event due to a lack of rare alleles, which were removed through the very bottlenecks they were attempting to date. Thus, in some cases the detection of recent bottlenecks is an empirically intractable problem. However, because whole genome sequence data are much more likely to capture the rare allele frequency data required to time recent bottlenecks, WGR may give better resolution in examples such as this. In summary, although other sequencing technologies, such as transcriptome sequencing and microsatellite markers, have shown considerable success in reconstructing invasion histories (e.g. , Fontaine et al., 2020; Popovic, Matias, Bierne, & Riginos, 2020), WGR data can increase resolution and will be especially useful in estimating the time of a recent invasion event.