DNA-based approaches for evaluating historical demography in terrestrial vertebrates

Abstract

Contemporary DNA sequences can provide information about the historical demography of a species. However, different molecular markers are informative under different circumstances. In particular, mitochondrial (mt)DNA is uniparentally inherited and haploid in most vertebrates and thus has a smaller effective population size than diploid, biparentally inherited nuclear (n)DNA. Here, we review the characteristics of mtDNA and nDNA in the context of historical demography. In particular, we address how their contrasting rates of evolution and sex-biased dispersal can lead to different demographic inferences. We do so in the context of an extensive review of the vertebrate literature that describes the use of mtDNA and nDNA sequence data in demographic reconstruction. We discuss the effects of coalescence, effective population size, substitution rates, and sex-biased dispersal on informative timeframes and expected patterns of genetic differentiation. We argue that mtDNA variationin species with male-biased dispersal can imply deviations from neutrality that do not reflect actual population expansion or selection. By contrast, mtDNA can be more informative when coalescence has occurred within the recent past, which appears to be the case with many vertebrates. We also compare the application and interpretation of demographic and neutrality test statistics in historical demography studies.

Demographic histories of three predatory lady beetles reveal complex patterns of diversity and population size change in the United States

“…Estimates of Tajima's D, Fu and Li's D* and F* statistics were largely consistent in their signage across all states, with statistically significant D (P < 0.05) when C. septempunctata from all states were analyzed together. Additional tests of neutrality with more loci, and a combination of mitochondrial and nuclear loci, Table 6 Tajima's D, Fu and Li's D* and F* test estimates from the dataset of Greenstone et al (2011) are thus required to provide more definitive predictions of population size expansion versus natural selection signatures in the populations analyzed (Fahey et al, 2014).…”

Multilocus phylogeography of a widespread savanna–woodland‐adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa's Zambezi region

“…Fu's F s (Fu ) and Tajima's D (Tajima ) were also calculated, and negative and significant values of each of these statistics indicate recent population expansion (see Fahey et al . ). Significance was assessed by comparison of observed data to expectations under neutrality.…”

“…For distributions with nonsignificant raggedness indices, expansion time was estimated following Schenekar & Weiss (2011). Fu's Fs (Fu 1997) and Tajima's D (Tajima 1989) were also calculated, and negative and significant values of each of these statistics indicate recent population expansion (see Fahey et al 2014). Significance was assessed by comparison of observed data to expectations under neutrality.…”

Evidence for geographic substructuring of mtDNA variation in the East European Hermit beetle (Osmoderma barnabita)

“…Overall, the haplotype network showed a star-shaped topology as characteristic of population expansion after a bottleneck, wherein newer mutations form groups of (mostly) lower-frequency haplotypes budding from a central haplotype (Figure 2; see Slatkin and Hudson 1991, Avise 2000, Charlesworth and Charlesworth 2012, Fahey et al 2014. All tests of expansion proved significant and attested to a rapid growth of the European population.…”