Effects of recent population bottlenecks on reconstructing the demographic history of prairie‐chickens

Abstract

Current methods of DNA sequence analysis attempt to reconstruct historical patterns of population structure and growth from contemporary samples. However, these techniques may be influenced by recent population bottlenecks, which have the potential to eliminate lineages that reveal past changes in demography. One way to examine the performance of these demographic methods is to compare samples from populations before and after recent bottlenecks. We compared estimates of demographic history from populations of greater prairie-chickens (Tympanuchus cupido) before and after recent bottlenecks using four common methods (nested clade analysis [NCA], Tajima's D, mismatch distribution, and MDIV). We found that NCA did not perform well in the presence of bottleneck events, although it did recover some genetic signals associated with increased isolation and the extinction of intermediate populations. The majority of estimates for Tajima's D, including those from bottlenecked populations, were not significantly different from zero, suggesting our data conformed to neutral expectations. In contrast, mismatch distributions including the raggedness index were more likely to identify recently bottlenecked populations with this data set. Estimates of population mutation rate (theta), population divergence time (t), and time to the most recent common ancestor (TMRCA) from MDIV were similar before and after bottlenecks; however, estimates of gene flow (M) were significantly lower in a few cases following a bottleneck. These results suggest that caution should be used when assessing demographic history from contemporary data sets, as recently fragmented and bottlenecked populations may have lost lineages that affect inferences of their demographic history.

Assessing the genetic diversity of five Tanzanian chicken ecotypes using molecular tools

“…Furthermore, mtDNA analysis results indicated that Unguja, Pemba and Morogoro chickens shared a rather equal distribution of haplotypes D and E. These results obtained from mtDNA and microsatellite analysis suggest that effects of genetic drift were stronger within these populations than gene flow between island and mainland populations (Johnson et al, 2003). This is further supported by positive Tajima's D-value in Unguja, which might indicate a decrease in population size (Johnson et al, 2007).…”

“…A low genomic evolutionary rate and elevated inbreeding frequency may have contributed to the low genetic variation observed in this population. Demographic analyses (Tajima's D) using mtDNA sequence polymorphism showed a signal of population expansion in the Kuchi population characterized by an excess of rare variants consistent with population growth (Tajima, 1989;Aris-Brosou & Excoffier, 1996;Schmidt & Pool, 2002;Johnson et al, 2007).…”

Phylogeography and subspecies status of Black Grouse

“…Analyses of mismatch distributions can be used to detect and date historical population expansions (Prairie Chicken; Johnson et al 2007;Johnson 2008; Great Reed Warbler (Acrocephalus arundinaceus), Hansson et al 2008). For Black Grouse, the bell-shaped mismatch distribution, the star-shaped phylogeny with a central common haplotype and low nucleotide diversity are consistent with a demographic population expansion.…”

“…There have been several studies assessing patterns of genetic variation to infer population expansions from refugia (Taberlet et al 1998), allowing inferences about the processes that led to current levels of genetic diversity and population structure (Johnson et al 2007). This information is important for conservation management purposes, and for revising the traditional species and subspecies designations (Avise and Ball 1990;Moritz 1994).…”

Museum collections reveal that Buff-breasted Sandpipers (Calidris subruficollis) maintained mtDNA variability despite large population declines during the past 135 years

“…Historic DNA (hereafter, hDNA) isolated from museum specimens allows conservation geneticists to examine effects of historic events directly instead of relying on inference from study of contemporary specimens (Ramakrishnan and Hadly 2009). If low genetic diversity is the result of recent population declines, contemporary sampling may underestimate the loss of unique alleles or lineages not observed in contemporary samples (Johnson et al 2007), and researchers might misinterpret the impact of population declines on their study system. Using historic samples allows conservation geneticists to elucidate finescale population trends, and thus hDNA can provide a historical perspective on large-scale population declines that may not be apparent from contemporary sampling alone (Wandeler et al 2007;Mourier et al 2012).…”