Recent effective population size estimated from segments of identity by descent in the Lithuanian population

Abstract

The effective population size (Ne) quantifies the rate at which genetic diversity is eroded by genetic drift, a fundamental process of evolutionary change, and also provides an insight into the demographic history and dynamics of modern human populations. The main interest of this study was to reconstruct the recent effective population size, by using inferred long segments of identity by descent (IBD), and to estimate the effective/census size ratio in the Lithuanian population. We used Illumina 770K HumanOmniExpress-12v1.0 array data of 295 unrelated individuals of the Lithuanian population. IBDseq v. r1206 and IBDNe v. 04Sep15.e78 software packages were used to detect IBD segments and to estimate Ne, respectively. We estimated the effective population size in Lithuania 50 generations (g) ago to be 11900, whereas for g = 0 (1991) the effective population was 417000 (95% confidence interval, CI [218000; 1150000], and the census size was 3701968. We evaluated the ratio of effective size to census (N) size. The estimates of Ne were approximately one-tenth of the census size. We conclude that natural levels of fluctuations in the Lithuanian population size probably caused the small values of Ne/N. Because of extrapolation of slowing growth rates and migration of the Lithuanian population, this estimate might be correct, as the census size is expected to be several times larger than the Ne.