Genetic signatures of lineage fusion closely resemble population decline

Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi-locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo-observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non-fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage ..., All pseudo-observed datasets (PODs) were simulated in DIY-ABC v2.1.0 (Cornuet et al., 2014) using the HKY model of nucleotide sequence evolution (Hasegawa et al., 1985) with proportion of invariant sites = 10% and gamma = 2.0, and a mutation rate (µ) of 1×10-7 substitutions per site per generation. Summary statistic distributions were estimated via 1,000 simulations using the “Coalescent Simulations (n-loci | 1-pop)” feature in DnaSP V6.12.03 (Rozas et al., 2017). Simulations were seeded using values for θ per gene (Watterson, 1975), number of sampled individuals, DNA sequence haplotype length, and number of diploid autosomal loci from the associated POD. A subset of PODs were analyzed using Extended Bayesian Skyline Plots (EBSPs; Heled & Drummond, 2008), implemented in BEAST V2.7.3 (Bouckaert et al., 2014), using the true model nucleotide sequence evolution and mutation rate that generated the PODs, clock model = strict, operator weights = auto-optimized, with other priors as defau..., , # Genetic signatures of lineage fusion closely resemble population decline

All pseudo-observed datasets (PODs) were simulated in DIY-ABC v2.1.0 (Cornuet et al., 2014) using the HKY model of nucleotide sequence evolution (Hasegawa et al., 1985) with proportion of invariant sites = 10% and gamma = 2.0, and a mutation rate () of 110-7 substitutions per site per generation.

Summary statistic distributions were estimated via 1,000 simulations using the Coalescent Simulations (n-loci | 1-pop) feature in DnaSP V6.12.03 (Rozas et al., 2017). Simulations were seeded using values for per gene (Watterson, 1975), number of sampled individuals, DNA sequence haplotype length, and number of diploid autosomal loci from the associated POD.

A subset of PODs were analyzed using Extended Bayesian Skyline Plots (EBSPs; Heled & Drummond, 2008), implemented in BEAST V2.7.3 (Bouckaert et al., 2014), using the true model nucleotide sequence evolution and mutation rate that generated the PODs, clock mode...