Effective Population Size Estimation Using PSMC

We used pairwise sequentially Markovian coalescent (PSMC) models to estimate the effective population size of each species^{84 (link)}. Fastq sequences were obtained using bam format aligned sequences of one randomly selected father per species and were converted into fastq format using samtools mpileup command and vcf2fq. As recommended, the minimum depth was set to one-third of the average for the sample and twice the average for the maximum. For mammals, fish and reptiles, the parameters of the PSMC were set to –N25 for the maximum number of iterations of the algorithm, –t15 as the upper limit for the time to the most recent common ancestor, –r5 for the initial θ/ρ value, and finally the atomic intervals –p of ‘4 + 25 × 2 + 4 + 6’. These parameters were used previously for PSMC analysis of various species, including primates^{84 (link),85 (link)}, cetaceans^{86 (link)}, Felidae^{87 (link)}, fishes^{88 (link),89 (link)} and turtles^{90 (link)}. For birds, we used different parameters according to the literature with –N30 –t5 –r5 (ref. ^{91 (link)}). Finally, to simulate the history inferred by PSMC, we parameterized the generation time and the mutation rate inferred from the UCE alignment. We then explored the effect of the harmonic mean N_e over windows of 30,000 years to 1,000,000 years. We also compared N_e estimated obtained with this method with those estimated based on N_e = π/4μ. Nucleotide diversity (π) was calculated using ANGSD^{92 (link)}. This approach was implemented in three consecutive steps. From the alignment files, a global estimate of the site frequency spectrum was inferred using a maximum likelihood method, then the empirical π value was estimated per site, and finally, a sliding window approach was used to estimate π for each species. We used a window size of 50 kb and a step size of 10 kb together with an average pairwise estimation of the π to obtain global estimates of π. This analysis was restricted to unrelated individuals from each species, which corresponded to the 2 unrelated parents for 55 species, between 3 and 7 individuals for 10 species, and 3 species were excluded from this analysis as the parents were first-degree relatives.