Figure 1

Phylogenetic relationships and changes in effective population sizes of two penguin species. (A) Phylogeny of two penguins and six closely related aquatic species (northern fulmar Fulmarus glacialis; great cormorant Phalacrocorax carbo; crested ibis Nipponia nippon; dalmatian pelican Pelecanus crispus; little egret Egretta garzetta; red-throated loon Gavia stellata) (blue names), and a land bird (zebra finch Taeniopygia guttata). The estimates of topology and divergence times are from our avian phylogenomic study [24]. Horizontal bars at each node represent 95% credibility intervals of estimated divergence times. Above the tree are the geological timescale and temperature changes over the past 65 million years, relative to the present [26]. PETM, Paleocene–Eocene Thermal Maximum. (B) Dynamic changes of effective population sizes (N _e ) of two penguins inferred by the pairwise sequentially Markovian coalescent (PSMC) method. The thick curves depict the estimated N _e values of the two penguins, and the thin curves represent PSMC bootstrapping estimates. (C) Enlargement of the period from 100 KYA to 10 ka in panel (B). MIS 4, Marine Isotope Stage 4; LGM, last glacial maximum. Temperature change data are from [33].