Fig 1.
Map of all sampling locations.
All sampling occurred in southern New Zealand during the breeding seasons of 2017, 2018, and 2022. Colored points represent sampling locations for tawaki (purple, green, orange, yellow; n = 55), erect-crested penguins (red, blue; n = 54), and eastern rockhopper penguins (blue; n = 17).
Table 1.
Cross validation (CV) and cluster assignment (K).
Fig 2.
Principal components analysis (PCA) of all ddRAD-seq data.
Tawaki (circle), erect-crested penguins (square), and eastern rockhopper penguins (asterisk) colors denote the region in which the samples were collected. The first two principal components PC1 and PC2 represent 60.4% of the variance and separate the samples into three distinct genetic clusters.
Fig 3.
Heat map resulting from the population assignment analysis performed using fineRADstructure on all ddRAD-Seq data combined. Tick marks in both horizontal and vertical axes represent individual samples. The coancestry matrix shows the pairwise genetic similarity between individuals. Inferred populations are indicated by the dendrogram on the right. Overall, tawaki exhibit the lowest degree of coancestry whereas the eastern rockhopper penguins exhibit very high coancestry.
Fig 4.
Principal components analysis (PCA) for erect-crested penguins.
All ddRAD-seq data for erect-crested penguins from the Anchorage Bay (circle), South Coast (triangle), and Proclamation Island (square) colonies. The first two principal components PC1 and PC2 represent 20.8% of the variance and separate the samples into two distinct genetic clusters: Antipodes Island (blue) and Bounty Islands (red). Note six individuals that fall outside of the main clusters.
Fig 5.
ADMIXTURE plot for erect-crested penguins.
ADMIXTURE plot from ddRAD-Seq data from erect-crested penguins showing assignments to population 1 or 2 based on K = 2. Six individuals including three from the Bounty Islands and three from the Antipodes Islands and falling outside the clusters on the PCA appear as ‘hybrids’ between the two groups.
Table 2.
Summary statistics for ddRAD-Seq data.
Fig 6.
Estimates of changes in historical effective populations size (Ne).
Historical changes to the effective population size (Ne) of A) tawaki, B) eastern rockhopper penguin, C) Antipodes Islands erect-crested penguins, and D) Bounty Islands erect-crested penguins. Shading represents the 95% confidence interval for the Ne estimates.