Fig 1.
Map of South America showing sampling locations of the Humboldt penguin: CHI (Chiloé), PUP (Pupuya), ALG (Algarrobo), CAC (Cachagua), TIL (Tilgo), PAJ (Pajaros), CHO (Choros), CHA (Chañaral), GRA (Isla Grande), AZU (Pan de Azucar), and PSJ (Punta San Juan).
Table 1.
Summary statistics of Humboldt penguins based on the 13 microsatellites: Sample size (n), mean number of alleles (Na), Shannon Index (I), expected (He) and observed (Ho) heterozygosity, inbreeding coefficient (FIS), and mitochondrial DNA control region and nuclear RAG1 intron: sample size (n), haplotype diversity (Hd), nucleotide diversity (π) and Neutrality test of Fu’s Fs (Fs), Tajima'D (D) with respective probability (p).
In bold, values that were significant for Fs (p < 0.02) and D (p < 0.05). Population reference: CHI (Chiloé), PUP (Pupuya), ALG (Algarrobo), CAC (Cachagua), TIL (Tilgo), PAJ (Pajaros), CHO (Choros), CHA (Chañaral), GRA (Isla Grande), AZU (Pan de Azucar), PSJ (Punta San Juan).
Fig 2.
Bayesian STRUCTURE of the Humboldt penguin, delta K = 3, using admixture model.
1- Punta San Juan; 2- Isla Pan de Azucar; 3- Isla Grande de Atacama; 4- Chañaral; 5- Choros; 6- Pájaros; 7- Tilgo; 8- Cachagua; 9- Algarrobo; 10- Pupuya; 11- Chiloé.
Fig 3.
DAPC based on 10 microsatellites of the Humboldt penguin (Spheniscus humboldti): CHI (Chiloé), PUP (Pupuya), ALG (Algarrobo), CAC (Cachagua), TIL (Tilgo), PAJ (Pajaros), CHO (Choros), CHA (Chañaral), GRA (Isla Grande), AZU (Pan de Azucar), and PSJ (Punta San Juan).
Fig 4.
Pairwise RST based on 10 microsatellites (a), pairwise ϕST based on RAG1 (b) of the Humboldt penguin (* p value < 0.05).
Table 2.
Frequency of Humboldt penguin assignment to each population, estimated by maximum likehood based on allele frequencies, where rows represent immigrants and columns represent emigrants.
Population reference: CHI (Chiloé), PUP (Pupuya), ALG (Algarrobo), CAC (Cachagua), TIL (Tilgo), PAJ (Pajaros), CHO (Choros), CHA (Chañaral), GRA (Isla Grande), AZU (Pan de Azucar), and PSJ (Punta San Juan).
Table 3.
Inference of theta (θ) of each population and historical migrate number of among Humboldt penguin population, estimated by maximum likelihood based on allele frequencies on MIGRATE software, where rows represent immigrants and columns represent emigrants.
Population reference: CHI (Chiloé), PUP (Pupuya), ALG (Algarrobo), CAC (Cachagua), TIL (Tilgo), PAJ (Pajaros), CHO (Choros), CHA (Chañaral), GRA (Isla Grande), AZU (Pan de Azucar), and PSJ (Punta San Juan).
Fig 5.
Haplotype network for the D-loop region and RAG1 from Humboldt penguin sequences.
Node size corresponds to haplotype frequency.