Table 2.

Details of the individuals sequenced

Genus	Species	Locality	Geographic position		Total genomic reads	MtDNA		Coverage	Genome lenght (bp)		Genbank
			Latitude (S)	Longitude (W)		Total Reads	Used Reads		all genes	+ D-loop
Pygoescelis	P. antarcticus	Antarctica, South Shetland Islands, Narebski base	62° 13’	58° 45’	80,496,366	15,788	11,347	36	15,491	16,664	KU356673
		Antarctic Peninsula, Kopaitic	63° 19’	57° 54’	52,990,428	9298	6359	20	15,490	16,653	KU356674
	P. papua	Elephant Island, South Shetlands Islands	61° 06’	55° 09’	7,341,640	2630	1647	7a	–	–	–
		Antarctic Peninsula, Gabriel Gonzalez Videla base	64° 48’	62° 51’	158,565,602	34,092	25,947	82	15,500	16,704	KU356677
	P. adeliae	Antarctica, South Shetland Islands, Arctowski base	62° 09’	58° 28’	52,997,551	8162	5049	16	15,493	16,764	KU356675
		Antarctica, Ross Sea, Cape Crozier	77° 29’	69° 20’	68,998,340	13,000	7956	26	15,493	16,765	KU356676
Spheniscus	S. mendiculus	Galapagos Islands, Isabela Island	00° 35’	91° 05’	69,908,826	13,006	7360	24	15,516	16,367	KU361807
	S. humboldti	South America, Peru, Punta San Juan	15° 21’	75° 11’	64,663,956	21,786	13,908	43	15,519	16,658	KM891593
		South America, Chile, Cachagua	32° 35’	71° 27’	55,087,204	14,606	9269	28	15,519	16,660	KU361805
	S. magellanicus	South America, Chile, Chiloé Island, Puñihuil	41° 55’	74° 02’	61,046,791	11,456	5984	19	15,520	16,427	KU361804
		South America, Chile, Magdalena Island	52° 51’	70° 36’	54,372,256	11,108	6490	20	15,514	16,659	KU361806
		South America, Argentina, Puerto Deseado	47° 45’	65° 43’	67,969,432	10,640	5483	18	15,520	16,549	KU361803

^aGenome not included in all analyses due the low coverage