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Samples of skin tissue were collected by biopsy darting from humpback whales (Megaptera novaeangliae) in six seasonal habitats representing three stocks and four regions: Groups IV (western Australia), V western component (eastern Australia), V eastern component (New Zealand and Tonga) and VI (the Antarctic Peninsula and Gorgona Island, Colombia, South America) of the Southern Hemisphere. A variable section of the mitochondrial DNA control region was amplified and sequenced from 84 of these individuals, distinguishing a total of 48 unique sequences (i. e., mtDNA nucleotypes). Phylogenetic reconstructions suggested that these nucleotypes form three clades, corresponding to those previously described in a world‐wide survey of humpback whale mtDNA variation, although bootstrap support for two of the clades was relatively low (<50%). An analysis of variance adapted for molecular information showed significant differentiation of nucleotypes among the three Groups (Stocks) and heterogeneity of haplotype diversity among the four regions. A pattern of interchange within and between oceanic basins was demonstrated by the presence of shared identical nucleotypes among humpback whales in regions of the Southern and Northern Hemispheres.

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Latitudinal preferences within the breeding range have been suggested for Breeding Stock G humpback whales that summer in different feeding areas of the eastern South Pacific. To address this hypothesis, humpback whales photo‐identified from the Antarctic Peninsula and the Fueguian Archipelago (southern Chile) were compared with whales photo‐identified from lower latitudes extending from northern Peru to Costa Rica. This comparison was performed over a time span that includes 18 austral seasons. A total of 238 whales identified from the Antarctic Peninsula and 25 whales from the Fueguian Archipelago were among those photo‐identified at the breeding grounds. Our findings showed that humpback whales from each feeding area were resighted unevenly across the breeding grounds, which suggests a degree of spatial structuring in the migratory pathway. Humpback whales that feed at the Antarctic Peninsula were more likely to migrate to the southern breeding range between northern Peru and Colombia, whereas whales that feed at the Fueguian Archipelago were more likely to be found in the northern range of the breeding ground off Panama. Further photo‐identification efforts and genetic sampling from poorly sampled or unsampled areas are recommended to confirm these reported connectivity patterns.

Humpback whales undertake seasonal migration between productive high-latitude areas where they feed in summer and low-latitude tropical waters where mating and calving occur during winter. In the eastern south Pacific, the species breeds off Colombia and Ecuador, and feeds primarily in the western Antarctic Peninsula and in the waters of the Strait of Magellan (SM), recently described as a new feeding ground for humpback whales. Comparison of fluke photographs of 62 individuals from the SM obtained during the austral summer from 1999 to 2005 and 1,042 individuals from Colombia, provided conclusive matches for six individuals, with an overall interchange index of 0.093. Eight migratory trips between summer and winter grounds were registered for four whales during a complete migratory round-trip in consecutive years. The minimum distance traveled in a one-way trip ranged from 6,650 to 7,000 km. The duration of the two fastest trips between these migratory destinations was 88 and 99 days, with a mean speed of migration of 76 and 67 km day -1 respectively. Five of the whales present in both areas were males and three mitochondrial DNA haplotypes were identified: EM-1 for three individuals, EM-2 for two and EM-3 for the last one, all of which have been previously described for humpback whales from Colombia. All six individuals were seen several days in each season in the SM (as many as 39 days in one case), with an average stay of 72 ± 40 days (n = 20) per year, ranging from 3 to 125 days. On average, each of the six individuals was seen in the SM during 71 ± 18 % of the seven monitored summers. Three individuals were re-sighted in the SM six out of the seven surveyed years, during four to six consecutive years. These results provide the first direct evidence to include humpback whales that feed in the Strait of Magellan as part of the eastern south Pacific population of whales that feed off Colombian waters.Key words: Colombia, humpback whales, migration, photo-identification, Strait of Magellan. RESUMENLa ballena jorobada migra estacionalmente entre latitudes altas donde se alimenta en verano y latitudes bajas donde cría y se aparea en invierno. En el Pacífico sureste, la especie se reproduce en Colombia y Ecuador y se alimenta principalmente al oeste de la península Antártica, y en el estrecho de Magallanes (EM) recientemente descrito como nueva área de alimentación. Al comparar las fotografías de las colas de 62 ballenas individualizadas en el EM durante el verano austral entre 1999 y 2005 con 1.042 individuos de Colombia, se encontró a seis individuos comunes, lo que representa un Indice de Intercambio migratorio de 0,093. Se registraron ocho migraciones para cuatro de estas ballenas entre el EM y Colombia en el ciclo migratorio de años consecutivos. La distancia mínima recorrida en una sola dirección varió entre 6.650 y 7.000 km. La duración de los dos viajes más rápidos registrados entre estos dos destinos fue de 88 y 99 días, con una velocidad promedio de migración de 76 y 67 km día -1 respectivamente...

From 2003 to 2009, we surveyed Las Perlas Archipelago off the Pacific coast of Panama 53 times between the months of August and October to estimate abundance of humpback whales and to test for a migratory connection with populations from the southern hemisphere. We identified 295 individuals using photo-identification of dorsal fins, including 58 calves, and the population estimate for a single season was 100-300 solitary adults plus 25-50 mothers with calves; the estimated population of animals across all seasons using a mark and recapture model was over 1,000. Eight of the 139 fluke identifications were matched to whales in photograph catalogues from the Antarctic Peninsula and a ninth was matched to a whale sighted in Chilean waters; four of these nine individuals have also been sighted in Colombia. We conclude that Panama (Las Perlas Archipelago in particular) is an important calving area for humpback whales in the Southern Hemisphere. These data should provide a foundation for monitoring of population change and to increase awareness in Panama about the need to manage vessel traffic and tourism related to the whales at Las Perlas.

Humpback whales wintering in tropical waters along the Atlantic and Pacific coasts of the South American continent are thought to represent distinct populations or “stocks.” Here we present the first analysis of genetic differentiation and estimates of gene flow between these breeding stocks, based on both mitochondrial DNA (mtDNA) control region sequences (465 bp) and 16 microsatellite loci from samples collected off Brazil (n = 277) and Colombia (n = 148), as well as feeding areas near the western Antarctic Peninsula (n = 86). We found significant differentiation between Brazilian and Colombian breeding grounds at both mtDNA (FST = 0.058) and microsatellite (FST = 0.011) markers and corroborated previous studies showing genetic similarity between humpbacks from Colombia and those from Antarctic Peninsula feeding areas. Estimates of long‐term gene flow between Brazil and Colombia were low to moderate, asymmetrical, and mostly mediated by males. Assignment procedures detected some cases of interchange and individuals of admixed ancestry between breeding grounds, indicating limited mixing of individuals between these stocks. Overall, results highlight the differentiation of humpback whale breeding populations with adjacent feeding grounds. This appears to be a remarkable example of fidelity to seasonal habitat in the absence of any contemporary barriers.