The Juan Fernández Fur Seal is a polygynous species. Based on sealer observations made during the late 18th century, the breeding season lasts from mid-November through the end of January, and the colonies are essentially vacated by early September, and no later than mid-October (Francis et al. 1998).
Juan Fernández Fur Seals are sexually dimorphic from the time of birth (Osman et al. 2010) and the differences in length and weight increase with age. Adult males reach 2 m length and weigh 140 kg. Lactating females are on average 1.42 m in length and 48.1 kg in weight (Francis et al. 1998). Newborn pups are approximately 65-68 cm long and weigh 6.2-6.9 kg, and are born with a black coat. Male pups are significantly larger and heavier than female pups at birth, but they do not grow faster than females nor do they show significant differences in body condition. Differences in the growth rates of male and female Juan Fernández Fur Seal pups appear to originate before birth and are not accentuated during the nursing period (Osman et al. 2010).
Males defend territories on land that typically cover about 36 m² and that include an average of four females; some males also hold larger territories in the water (Francis et al. 1998). Most adult females give birth within a few days of arriving at the rookery. Mean time from birth to the first foraging trip is 11.3 days. Although females can be gone for as little as a day, the mean length of foraging trips is 12.3 days, with the longest recorded trip lasting 25 days. Mean duration of pup attendance between foraging trips is 5.3 days with a range of 0.3–15.8 days. Based on the onset of pupping and the observations at vacant colonies in early September, pups appear to be weaned at 7-10 months old (Francis et al. 1998).
Juan Fernández Fur Seal females travel long distances to find adequate quantities of prey making some of the longest foraging trips of any otariid (Francis et al. 1998, Osman 2007). Most trips were made to the southwest and west of the Juan Fernández Islands, far offshore, to deep oceanic areas more than 550 km from the island (mean = 653 km) and up to 889 km distant. The mean dive depth was only 12.3 m and the mean dive duration was 51 seconds, suggesting mostly surface feeding (Francis et al. 1998). Osman (2007) analysed 27,541 dives made by five females from Alejandro Selkirk Island during a single foraging trip, obtaining a median dive depth of 4 m and median dive duration of 0.33 minutes. Maximum depth attained by any seal was 169.5 m during a dive lasting 3.1 minutes and the longest dive lasted 5.1 minutes with a maximum depth of 24 m. The median maximum depths ranged from 3.5 m to 4.5 m (Osman 2007). Francis et al. (1998) reported that nearly all foraging-type dives occur at night; however (Osman 2007) found feeding during daytime to be more frequent.
Juan Fernández Fur Seals feed extensively on vertically-migrating prey (Francis et al. 1998). Their diet is one of the least diverse of any otariid. Coupled with the long foraging trips made by lactating females, this pattern reflects the low productivity of their oceanic feeding areas (Acuña and Francis 1995). The diet composition of Juan Fernández Fur Seals was assessed by analysing 437 scats collected during five reproductive seasons (1987–1991). The study yielded 4,172 fish otoliths and cephalopod beaks, with 13 prey species identified. Myctophidae represented most of the items (80.3%), followed by Scomberesocidae (10%), Carangidae (9.5%), Engraulidae (1.0%), and Bathylagidae (0.7%). Cephalopod families included Onychoteuthidae (27.1%), Ommastrephidae (3.7%), and Tremoctopodidae (0.7%) (Acuña and Francis 1995). Scat samples from females contained larger numbers of the Squid Onychoteuthis banksi than did the samples from subadult males and juveniles.
Two-thirds of the 60 Juan Fernández Fur Seal pups found dead on Alejandro Selkirk Island during the 1991 and 1992 breeding seasons had Hookworms (Uncinaria sp.), with a mean infection of 17 parasites per host (Sepúlveda 1998). Blue Sharks, Great White Sharks, and Killer Whales are suspected predators, and Leopard Seals that infrequently visit the islands may also prey on Juan Fernández Fur Seals (Torres 1987).
The number of Juan Fernández Fur Seals harvested between 1793 and 1807 has been estimated to be in the order of millions (Busch 1985, Hubbs and Norris 1971) but no reliable estimates are available. By 1872, approximately 38,000 animals had been killed for the fur trade with China, and during 1801, “a single ship carried one million skins to the London Market” (Bush 1985). By 1891, the Juan Fernández Fur Seal population was estimated to be just 300-400 animals; by 1900 and until the middle of the 20th century the species was presumed extinct (Scheffer 1958, Hubbs and Norris 1971, Gerber and Hilborn 2001). In 1965, the species was rediscovered when small groups of Fur Seals were sighted on Alejandro Selkirk and Robinson Crusoe Islands (Bahamonde 1966, Aguayo 1979). The overall abundance of the Juan Fernández Fur Seal recovered from 750 individuals in 1969 to 32,278 in 2005. On Robinson Crusoe Island, the number of pups increased from 125 in 1983 to 2,732 in 2005. On Santa Clara the number of pups increased from 575 in 1998 to 1,325 in 2005, and on Alejandro Selkirk Island 548 pups were sighted in 1983 while 6,941 were observed in 2005 (Osman 2007).
In 2005, 63% of the total 10,998 pups were born on Alejandro Selkirk Island, which is the only clearly increasing colony (Osman 2007). Robinson Crusoe and Santa Clara populations are stable, suggesting that the quality of the breeding habitat may be important to the recovery of this species. Overall, the population is apparently stabilizing, as the per capita population growth rate oscillates between negative and positive values (Osman 2007). The current Juan Fernández Fur Seal population remains small and represents a much reduced fraction of its population prior to the seal exploitation period.
Mitochondrial DNA from 28 Fur Seals from both islands of Juan Fernández was used to evaluate the potential negative effect of the population bottleneck. Contrary to expectations, no significant reduction in genetic variability was identified (Goldsworthy et al. 2000). Similar results were obtained for the Guadalupe Fur Seal (Bernardi et al. 1998). However, when the genetic material from recent animals was compared to the genetic material from specimens collected prior to the seal exploitation, significantly reduced genetic variability was evident (Weber et al. 2004).