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Intercolony variation in reproductive skipping in the African penguin mark-recapture data

Cite this dataset

Leith, Freddie et al. (2022). Intercolony variation in reproductive skipping in the African penguin mark-recapture data [Dataset]. Dryad.


In long-lived species, reproductive skipping is a common strategy whereby sexually mature animals skip a breeding season, potentially reducing population growth. This may be an adaptive decision to protect survival or a non-adaptive decision driven by individual-specific constraints. Understanding the presence and drivers of reproductive skipping behaviour can be important for effective population management, yet in many species such as the endangered African penguin (Spheniscus demersus), these factors remain unknown. This study uses multistate mark-recapture methods to estimate African penguin survival and breeding probabilities at two colonies between 2013 and 2020. Overall, survival (mean ± SE) was higher at Stony Point (0.82 ± 0.01) than Robben Island (0.77 ± 0.02). Inter-colony differences were linked to food availability; under decreasing sardine (Sardinops sagax) abundance, survival decreased at Robben Island and increased at Stony Point. Additionally, reproductive skipping was evident across both colonies; at Robben Island, the probability of a breeder becoming a nonbreeder was ~0.22, versus ~0.1 at Stony Point. Penguins skipping reproduction had a lower probability of future breeding than breeding individuals; this lack of adaptive benefit suggests reproductive skipping is driven by individual-specific constraints. Lower survival and breeding propensity at Robben Island places this colony in greater need of conservation action. However, further research on the drivers of inter-colony differences is needed.


Mark-recapture data of African penguins were collected over an 8-year period (2013-2020) across two colonies in the Western Cape, South Africa. From 2013, penguins were captured in each colony and injected with passive integrated transponders (PITs). As part of routine nest monitoring, the presence and breeding status (breeding or nonbreeding) of tagged birds was identified, and captured untagged birds were tagged.

Data were analysed using multi-state mark recapture models, with a group effect to evaluate colony differences, and 3 breeding states (breeder, nonbreeder, and pre-breeder). Pre-breeder was a state assigned to any non-breeding individual not yet encountered breeding to ensure all 'non-breeders' were skipping reproduction and not young birds yet to breed for the first time. 

Known parameters were fixed to improve model performance; since only breeders were marked in 2013 across both colonies (with nonbreeders marked in subsequent years, Table A1), survival and transition rates for nonbreeders and prebreeders were fixed to zero during 2013–14, as was recapture in 2014 in both colonies. Additionally, no nonbreeders were marked in 2014 at Robben Island, so prebreeder survival and transition during 2014–15, and prebreeder recapture in 2015 were also fixed to zero for this colony. Finally, impossible transitions (ψ[prebreeder to nonbreeder], ψ[nonbreeder to prebreeder], and ψ[breeder to prebreeder]) were fixed to zero at both colonies.

Usage notes

Program MARK and the ‘RMark’ package in R (White & Burnham 1999; Laake 2013) were used to analyse the data.


Association of Zoos and Aquariums

Department of Environment, Forestry and Fisheries

Pew Charitable Trusts

Bristol Zoological Society

Earthwatch Institute

The Leiden Conservation Foundation

The San Diego Zoo Wildlife Alliance