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eDNA - How genetic material can be used to track an endangered species of penguin




The African penguin (Spheniscus demersus) is Africa’s only species of penguin and is found nowhere else in the world [1]. The Benguela upwelling ecosystem, located off the coast of South Africa, plays a vital role in providing foraging grounds for them to raise their chicks at surrounding breeding colonies [2]. However, localised fishing pressure, combined with environmental changes have significantly reduced and shifted prey availability for these marine predators [3]. The combination of climate change with intensive fishing pressure, has had a synergistic effect on the distribution of high-quality prey species, such as sardines and anchovies, causing them to move east [4]. Subsequently, a spatial mismatch between the foraging ranges of breeding penguins and spawning aggregations of pelagic fish stocks has developed [5]. This has caused severe declines in Western Cape penguin populations [3], causing >60% population decline between 2001-2009 [5]. The species is currently classified as endangered on the IUCN’s Red List of Threatened species [6].


Juvenile and non-breeding African penguins are severely understudied, despite the importance of their survival for recruitment into the breeding population [5]. Furthermore, their dispersal has important implications for gene flow and subsequent adaptability towards changing environmental conditions [7]. While it is known that eastward shifts in prey species have caused severe declines in breeding colonies, the impact on juvenile penguins and their foraging ranges is unknown. Until now, scientists have been using satellite transmitters to try and improve our understanding of the foraging ranges and dispersal of juvenile penguins [5,7], however, these have limitations. Firstly, attaching trackers is highly invasive and can cause modifications to individual behaviour [8], which has ethical implications and can reduce data reliability. Trackers are also expensive [9], which can be costly if lost in the field, as well as limiting the total number of penguins tracked due to research budgets. An alternative tracking approach is an up-and-coming technique known as environmental DNA (eDNA), which uses genetic material left behind in the environment to detect species presence [10].


Figure 1 - The African penguin (Spheniscus demersus)



What is eDNA?

eDNA uses genetic material in an environment, such as faeces, mucous, feathers and blood, to detect whether a target species is present or has recently been present [10]. The method works by targeting a specific gene belonging to the species of interest and isolating it from the relevant environment. So far, this has been successful in a range of systems, including terrestrial and aquatic sediments, seawater, freshwater, and air [11,12]. Using eDNA offers many advantages, including increased sample site coverage per unit effort [10,13] and detecting species in areas where they have not been found before [14,15]. For example, eDNA has already been used to complement traditional biodiversity survey techniques and to detect the early presence of invasive species [16].



How can eDNA be used to help African penguins?

Researchers at the University of the West of England (UWE) and Bristol Zoological Society have been developing an eDNA method for the African penguin, targeting the mitochondrial cytochrome b gene from aquatic samples. It is hoped that in time, this method can complement existing satellite tracking techniques, helping to infer foraging and dispersal ranges of juvenile penguins by collecting and analysing aquatic ocean samples. However, the technique must first undergo vigorous testing before being implemented in the field [17].


The first step requires the development of primers [18], small fragments of single-stranded DNA which target the cytochrome b gene for replication. Primers must be species-specific and bind only to the African penguin cytochrome b gene, to avoid replicating any other genetic material found in the water [17]. This occurs by running the primer DNA sequence against DNA sequences belonging to geographically relevant species on an online database called BLAST. This ensures that enough mismatches exist between primers and other DNA sequences potentially found in the target environment to avoid non-specific binding [18]. The next step is to ensure that these primers can replicate African penguin DNA using a process called PCR (polymerase chain reaction). PCR involves programmed cycles of heating and cooling which replicates the target DNA, allowing researchers to identify whether African penguin DNA is present in a sample [17]. After this, the testing of environmental water samples can occur. Due to covid restrictions this year, researchers have been using water samples taken from the African penguin enclosure at Bristol Zoo. Doing this has provided them with the opportunity to assess whether the method can detect African penguin DNA from zoological seawater samples. Excitingly, this has been met with success and is the first research to successfully apply the eDNA method to any penguin species.


Figure 2 - Water sample collection at Bristol Zoo Gardens



What next?

While eDNA monitoring of penguins in captivity has proven to be a success, additional factors may affect results in the field. Due to this, an in-depth understanding of how African penguin DNA reacts under natural conditions will be needed. Environmental DNA degrades over time [19], meaning knowing how long DNA can persist in the water column is important to infer how long ago an individual may have been present. Research undertaken at UWE has started to investigate this, looking at the effects of UV light and different temperature conditions on eDNA degradation. However, further work is required to assess the impact of natural processes such as currents and tides on the dispersion of eDNA, as well as how the greater dilution of eDNA in the ocean may affect detection success [20]. Nevertheless, research conducted on zoo-housed penguin eDNA has provided a useful starting point in the development of this method and is encouraging for the future use of eDNA in monitoring this endangered species. With a greater understanding of the distribution of juvenile African penguins, targeted conservation management can be used to increase survival rates of them, helping to improve breeding success and hopefully bolstering future populations of African penguins.


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