Conservation genetics

The study of conservation genetics allows populations to be sampled and analysed to aid in the preservation of biodiversity (Allendorf, Hohenlohe, Luikart, 2010). Many populations have been isolated and fragmented due to a combination of human activity and natural barriers, this can reduce or completely halt the connectivity of species (Noss, 1991). Furthermore, when this connectivity is reduced or halted, the genetic variation between these populations can be reduced (Bailey, 2007; Peterken, 2002), when this variation is reduced they may become totally adapted to that environment which reduces the species ability to adapt to change (Waldvogel, et al.

, 2020). Moreover, this reduction in gene flow can ultimately result in inbreeding which will further lower the species fitness and may result in an extinction vortex, the use of genetics can also be used to rescue such populations to avoid inbreeding (Keller, Waller, 2002; Whiteley, Fitzpatrick, Funk, Tallmon, 2015). Therefore, analysing population genetic structure is essential in population management to prevent such negative consequences from happening, which ultimately could lead in the collapse of ecosystems.

When studying phylogenetic relationships of organisms, DNA (deoxyribonucleic acid) can be compared to determine the evolutionary history which they share which can determine how closely related they are by considering the level of variation they exhibit, species which are more closely related will show lower variation than those which are more distantly related (Baum, 2008).

The small spotted catshark Scyliorhinus canicula

The small spotted catshark Scyliorhinus canicula (Linnaeus, 1758) is one of the most abundant species of cartilaginous fish (Chondrichthyes) within the Northeast Atlantic and Mediterranean Sea.

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S. canicula belongs to the Scyliorhinidae family. It inhabits continental shelf areas, along with the upper portion of continental slopes, being distributed throughout the Mediterranean Sea, North-eastern Atlantic Ocean, North Sea, reaching down to the North-West coast of Africa (Soares & De Carvalho, 2019; FIGURE 1). The species can reach up to 1m in length (Compagno et al., 2005) and weigh up to 3kg (Burnie & Wilson, 2001) and can be found in depths of 10m ranging down to 400m (Ebert & Stehmann 2013). S. canicula is an opportunistic predator species which consumes a wide variety of fish and invertebrates such as hermit crabs, shrimp, polychaetas, molluscs, and decapods along the sea floors classifying them as demersal fish (Ford 1921; Lyle 1983). Female S. canicula are able to store sperm for extended durations which enables long periods of oviposition (Sumpter et al. 1978). Oviposition takes place year-round, however within the waters surrounding the British Isles oviposition peaks over the summer and halts between August and October (Ellis & Shackley 1995; Capapé et al. 2008; Ford 1921; Kousteni et al. 2014). Eggs generally attach to macro algae (Ebert & Stehmann 2013) and develop for 5-11 months before spawning, dependent on water temperature, with colder waters increasing development (Ellis & Shackley, 1997).

S. canicula is currently listed as “least concern” (The IUCN Red List of Threatened Species, 2016). However, within a study on fish stocks, S. canicula has been shown to overexploited from 1994-2010 within the Mediterranean (Cardinale & Osio 2013). S. canicula is generally considered bycatch and usually discarded upon capture, however, in some regions the shark has a moderate economic value and is used for human consumption, oil extraction, and for use as bait, the method of capture is mainly through trawling which is highly invasive (Springer 1979; Compagno 1984). Despite not being at risk of extinction their populations should be monitored to ensure their stocks are sustainable. Their generalist feeding behaviour helps maintain the populations of several benthic invertebrate species, which if were to grow uncontrollably or become depleted from over-prayed upon could have rippling negative effects on the ecosystem.

Various studies have discussed the wide distribution range of S. canicula along with its intraspecific variation and identified various populations (Rodríguez-Cabello et al. 1997; Ellis & Shackley 1997; Rodríguez-Cabello et al. 2004; Barbieri et al. 2014; Kousteni et al. 2014). The studies found there is morphological variation within different regions and species do not travel long distances and remains within certain areas.

FIGURE 1. The regions within the Mediterranean where Scyliorhinus canicula samples were collected within the study by Barbieri et al. (2014) 1 – Catalan Sea; 2 – Ligurian Sea; 3 – South Tyrrhenian Sea; 4 – Strait of Sicily; 6, North Adriatic Sea ; a – Atlantic Ocean; b – Strait of Sicily ; c – Ionian Sea; d – Levantine Sea; e – Levantine Sea; and f – North Adriatic Sea (Barbieri et al., 2014)

Mitochondrial DNA

Mitochondrial deoxyribonucleic acid (mtDNA) is a useful marker for analysis as it is more robust and more abundant when compared to nuclear DNA, each mitochondrion contains several copies of mtDNA and each cell typically contains thousands of mitochondrion (Pereira, Carneiro, Van Asch, 2010). mtDNA is inherited through the maternal line a provides a lineage for phylogenetic pathways as there is no recombination of the genetic sequence between new generations (Rokas, Ladoukakis, Zouros, 2003). The mitochondrial genome contains 37 genes, one of which is the cytochrome c oxidase which can be used to provide information of interspecies and intraspecies variation (Schon, 2000; Meyer, Paulay, 2005).

Barbieri et al. (2014) sequenced the subunit I of the cytochrome c oxidase (COI) gene in S. canicula populations across the Mediterranean Sea (FIGURE 1) to investigate the population genetic structure of the species and determine the connectivity between said populations. The results detected 27 COI haplotypes present, with moderate to high COI variability, with significant genetic structuring within the study area. Furthermore, the results suggest the Strait of Sicily is not an effective barrier for restricting gene flow, as western and eastern samples were not genetically divergent but found that populations from Adriatic Sea and Ionian Sea are genetically differ from those of other regions. Similarly, a study by Kousteni et al. (2014) investigated genetic structure and historical demography within S. canicula populations within the Mediterranean basin by use of the COI gene. They found strong genetic subdivision between western and eastern Mediterranean populations which suggests geographic isolation of the deep sea between sample sites enforces genetic differentiation of S. canicula due to their limited ability to disperse between sites and therefore geneflow is restricted. Moreover, the study concluded that S. canicula exhibits multiple genetic stocks across the Mediterranean. In contrast Soares & De Carvalho (2019) suggest that the findings of these studies may be due to the presence of Scyliorhinus duhamelii within the analysis which is morphologically similar and inhabits similar distributions.

Aims and Objectives

This study sets out to analyse mtDNA from samples of Scyliorhinus canicula obtained from the British isles and make comparisons of haplotypes against previous research conducted throughout the Mediterranean, the results of this study will reveal the similarities and/or differences of the geographical regions, adding to the scientific literature, broadening the range of scientific data of the Scyliorhinus canicula. This study investigates whether the 578bp region of the cytochrome c oxidase subunit I (COI) gene is informative in identifying Scyliorhinus canicula haplotypes within the continental shelves of the British Isles. Additionally, whether this data can provide information on the genetic structure and connectivity within populations from the Mediterranean Sea and wider Atlantic regions.