The Inclusion Of Genetic Analyses In Marine Conservation

Climate change and anthropogenic measures are an increasing obstacle for global biodiversity. As global biodiversity continues to be threatened and ecological systems disturbed, measures for conserving biodiversity can become challenging (Sutherland et al., 2010).Similar to other ecological systems, marine environments face several anthropogenic challenges, such as overfishing, chemical contamination, pollution and habitat loss (Korpinen et al., 2016). Along with climate change, these factors all contribute to the ongoing decrease in genetic diversity of marine species (Pinsky et al., 2014). Ellegren et al. (2018) defined genetic diversity as the variation in DNA sequences amongst individuals of a known population. There are many components that contribute towards genetic diversity but it is broadly recognized that the life history of a species is what shapes genetic diversity (Ellegren et al., 2018).

Evolutionary processes and genetic diversity are the foundation for building resilience in species populations, community ecology and ecosystem functions. As a result, resilience depends on the ability of a population to withstand extreme changes in the environment (Sgro et al., 2010). There are two parts to genetic diversity, (1) neutral diversity and (2) adaptive diversity. Neutral diversity reflects an element of the genome that does not undergo natural selection and comprises of components such as mutation, migration and genetic drift. Adaptive diversity consists of an organism’s ability to adapt to a new environment (Sgro et al., 2010). Climatic fluctuations in small sized populations are at a higher risk of extinction than loss of genetic diversity. Therefore, an important factor of resilience is to maintain a species’ population at a large and effective size to preserve genetic diversity and ongoing evolution (Sgro et al., 2010).

An alternative measure by Oterga-Cisnero et al. (2018) focused on a trait- based approach to assess the sensitivity of 40 marine species in Southern Benguela ecosystem, to climate change. Changes in the water temperature and environmental conditions have been previously recorded and observed to have effects on the marine life present. Oterga-Cisnero et al. (2018) accounted for abundance, distribution and phenology as the total sensitivity score in relation to climate change. An overview of species most likely to be affected by climate change was estimated using various attributes such as fecundity, stock status, life cycles and additional stressors etc. Using a logic rule, the results were analyzed and compared to overall sensitivity (low, medium-low, medium-high and high) and data quality (low, medium and high). While most species scored a medium-low or medium-high sensitivity value only a few scored high sensitivity values. Nevertheless, it was found that the species that scored high sensitivity values all had a depleted stock status, emphasizing that they are vulnerable to disturbances and climatic changes (Oterga-Cisnero et al., 2018).

In this study we used eight (8) of the forty (40) species in the study done by Oterga-Cisnero et al. (2018) to compare their genetic diversity to their sensitivity scores. We aim to assess whether their genetic diversity values are congruent to their sensitivity scores. Genetic diversity will be measured using microsatellite loci, single nucleotide polymorphisms (SNPs) or mitochondrial (mt) DNA markers.

West coast rock lobster (Jasus lalandi)

The west-coast rock lobster, Jasus lalandii, has been under intense measures of exploitation by anthropogenic procedures which in result has drastically impacted its population numbers (Matthee et al. 2007). Genetic diversity for the west-coast rock lobster was determined using mitochondrial (mt) DNA. Results include J. lalandii had a nucleotide diversity value of 0.002 (s.d. ± 0.001). While most individuals shared a common haplotype diversity value of 59.6%, contrarily there was no significant variation among populations. The sensitivity score of J. lalandii, in relation to climate change was medium-high. Although juvenile and adult J. lalandii species are expected to adapt to ongoing climate change aspects, J. lalandii still faces difficulties due to its extensive larval phase thus making it vulnerable to variability in climate (Ortega-Cisneros et al., 2018). This is congruent with the findings of Matthee et al. (2007), in which Mathee states that strong differential selection pressures can be the cause of low haplotype and nucleotide diversity.

Black musselcracker (Cymatoceps nasutus)

Black musselcracker, Cymatoceps nasutus, is generally an inshore and offshore (80m) species and is increasing popular amongst kayakers. C. nasutus is both commercially recreationally sought after. Due to this, exploitation generally occurs which result in decreased population numbers. Genetic diversity was determined using mtDNA and nuclear (n) DNA. The mtDNA haplotype diversity was high (h= 0.878) and ranged from 0.795 - 0.903. Nucleotide diversity (π) was found to be constant and ranged from 0.005 – 0.008. Genetic diversities ranged from 0.123 – 0.220 and the total sample 0.180. The average number of alleles per locus ranged from 1.333 – 2.000. While the expected heterozygosity was 0.180 and the observed heterozygosity was 0.177. The sensitivity score for C. nasutus was medium high. Similar to that of J. lalandii, the exploitation and life history of C. nasutus is also what makes it vulnerable to changes in its environment and climate.

Abalone (Haliotis midae)

The abalone industry in South Africa makes up the largest sector in terms of revenue. The abundance and extensive distribution of the endemic abalone species, Haliotis midae, is rapidly leading to an increase in its market value (Rhode et al. 2012). Thus, making H. midae, a target for exploitation. Together with habitat loss, climate change and predation pressures, there has since been a decline in H. midae populations (Beste-van der merwe et al. 2011). It is therefore important to establish the genetic diversity of H. midae to ensure the sustainability and conservation of H. midae (Beste-van der merwe et al. 2011; Rhode et al. 2012). Genetic diversity was determined using microsatellites and SNPs. The microsatellite loci displayed high levels of genetic variation with the total number of alleles per locus ranging from 12-43. Observed and expected heterozygosity ranged from 0.35 – 0.848 and 0.53 - 0.939. For the SNPs values, observed and expected heterozygosity ranged from 0.121 - 0.870 and 0.232 – 0.489. According to Orterga-Cisneros et al. (2018), H. midae has a relatively high sensitivity score. With its constant exploitation H. midae has resulted in a depleted stock status, therefore making it increasingly vulnerable to ongoing climate change.

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Brown Mussel (Perna perna)

Perna perna is a subtropical rocky shore species that is both ecologically and economically significant as it is a central source of food (Coelho et al., 2012). Genetic diversity for P. perna was determined using 10 microsatellite loci markers. An average of 11 alleles per locus ranged from 5-27. The expected and observed heterozygosity values varied from 0.31- 0.95 and 0.23 – 1.0. The results from Coelho et al. (2012) indicates that the microsatellite loci can be an effective measure to identify processes affecting species boundaries. The sensitivity score for P. perna was medium-high.

Kingklip (Genypterus capensis)

Genetic diversity for kingklip, Genypterus capensis, was determined using mtDNA and microsatellites. Historical haplotype diversity (h= 0.902) for kingklip (as well as nucleotide diversity (∏= 0.009) values were high due to fast growth from a population with a low effective population size (Henriques et al., 2017). This is similar to the Cape hake, Merluccius capensis, which occurs with this species. Contemporary genetic diversity scores of H= 0.777; allelic richness, AR = 18.601 are lower than historical figures and figures of other commercially exploited marine fishes. This is due to the removal of large female fish during commercial exploitation which results in a decreased effective population sizes (Hauser et al., 2003). Kingklip is listed as having a medium-low sensitivity score according to Ortega-Cisneros et al. This is in congruence with the genetic diversity scores found in Henriques et al. as high genetic diversity reduces the sensitivity of the species to climate change and other disturbances. Although this species has been exploited for a long time genetic diversity has not decreased drastically.

White Steenbras (Lithognathus lithognathus)

White or West Coast Steenbras, Lithognathus lithognathus, is an endemic species that has historically been commercially exploited in the Western Cape and still today. Genetic diversity was determined using mtDNA and microsatellites (Bennet et al., 2017). High haplotype and nucleotide diversities were found with overall values of h=0.985 and ∏= 0.011 at the population scale. This species has been listed as having a high sensitivity (see Table 1) with a medium data quality score. Genetic diversity values and the sensitivity scores are compatible as this species exhibits high genetic diversity similar to that of kingklip. However, this species is endemic and thus is more prone to negative population effects due to intensive harvesting within its restricted range. The sensitivity score reflect the rarity of this species.

Yellowtail (Seriola lalandi)

Genetic diversity was measured using mtDNA and microsatellites. Swart et al (2016) found high observed heterozygosity per population (H0= 0.722). Haplotype diversity was high while nucleotide diversity was low across populations as can be seen in Table 1. Yellowtail is listed as having a medium-low sensitivity. This is somewhat congruent with the genetic diversity scores as the individual populations have lower genetic diversity scores relative to other species with the same rating. Although genetic diversity is lower, the low sensitivity rating is largely due to the relative abundance of the species as it occurs in both hemispheres.

Deep water hake (Merluccius paradoxus)

Deep-water hake, Merluccius paradoxus, is a demersal fish species found in Namibian and South African waters and is an important commercial species. Genetic diversity values for this were obtained by Von der Heyden et al. using mtDNA and microsatellites. Genetic diversity is average for this species with h=0.51 ±0.016 and π = 0.0013 ± 0.001. This is congruent with a sensitivity rating of medium-low as the species is commercially exploited and has a low haplotype diversity relative to other species such as kingklip and white Steenbras. A relatively low haplotype diversity suggests that this species arose later than others and so contains less evolutionary history.

Shallow water hake (Merluccius capensis)

Von der Heyden et al. also determined genetic diversity of shallow-water hake, M. capensis, using mtDNA and microsatellites. Genetic diversity values of h=0.88 ± 0.02 and π = 0.006± 0.0036 were found. These values are consistent with a medium-low sensitivity rating as the species is commercially exploited. This species has greater genetic diversity than deep-water hake. The sensitivity score of medium-low is more suitable for this species than for deep-water hake.

Discussion

Genetic diversity measures are important to consider in conjunction with sensitivity analyses in order to investigate the true vulnerability of species and ensure that resources are used efficiently and effectively for conservation. For the 8 species listed above, we found that most of the genetic diversity measures were congruent with the sensitivity analysis scores. Species with high levels of genetic diversity were scored with high or medium-high sensitivity. However, the black musselcracker and West Coast rock lobster had low genetic diversity measures but were given medium-high sensitivity scores. In these cases, it can be seen that genetic analyses alone would have been insufficient to determine whether these species require protection. The sensitivity analyses revealed exceptionally high exploitation of these species resulting in high sensitivity to climate change as well as a decline in genetic diversity with ongoing exploitation. While sensitivity analyses are useful and are based on various traits such as abundance and phenology, genetic approaches are further elaborative. Genetics analyses are useful in accounting for the genetic structure of populations based on life history (Galarza et al., 2009). It is important to consider the unique sensitivities and evolutionary and genetic histories of each species for the development of good conservation planning particularly in marine conservation and the use of MPAs. Population genetics analyses are vital to the establishment of more effective MPAs as they can be used to estimate gene flow and connectivity between MPAs, identify areas of special interest for protection, and be used to analyse and improve existing MPAs (von der Heyden at al., 2009). This will improve the protection of commercially exploited species in order to replenish fish stocks for future sustainable use if used correctly in conjunction with sensitivity analyses.

Conclusion

Due to a multitude of anthropogenic effects and the onset of climate change it has become increasingly important to protect species, especially those that we rely on, from extinction at local and global scales. Intuitively, it would be beneficial to combine various tools used for conservation planning to improve conservation and identify deficient areas. We found that genetic diversity measures were helpful in elucidating sensitivity scores for the 8 species chosen. We also found that although both tools are powerful, their combined use can lead to improved conservation planning. The use of genetic analyses in conjunction with sensitivity analyses can be used to improve conservation of marine ecosystems and subsequently, individual species with high economic value.