Temporal changes in allele frequencies but stable genetic diversity over the past 40 years in the Irish Sea population of thornback ray, Raja clavata

Abstract

Rays and skates are an unavoidable part of the by-catch in demersal fisheries. Over the past 40 years, the thornback ray (Raja clavata) has decreased in numbers and even disappeared in some areas, leading to concerns about genetic risk. For this reason, the effective population size (N e ), the migration rate (m) and temporal changes in the genetic diversity were estimated for the population of thornback rays in the Irish Sea and Bristol Channel. Using genotyped, archived and contemporary samples (1965 and 2003-2004), N e was estimated at 283 individuals (95% CI ¼ 145-857), m at 0.1 (95% CI ¼ 0.03-0.25) and the N e /N ratio between 9 Â 10 -5 and 6 Â 10 À4 . Although these results must be treated with caution, due to the small sample sizes, this is the first attempt to estimate N e in an elasmobranch species. The low N e /N ratio suggests that relatively few individuals contribute to the next generation. The combined effect of sex bias, inbreeding, fluctuations in population size and, perhaps most important, the variance in reproductive success may explain the low N e /N ratio. In addition, the relatively high gene flow between Irish Sea population and other source populations is likely to have had an impact on our estimate, which may be more relevant at the metapopulation scale. No significant loss of genetic diversity was found over the 40-year timeframe and long-term maintenance of the genetic diversity could be due to gene flow.

Temporally stable genetic structure of heavily exploited Atlantic herring (Clupea harengus) in Swedish waters

“…Similarly, a decrease in genetic diversity was detected in a comparison before and after heavy exploitation of orange roughy (Hoplostethus atlanticus; Smith et al, 1991). In contrast, there was no significant loss of genetic diversity over 40 years and with declining population sizes in the thornback ray (Raja clavata; Chevolot et al, 2008). However, as with our herring data, these samples do not predate major exploitation so genetic diversity may have been lost before sampling.…”

The relationship between abundance and genetic effective population size in elasmobranchs: an example from the globally threatened zebra shark Stegostoma fasciatum within its protected range

“…Ratios approaching unity were generated when combining separate studies of N e and N c for a population of grey nurse sharks (Ahonen et al 2009;Otway and Burke 2004). In contrast, the N e /N c ratio for the thornback ray was orders of magnitude smaller than for other elasmobranchs (10 -3 , Chevolot et al 2008). These disparate findings raise questions about the effects of life history strategies on N e and N c estimates within elasmobranchs as well as potential effects due to population structuring and immigration.…”

“…To date, no other studies have directly compared N e and N c in an elasmobranch species, although comparison of the N e estimates of grey nurse sharks Carcharias taurus with published census information for mature adults results in a ratio of similar magnitude (mean N e = 126, 95 % CI 67-474, Ahonen et al 2009;mean N c = 178, 95 % CI 58-321, Otway and Burke 2004). In contrast, comparison of N e estimates obtained using temporal comparisons (Wang and Whitlock 2003) between samples taken 40 years apart for the thornback ray Raja clavata with very large census sizes of 500,000-3 million adult individuals for this species, resulted in very low N e / N c ratios (between 9 9 10 -5 and 1.8 9 10 -3 , Chevolot et al 2008). The variation in N e /N c ratios among elasmobranch species to date emphasizes the size of the knowledge gap that must be addressed before genetic N e is useful for the conservation of threatened, endangered and protected species.…”

“…The use of ? follows the notation from the publication and indicates inestimable upper confidence limits a Portnoy et al f Chevolot et al (2008) 2013) due to over-fishing will affect N e /N c ratios as changes to N e are likely to lag behind changes in N c depending on the number of generations over which these changes occur, the degree of generational overlap (Palstra and Fraser 2012;Waples et al 2014), and the age composition of the individuals removed from the population. In simulated data with discrete generations, N e estimated using the LD method was able to detect early population declines (Antao et al 2010).…”

“…Few studies have investigated contemporary N e for elasmobranch populations (Ahonen et al 2009;Chapman et al 2011;Chevolot et al 2008;Portnoy et al 2009). Portnoy et al (2009) found that N e estimates generated from microsatellite data in sandbar sharks Carcharhinus plumbeus were similar in magnitude to N c estimates of mature adult sharks with resulting ratios of N e /N c * 0.5-1.…”