Rupert A. Collins's research while affiliated with University of Bristol and other places

... Trachurus trachurus (Atlantic horse mackerel)[50][51][52][53].DATA VALIDATION AND QUALITY CONTROLSequencingCLR sequencing (PacBio) generated 3.74 M reads with a total of 58.25 Gbp, which is approximately 93× physical coverage of the genome. The mean and N50 read lengths were 15,591.278 ...

... Current methods for obtaining census data on cartilaginous fish are based on the visual identification of caught individuals, which is invasive and expensive, often speciesselective and dependent on taxonomic expertise (Boussarie et al., 2018). The recent development of environmental DNA (eDNA) offers a powerful, cost-effective, noninvasive alternative (Taberlet et al., 2012;Thomsen et al., 2012), which has been shown to be effective in tracking the presence of cartilaginous fish in various environments (Bakker et al., 2017;Boussarie et al., 2018;West et al., 2021;Dunn et al., 2022;Liu et al., 2022). Spatial models are continuously developed for studying the impact of demersal fisheries, and the spatial origin of catches, using satellite-based information on fishing activities (D'Andrea et al., 2020;Russo et al., 2018Russo et al., , 2019; eDNA could enhance these models, being itself an important source of biological information. ...

... Insights into the spatial distribution of AIS and patterns of secondary spread are essential in devising successful containment strategies (Vimercati et al. 2019;Araya-Donoso et al. 2022;Greenhalgh et al. 2022). However, conventional aquatic species surveillance can be labour-intensive and costly when conducted on vast spatiotemporal scales and when a priori knowledge of occurrence and ecological habitat preferences is unavailable (Mueller et al. 2017;Vimercati et al. 2019;Da Silva Neto et al. 2020). ...

... We first downloaded an accurate and updated list of Mediterranean chondrichthyan species following the steps available at github.com /genner-lab/meta-fish-lib (Collins et al., 2021). The list was then validated according to the recent literature (Serena et al., 2020;F. ...

... Some automation of both approaches has been achieved in field deployable remote automated underwater vehicles and there is significant capacity to improve this further 99 . Living filters such as mussels and other shellfish also concentrate exogenous nucleic acids and may be suitable for monitoring, including some in pre-existing populations, but this concept remains very much in early development 96,100 . ...

... However, we maintained the data for this species in our analysis (Table S2), as the interviewed fishers noticed the difference in the photograph shown and, although they provided information for the related species (filhote , Table S2), they alerted us that the fish shown is not usually found in the Tapajos River. In the Negro River, we included two photographs of the species Myloplus nigrolineatus (pacu galo, Table S1), which has morphological differences between females (Fig. S7a) and males ( Fig. S7b) (Ota et al. 2020, Silvano 2020. Nevertheless, at least half of the interviewed fishers in the Negro River accurately mentioned that these two fish would be f