First estimates of population size and home range of Caribbean reef and nurse sharks using photo-identification and BRUVS

The assessment of parameters population size and individual home range is important for effective conservation management of sharks. This study uses the novel application of photo identification (photo-ID) to BRUVS footage as a non-invasive alternative to tagging in order to generate individual capture histories. These were used in mark-recapture models to estimate effective population sizes and to determine home ranges. In the Cayman Islands a total of 499 shark sightings of six coastal shark species were recorded on BRUVS from 2015 - 2018, but re-sighting rates were only sufficient for the determination of population parameters for two species - Caribbean reef shark (Carcharhinus perezi) and nurse shark (Ginglymostoma cirratum). The calculated super-population sizes for Caribbean reef shark (180 ± 37 SE) and nurse shark (336 ± 61 SE) were greater than the estimates for each species based on a closed-population model (Caribbean reef shark: 128 ± 40 SE, nurse shark: 249 ± 48 SE), though both measures indicated that there were about twice as many nurse sharks (1.3 - 1.8 sharks/km2) as Caribbean reef sharks (0.7 – 1 shark/km2) within the study area. The demographic compositions included numerous immature individuals, indicating that breeding of both species takes place within the study area of 188 km2. Most recognizable individuals of both species showed linear home ranges of <20 km, but a few individuals were observed to have moved longer distances (Caribbean reef shark: 125.37 km, nurse shark: 156.07 km). The data indicate that the home ranges and long-distance movements of individual sharks observed within the islands’ marine protected areas (MPAs) often extend to areas beyond the MPA’s boundary, potentially exposing them to fishing activities. This study provides the first estimates of population size for Caribbean reef and nurse sharks in the Cayman Islands and the first estimate of a Caribbean reef shark population globally

Genetic Connectivity of a Coral Reef Ecosystem Predator: The Population Genetic Structure and Evolutionary History of the Caribbean Reef Shark (Carcharhinus perezi)

Aim The Caribbean reef shark (Carcharhinus perezi) is one of few extant reef sharks inhabiting the Atlantic Ocean. Its variability in movements across habitat types suggests the possibility of a complex genetic population structure. Here, we use mitochondrial and nuclear DNA to investigate the genetic connectivity of the Caribbean reef shark across contemporary and evolutionary time-scales and relate our findings to the ecology of this understudied species. Location Tropical western Atlantic and Caribbean. Methods Samples were obtained from 216 individuals from six western Atlantic and Caribbean locations. Individuals were genotyped at seven nuclear microsatellite DNA loci and sequenced at two mitochondrial (control region [CR]; NADH dehydrogenase subunit 4 [ND4]) and one nuclear locus (lactate dehydrogenase [LDH]). Analyses to resolve the population genetic structure and evolutionary history of this species were adopted. Results Sequencing of the CR (1,068 bp, n = 216), ND4 (741 bp, n = 213) and LDH (258 bp, n = 165) loci, resolved 11, 8 and 13 unique haplotypes (or alleles), respectively. Overall, Caribbean reef sharks showed low levels of genetic diversity and most marker sets identified strong genetic differences (FSTand ΦST) between sharks sampled in Brazil versus all other locations (msat FST \u3e 0.017; CR-ND4 ΦST \u3e 0.013). Mitochondrial DNA showed evidence of increased genetic partitioning among western North Atlantic sampling sites, although widespread haplotype sharing (~85%–92%) and a shallow population history were found. Main Conclusions Findings of genetic differentiation are concordant with previous movement studies showing residency and/or site-fidelity to specific locations by individuals. However, similar to other reef shark studies, we found that the level of genetic connectivity among populations was context dependent—i.e., sharks occupying isolated habitats showed greater genetic differentiation compared with those sharks occupying semi-isolated or continuous reef habitats. Furthermore, low genetic diversity and a shallow mitochondrial population history were found, suggesting historical demographic fluctuations, including population collapse and more recent expansions

Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers

Phylogeographic inference has provided extensive insight into the relative roles of geographical isolation and ecological processes during evolutionary radiations. However, the importance of cross-lineage admixture in facilitating adaptive radiations is increasingly being recognised, and suggested as a main cause of phylogenetic uncertainty. In this study, we used a double digest RADseq protocol to provide a high resolution (∼ 4 Million bp) nuclear phylogeny of the Delphininae. Phylogenetic resolution of this group has been especially intractable, likely because it has experienced a recent species radiation. We carried out cross-lineage reticulation analyses, and tested for several sources of potential bias in determining phylogenies from genome sampling data. We assessed the divergence time and historical demography of T. truncatus and T. aduncus by sequencing the T. aduncus genome and comparing it with the T. truncatus reference genome. Our results suggest monophyly for the genus Tursiops, with the recently proposed T. australis species falling within the T. aduncus lineage. We also show the presence of extensive cross-lineage gene flow between pelagic and European coastal ecotypes of T. truncatus, as well as in the early stages of diversification between spotted (Stenella frontalis; Stenella attenuata), spinner (Stenella longirostris), striped (Stenella coeruleoalba), common (Delphinus delphis), and Fraser’s (Lagenodelphis hosei) dolphins. Our study suggests that cross-lineage gene flow in this group has been more extensive and complex than previously thought. In the context of biogeography and local habitat dependence, these results improve our understanding of the evolutionary processes determining the history of this lineage

Individual residency behaviours and seasonal long-distance movements in acoustically tagged Caribbean reef sharks in the Cayman Islands

Understanding how reef-associated sharks use coastal waters through their ontogeny is important for their effective conservation and management. This study used the horizontal movements of acoustically tagged Caribbean reef sharks (Carcharhinus perezi) to examine their use of coastal space around the Cayman Islands between 2009 and 2019. A total of 39 (59.1%) tagged sharks (male = 22, female = 17, immature = 18, mature = 21) were detected on the islands wide network of acoustic receivers. The detection data were used to calculate values of Residency Index (RI), Site-Fidelity Index (SFI) and minimum linear displacement (MLD), as well as for network analysis of individual shark movements to test for differences between demographics, seasons, and diel periods. Sharks were detected for up to 1,598 days post-tagging and some individuals showed resident behaviour but the majority of tagged individuals appear to have been one-off or only occasional transient visitors to the area. Generally, individuals showed strong site-fidelity to different areas displaying linear home ranges of &lt; 20 km. The evidence indicates that there was no pattern of diel behaviour. Tagged sharks generally showed increased movements within and between islands during the summer (April-September), which may be related to breeding activity. Some individuals even made occasional excursions across 110 km of open water &gt; 2,000 m deep between Grand Cayman and Little Cayman. One mature female shark showed a displacement of 148.21 km, the greatest distance reported for this species. The data shows that the distances over which some sharks moved, greatly exceeded the extent of any one of the islands' marine protected areas indicating that this species may be more mobile and dispersive than previously thought. This study provides support for the blanket protection to all sharks throughout Cayman waters, which was incorporated within the National Conservation Act in 2015.</p

Individual residency behaviours and seasonal long-distance movements in acoustically tagged Caribbean reef sharks in the Cayman Islands

Understanding how reef-associated sharks use coastal waters through their ontogeny is important for their effective conservation and management. This study used the horizontal movements of acoustically tagged Caribbean reef sharks (Carcharhinus perezi) to examine their use of coastal space around the Cayman Islands between 2009 and 2019. A total of 39 (59.1%) tagged sharks (male = 22, female = 17, immature = 18, mature = 21) were detected on the islands wide network of acoustic receivers. The detection data were used to calculate values of Residency Index (RI), Site-Fidelity Index (SFI) and minimum linear displacement (MLD), as well as for network analysis of individual shark movements to test for differences between demographics, seasons, and diel periods. Sharks were detected for up to 1,598 days post-tagging and some individuals showed resident behaviour but the majority of tagged individuals appear to have been one-off or only occasional transient visitors to the area. Generally, individuals showed strong site-fidelity to different areas displaying linear home ranges of &lt; 20 km. The evidence indicates that there was no pattern of diel behaviour. Tagged sharks generally showed increased movements within and between islands during the summer (April-September), which may be related to breeding activity. Some individuals even made occasional excursions across 110 km of open water &gt; 2,000 m deep between Grand Cayman and Little Cayman. One mature female shark showed a displacement of 148.21 km, the greatest distance reported for this species. The data shows that the distances over which some sharks moved, greatly exceeded the extent of any one of the islands' marine protected areas indicating that this species may be more mobile and dispersive than previously thought. This study provides support for the blanket protection to all sharks throughout Cayman waters, which was incorporated within the National Conservation Act in 2015.</p

Application of Photo-Identification and Lengthened Deployment Periods to Baited Remote Underwater Video Stations (BRUVS) Abundance Estimates of Coral Reef Sharks

Baited Remote Underwater Video Stations (BRUVS) are widely used for monitoring relative abundances of fishes, especially sharks, but only the maximum number of individuals seen at any one time (MaxN) is usually recorded. In both the Cayman Islands and the Amirante Islands, Seychelles, we used photo-ID to recognise individual sharks recorded on BRUVS videos. This revealed that for most species the actual numbers of separate individuals (IndN) visiting the BRUVS were significantly higher than MaxN, with, for example, ratios of IndN to MaxN being 1.17 and 1.24 for Caribbean reef, Carcharhinus perezi, and nurse, Ginglymostoma cirratum, sharks in the Cayman Islands, and 2.46 and 1.37 for blacktip reef, C. melanopterus, and grey reef, C. amblyrhynchos, sharks, respectively, in the Amirantes. Further, for most species, increasing the BRUVS deployment period beyond the 60 min normally used increased the observed IndN, with more than twice as many individuals in the Cayman Islands and &gt;1.4 times as many individuals in the Amirantes being recorded after 120 min as after 60 min. For most species, MaxN and IndN rose exponentially with time, so data from different deployment periods cannot reliably be compared using catch-per-unit-effort (CPUE) calculated as catch-per-unit-time. In both study areas, the time of first arrival of individuals varied with species from &lt;1 min to &gt;2 h. Individually identifiable sharks were re-sighted after up to 429 days over 10 km away in the Cayman Islands and 814 days over 23 km away in the Amirantes, demonstrating that many individuals range over considerable distances. Analysis of Cayman re-sightings data yielded mean population estimates of 76 &plusmn; 23 (SE) and 199 &plusmn; 42 (SE) for C. perezi and G. cirratum, respectively. The results demonstrate that, for sharks, the application of both photo-identification and longer deployment periods to BRUVS can improve the precision of abundance estimates and provide knowledge of population size and ranging behaviour

Use of Photo-Identification and Mark-Recapture Methodology to Assess Basking Shark (Cetorhinus maximus) Populations.

Following centuries of exploitation, basking sharks (Cetorhinus maximus) are considered by IUCN as Endangered in the Northeast Atlantic, where they have now been substantially protected for over two decades. However, the present size of this population remains unknown. We investigated the use of photo-identification of individuals' dorsal fins, combined with mark-recapture methodology, to investigate the size of populations of basking shark within the west coast of Scotland. From a total of 921 encounters photographed between 2004 and 2011, 710 sharks were found to be individually identifiable based on dorsal fin damage and natural features. Of these, only 41 individuals were re-sighted, most commonly both within days of, and close to the site of, the initial encounter. A smaller number were re-sighted after longer periods of up to two years. A comparison of the distinguishing features of individuals on first recording and subsequent re-sighting showed that in almost all cases these features remained little changed, suggesting the low re-sighting rate was not due to a loss of distinguishing features. Because of the low number of re-sighting we were not able to produce reliable estimates for the long-term regional population. However, for one 50 km diameter study area between the islands of Mull, Coll and Tiree, we were able to generate closed-population estimates for 6-9 day periods in 2010 of 985 (95% CI = 494-1683), and in 2011 of 201 (95% CI = 143-340). For the same 2011 period an open-population model generated a similar estimate of 213 (95% CI = 111-317). Otherwise the low rate and temporal patterning of re-sightings support the view that such local basking shark populations are temporary, dynamic groupings of individuals drawn from a much larger regional population than previously supposed. The study demonstrated the feasibility and limitations of photo-identification as a non-invasive technique for identifying individual basking sharks