Conservation of A-to-I RNA editing in bowhead whale and pig

RNA editing is a post-transcriptional process in which nucleotide changes are introduced into an RNA sequence, many of which can contribute to proteomic sequence variation. The most common type of RNA editing, contributing to nearly 99% of all editing events in RNA, is A-to-I (adenosine-to-inosine) editing mediated by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. A-to-I editing at ‘recoding’ sites results in non-synonymous substitutions in protein-coding sequences. Here, we present studies of the conservation of A-to-I editing in selected mRNAs between pigs, bowhead whales, humans and two shark species. All examined mRNAs–NEIL1, COG3, GRIA2, FLNA, FLNB, IGFBP7, AZIN1, BLCAP, GLI1, SON, HTR2C and ADAR2 –showed conservation of A-to-I editing of recoding sites. In addition, novel editing sites were identified in NEIL1 and GLI1 in bowhead whales. The A-to-I editing site of human NEIL1 in position 242 was conserved in the bowhead and porcine homologues. A novel editing site was discovered in Tyr244. Differential editing was detected at the two adenosines in the NEIL1 242 codon in both pig and bowhead NEIL1 mRNAs in various tissues and organs. No conservation of editing of KCNB1 and EEF1A mRNAs was seen in bowhead whales. In silico analyses revealed conservation of five adenosines in ADAR2, some of which are subject to A-to-I editing in bowheads and pigs, and conservation of a regulatory sequence in GRIA2 mRNA that is responsible for recognition of the ADAR editing enzyme.

Shark Side of the Moon: Are Shark Attacks Related to Lunar Phase?

Animals across taxa have shown behaviors linked to moon phase (or the proxy of lunar illumination), and marine organisms are well-documented to calibrate certain activities with the moon. Few studies have looked at a possible connection between moon phase and shark attacks on humans, and the results have been preliminary or lacking relationships. We used nearly 50 years of shark attack data from across the globe to test for a relationship between shark attacks and moon phase. We examined factors of geography, shark species, and outcome of attack. From 12 relationships that we tested (totaling 120 comparisons), we found 12 significant outcomes, of which five were positive (i.e., more attacks than expected) and seven were negative (i.e., fewer attacks than expected). Specifically, all the instances of more shark attacks than expected occurred at lunar illumination >50%, while all the instances of fewer shark attacks than expected occurred at lunar illumination of <50%. The findings presented here provide global evidence that shark attacks may be related to moon phase, and such information could be useful toward evaluating attack risk and developing recommendations for water-based recreational activities.

DNA barcoding reveals overlooked shark and bony fish species in landing reports of small-scale fisheries from northern Peru

Species-level identification of commercially landed fish provides pivotal information for stock assessment and fishery management. However, there is a common lack of species determination in landing records from small-scale fisheries (SSFs) worldwide. Using DNA barcoding analyses, we detected four overlooked bony fish (yellow snapper, union snook, blackspot wrasse, and steeplined drum) and one shark species (the sicklefin smooth-hound) in official landing records of SSFs from northern Peru. Of particular concern is the sicklefin smooth-hound shark Mustelus lunulatus that was found to be overlooked and could mistakenly be landed as the humpback smooth-hound M. whitneyi. Increased efforts should be made to improve species identification capacities in Peruvian fishing landings. There is an urgent need to quantify the catch levels of members of the genus Mustelus to species level. This would contribute to a better understanding of the levels of exploitation in each particular species and to improved management decisions.

Dermal denticle diversity in sharks: novel patterns on the interbranchial skin

Shark skin is covered in dermal denticles – tooth-like structures consisting of enameloid, dentine, and a central pulp cavity. Previous studies have demonstrated differences in denticle morphology both among species and across different body regions within a species, including one report of extreme morphological variation within a 1 cm distance on the skin covering the branchial pouches, a region termed “interbranchial skin”. We used gel-based profilometry, histology, and scanning electron microscopy to quantify differences in denticle morphology and surface topography of interbranchial skin denticles among 13 species of sharks to better understand the surface structure of this region. We show that 1) interbranchial skin denticles differ across shark species, and 2) denticles on the leading edge of the skin covering each gill pouch have different morphology and surface topography compared to denticles on the trailing edge. Across all species studied, there were significant differences in denticle length (P = 0.01) and width (P = 0.002), with shorter and wider leading edge denticles compared to trailing edge denticles. Surface skew was also higher in leading edge denticles (P = 0.009), though most values were still negative, indicating more valleys than peaks. Overall, leading edge denticles were smoother-edged than trailing edge denticles in all of the species studied. These data suggest two hypotheses: 1) smoother-edged leading edge denticles protect the previous gill flap from abrasion during respiration, and 2) ridged denticle morphology at the trailing edge might alter water turbulence exiting branchial pouches after passing over the gills. Future studies will focus on determining the relationship between denticle morphology and water flow by visualizing fluid motion over interbranchial denticles during in vivo respiration.

Population genetics of the school shark (Galeorhinus galeus) in New Zealand, Australian and Chilean waters

<p>The school shark (Galeorhinus galeus) is a coastal bentho-pelagic species that is highly migratory and has a widespread distribution in temperate waters. This species matures late, has a relatively low fecundity and is slow growing, which makes it vulnerable to overfishing. They are commercially fished throughout their distribution, and some global stocks have been under pressure because of poor management. In Australia, longline and gillnet fisheries targeted pregnant females and juveniles around Victorian and Tasmanian nursery grounds, resulting in loss of historical inshore nursery habitat. School shark tagging programmes have reported migration between Australian and New Zealand stocks, but preliminary genetic studies have suggested that there are slight genetic differences between the stocks. Currently, the Australian and New Zealand school shark fisheries are assessed and managed as separate stocks. However, the question of whether this species is comprised of a single population or multiple sub-populations in the South Pacific remains unresolved. Given the commercial importance of the school shark fisheries and the concern about stock levels on the regional and trans-Tasman scales, knowledge of stock structure is essential for effective management. The aim of this thesis research was to determine the levels of genetic diversity and population structure of G. galeus in New Zealand and Australia, and compare these to a population in Chile, using mitochondrial DNA (mtDNA) sequencing and microsatellite DNA markers. The DNA sequence of an 893 base pair region of the mtDNA control region (CR) was determined using 475 school shark samples and nine microsatellite DNA loci were genotyped in 239 individuals. Analyses of the data revealed strong evidence of genetic differentiation between G. galeus populations in Australasia and Chile, suggesting restricted gene flow among populations in the western and eastern areas of the Pacific Ocean. The FST values ranged from 0.188 to 0.300 for CR mtDNA, and 0.195 to 0.247 for microsatellite DNA in G. galeus. However, there was no evidence of stock differentiation among New Zealand/Australian sample sites for either mtDNA or microsatellite DNA data. These results support the model of a single panmictic stock across the Tasman Sea. The similarity of the results obtained from the maternally inherited mtDNA and biparental inherited microsatellite loci did not support the suggestion of sex-biased dispersal of G. galeus in the New Zealand/Australia region and it was concluded that females and males had similar patterns of dispersal. Sharks can be either monogamous or polygamous, which is important when considering stock assessments and harvesting models. Multiple paternity has been reported in several shark species, however, the number of sires per litter varies considerably among species. An investigation of multiple paternity (MP) was conducted in G. galeus by assessing the levels of relatedness within progeny arrays using six polymorphic microsatellite DNA markers. Five “families” (mother and litters) were sampled from the North Island of New Zealand and a parentage analysis was conducted. The minimum number of males contributing to each progeny array was estimated by identifying the putative paternal alleles by allele counting and reconstructing multilocus genotypes method. The analysis showed the occurrence of genetic polyandry in G. galeus; two of five litters showing multiple sires involved in the progeny arrays (40%). The minimum number of sires per litter ranged from one to four. Although MP was only detected in two litters, this finding is consistent with the known reproductive characteristics of G. galeus. It can potentially store sperm for long periods of time and has a specific mating season when males and females typically mix on the edge of the continental shelf. Detecting MP within a litter has highlighted the importance of the post-copulatory selective processes in the G. galeus mating system, and this has implications for the management and conservation of genetic diversity.</p>

Population genetics of the school shark (Galeorhinus galeus) in New Zealand, Australian and Chilean waters

<p>The school shark (Galeorhinus galeus) is a coastal bentho-pelagic species that is highly migratory and has a widespread distribution in temperate waters. This species matures late, has a relatively low fecundity and is slow growing, which makes it vulnerable to overfishing. They are commercially fished throughout their distribution, and some global stocks have been under pressure because of poor management. In Australia, longline and gillnet fisheries targeted pregnant females and juveniles around Victorian and Tasmanian nursery grounds, resulting in loss of historical inshore nursery habitat. School shark tagging programmes have reported migration between Australian and New Zealand stocks, but preliminary genetic studies have suggested that there are slight genetic differences between the stocks. Currently, the Australian and New Zealand school shark fisheries are assessed and managed as separate stocks. However, the question of whether this species is comprised of a single population or multiple sub-populations in the South Pacific remains unresolved. Given the commercial importance of the school shark fisheries and the concern about stock levels on the regional and trans-Tasman scales, knowledge of stock structure is essential for effective management. The aim of this thesis research was to determine the levels of genetic diversity and population structure of G. galeus in New Zealand and Australia, and compare these to a population in Chile, using mitochondrial DNA (mtDNA) sequencing and microsatellite DNA markers. The DNA sequence of an 893 base pair region of the mtDNA control region (CR) was determined using 475 school shark samples and nine microsatellite DNA loci were genotyped in 239 individuals. Analyses of the data revealed strong evidence of genetic differentiation between G. galeus populations in Australasia and Chile, suggesting restricted gene flow among populations in the western and eastern areas of the Pacific Ocean. The FST values ranged from 0.188 to 0.300 for CR mtDNA, and 0.195 to 0.247 for microsatellite DNA in G. galeus. However, there was no evidence of stock differentiation among New Zealand/Australian sample sites for either mtDNA or microsatellite DNA data. These results support the model of a single panmictic stock across the Tasman Sea. The similarity of the results obtained from the maternally inherited mtDNA and biparental inherited microsatellite loci did not support the suggestion of sex-biased dispersal of G. galeus in the New Zealand/Australia region and it was concluded that females and males had similar patterns of dispersal. Sharks can be either monogamous or polygamous, which is important when considering stock assessments and harvesting models. Multiple paternity has been reported in several shark species, however, the number of sires per litter varies considerably among species. An investigation of multiple paternity (MP) was conducted in G. galeus by assessing the levels of relatedness within progeny arrays using six polymorphic microsatellite DNA markers. Five “families” (mother and litters) were sampled from the North Island of New Zealand and a parentage analysis was conducted. The minimum number of males contributing to each progeny array was estimated by identifying the putative paternal alleles by allele counting and reconstructing multilocus genotypes method. The analysis showed the occurrence of genetic polyandry in G. galeus; two of five litters showing multiple sires involved in the progeny arrays (40%). The minimum number of sires per litter ranged from one to four. Although MP was only detected in two litters, this finding is consistent with the known reproductive characteristics of G. galeus. It can potentially store sperm for long periods of time and has a specific mating season when males and females typically mix on the edge of the continental shelf. Detecting MP within a litter has highlighted the importance of the post-copulatory selective processes in the G. galeus mating system, and this has implications for the management and conservation of genetic diversity.</p>

The ichnospecies Linichnus bromleyi on a Miocene baleen whale radius preserving multiple shark bite-shake traces suggests scavenging

An isolated Miocene baleen whale left radius was marked repeatedly by shark bite-shake traces. The radius probably derives from the Plum Point Member of the Calvert Formation, Calvert Cliffs, Calvert County, Maryland, U.S.A. At least three successive bite-shake traces, made by multiple teeth, marking the radius are attributed to the trace fossil Linichnus bromleyi. These bite-shake trace consisting of shallow, thin arching gouges on a radius, likely indicates scavenging rather than active predation. The most likely means of producing the bundle of L. bromleyi within each of the three sets of traces would be through repeated biting as the shark re-positioned the prey in its mouth or, perhaps, by a shark species with multiple functional teeth within its tooth row. If the bite traces were produced by a non-serrated tooth (as they appear to have been), then the most likely candidate would be Carcharodon hastalis.

Global shifts in species richness have shaped carpet shark evolution

Background The evolutionary processes that shape patterns of species richness in marine ecosystems are complex and may differ between organismal groups. There has been considerable interest in understanding the evolutionary processes that led to marine species richness being concentrated in specific geographical locations. In this study we focus on the evolutionary history of a group of small-to-medium sized sharks known as carpet sharks. While a few carpet shark species are widespread, the majority of carpet shark species richness is contained within a biodiversity hotspot at the boundary of the Indian and Pacific oceans. We address the significance of this biodiversity hotspot in carpet shark evolution and speciation by leveraging a rich fossil record and molecular phylogenetics to examine the prehistoric distribution of carpet sharks. Results We find that carpet sharks species richness was greatest in shallow seas connected to the Atlantic Ocean during the Late Cretaceous, but that there was a subsequent loss of biodiversity in Atlantic waters. Fossil evidence from sites in close geographic proximity to the current center of carpet shark diversity are generally restricted to younger geologic strata. Conclusions From this data we conclude that (1) center of carpet shark biodiversity has shifted during the last 100 million years, (2) carpet sharks have repeatedly dispersed to nascent habitat (including to their current center of diversity), and (3) the current center of carpet shark biodiversity conserves lineages that have been extirpated from this prehistoric range and is a source of new carpet shark species. Our findings provide insights into the roles of marine biodiversity hotspots for higher-tropic level predators and the methods applied here can be used for additional studies of shark evolution.

A “Wicked Problem” Reconciling Human-Shark Conflict, Shark Bite Mitigation, and Threatened Species

Conservation measures often result in a “wicked problem,” i.e., a complex problem with conflicting aims and no clear or straightforward resolution without severe adverse effects on one or more parties. Here we discuss a novel approach to an ongoing problem, in which actions to reduce risk to humans, involve lethal control of otherwise protected species. To protect water users, nets are often used to catch potentially dangerous sharks at popular bathing beaches, yet in Australian waters one of the targeted species, the white shark (Carcharodon carcharias) is listed as Vulnerable, while bycatch includes the Critically Endangered grey nurse shark (Carcharias taurus). Recent, highly publicised, shark attacks have triggered demands for improved bather protection, whilst welfare and conservation organisations have called for removal of lethal measures. This leaves management and policy makers with a wicked problem: removing nets to reduce impacts on threatened species may increase risk to humans; or leaving the program as it is on the premise that the benefits provided by bather protection are greater than the impact on threatened and protected species. We used multivariate analysis and generalised additive models to investigate the biological, spatial-temporal, and environmental patterns influencing catch rates of threatened and of potentially dangerous shark species in the New South Wales shark nets over two decades to April 2019. Factors influencing catches were used to develop a matrix of potential changes to reduce catch of threatened species. Our proposed solutions include replacing existing nets with alternative mitigation strategies at key beaches where catch rate of threatened species is high. This approach provides stakeholders with a hierarchy of scenarios that address both social demands and threatened species conservation and is broadly applicable to human-wildlife conflict scenarios elsewhere.