Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis)

Population genomic and biophysical modeling show different patterns of population connectivity in the spiny lobster Jasus frontalis inhabiting oceanic islands

Knowledge about connectivity between populations is essential for the fisheries management of commercial species. The lobster Jasus frontalis inhabits two oceanic island groups, the Juan Fernández Archipelago and the Desventuradas Islands, separated by 800 km. Since this species is primarily exploited in the Juan Fernández Archipelago, knowledge of the connectivity patterns among islands is foundational for species management. Here, we used variability at single-nucleotide polymorphisms (SNPs) and individual-based modeling (IBM) to estimate the genetic structure and connectivity between J. frontalis populations in these island groups. The variability at 9090 SNPs suggests two genetic populations, one in the Juan Fernández Archipelago and one in the Desventuradas Islands. Furthermore, IBM suggests an asymmetric connectivity pattern, with particles moving from the Juan Fernández Archipelago to the Desventuradas Islands but not vice versa. Since the IBM analysis suggests asymmetric larval movement between the islands, and the genetic analysis indicates isolation between the Juan Fernández Archipelago and the Desventuradas Islands, larval retention mechanisms such as small-scale oceanographic processes or behavior could hinder larval movement between islands. This study highlights the importance of using more than one methodology to estimate population connectivity.

Genetic stock structure of the silky shark Carcharhinus falciformis in the Indo-Pacific Ocean

The silky shark, Carcharhinus falciformis, is a cosmopolitan species commonly caught as a bycatch for longline fisheries. However, the genetic stock structure for the Indo-Pacific Ocean is not well-defined yet. Here, we used eight microsatellite loci to examine the genetic stock structure and effective population size of 307 silky sharks across 5 Indo-Pacific sampling locations. A major genetic break was found between Aceh and the remaining locations (FST = 0.0505-0.0828, p = 0.001). The Indian Ocean displayed a slightly lower effective population estimate (Ne) compared to the Pacific Ocean, potentially due to the higher fishing pressure in the Indian Ocean region. The lowest Ne was found in the Aceh population (Ne = 2.3), suggesting it might be a small and endemic population. These findings offer valuable information for the conservation and management of the silky shark. We suggest that the population around Aceh waters constitutes a distinct stock and should be managed independently. Further investigations into migratory and movement patterns are needed to define the boundaries of different stocks, ensuring effective management the silky shark across the Indo-Pacific region.

Phylogeography of sharks and rays: a global review based on life history traits and biogeographic partitions

Considerable research exists on the life history traits, evolutionary history, and environmental factors that shape the population genetic structure of marine organisms, including sharks and rays. Conservation concerns are particularly strong for this group as they are highly susceptible to anthropogenic stressors due to a combination of life history traits including late maturity and low fecundity. Here, we provide a review and synthesis of the global phylogeography of sharks and rays. We examined existing data for 40 species of sharks belonging to 17 genera and 19 species of rays belonging to 11 genera. Median joining haplotype networks were constructed for each species for the mtDNA cytochrome C oxidase subunit I (COI), and an Analysis of Molecular Variance (AMOVA) was conducted to understand patterns of genetic diversity and structure across the three major ocean basins-the Indian, Atlantic and Pacific Oceans. Haplotype networks showed very shallow coalescence in most species, a finding previously reported for marine teleosts. Star topologies were predominant among sharks while complex mutational topologies predominated among rays, a finding we attribute to extremely limited dispersal in the early life history of rays. Population structuring varied amongst species groups, apparently due to differences in life history traits including reproductive philopatry, site fidelity, pelagic habitat, migratory habits, and dispersal ability. In comparison to reef-associated and demersal species, pelagic and semi pelagic species showed lower levels of structure between and within ocean basins. As expected, there is variation between taxa and groups, but there are also some broad patterns that can guide management and conservation strategies.

Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales

Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.

Population structure and genetic connectivity of the scalloped hammerhead shark (Sphyrna lewini) across nursery grounds from the Eastern Tropical Pacific: Implications for management and conservation

Defining demographically independent units and understanding patterns of gene flow between them is essential for managing and conserving exploited populations. The critically endangered scalloped hammerhead shark, Sphyrna lewini, is a coastal semi-oceanic species found worldwide in tropical and subtropical waters. Pregnant females give birth in shallow coastal estuarine habitats that serve as nursery grounds for neonates and small juveniles, whereas adults move offshore and become highly migratory. We evaluated the population structure and connectivity of S. lewini in coastal areas and one oceanic island (Cocos Island) across the Eastern Tropical Pacific (ETP) using both sequences of the mitochondrial DNA control region (mtCR) and 9 nuclear-encoded microsatellite loci. The mtCR defined two genetically discrete groups: one in the Mexican Pacific and another one in the central-southern Eastern Tropical Pacific (Guatemala, Costa Rica, Panama, and Colombia). Overall, the mtCR data showed low levels of haplotype diversity ranging from 0.000 to 0.608, while nucleotide diversity ranged from 0.000 to 0.0015. More fine-grade population structure was detected using microsatellite loci where Guatemala, Costa Rica, and Panama differed significantly. Relatedness analysis revealed that individuals within nursery areas were more closely related than expected by chance, suggesting that S. lewini may exhibit reproductive philopatric behaviour within the ETP. Findings of at least two different management units, and evidence of philopatric behaviour call for intensive conservation actions for this highly threatened species in the ETP.

Genomic Stock Structure of the Marine Teleost Tarakihi (Nemadactylus macropterus) Provides Evidence of Potential Fine-Scale Adaptation and a Temperature-Associated Cline Amid Panmixia

Tarakihi (Nemadactylus macropterus) is an important fishery species with widespread distribution around New Zealand and off the southern coasts of Australia. However, little is known about whether the populations are locally adapted or genetically structured. To address this, we conducted whole-genome resequencing of 175 tarakihi from around New Zealand and Tasmania (Australia) to obtain a dataset of 7.5 million genome-wide and high-quality single nucleotide polymorphisms (SNPs). Variant filtering, FST-outlier analysis, and redundancy analysis (RDA) were used to evaluate population structure, adaptive structure, and locus-environment associations. A weak but significant level of neutral genetic differentiation was found between tarakihi from New Zealand and Tasmania (FST = 0.0054–0.0073, P ≤ 0.05), supporting the existence of at least two separate reproductive stocks. No clustering was detected among the New Zealand populations (ΦST < 0.001, P = 0.77). Outlier-based, presumably adaptive variation suggests fine-scale adaptive structure between locations around central New Zealand off the east (Wairarapa, Cape Campbell, and Hawke’s Bay) and the west coast (Tasman Bay/Golden Bay and Upper West Coast of South Island). Allele frequencies from 55 loci were associated with at least one of six environmental variables, of which 47 correlated strongly with yearly mean water temperature. Although genes associated with these loci are linked to various functions, the most common functions were integral components of membrane and cilium assembly. Projection of the RDA indicates the existence of a latitudinal temperature cline. Our work provides the first genomic insights supporting panmixia of tarakihi in New Zealand and evidence of a genomic cline that appears to be driven by the temperature gradients, together providing crucial information to inform the stock assessment of this species, and to widen the insights of the ecological drivers of adaptive variation in a marine species.

Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis

Background

Whole mitochondrial genomes are quickly becoming markers of choice for the exploration of within-species genealogical and among-species phylogenetic relationships. Most often, ‘primer walking’ or ‘long PCR’ strategies plus Sanger sequencing or low-pass whole genome sequencing using Illumina short reads are used for the assembling of mitochondrial chromosomes. In this study, we first confirmed that mitochondrial genomes can be sequenced from long reads using nanopore sequencing data exclusively. Next, we examined the accuracy of the long-reads assembled mitochondrial chromosomes when comparing them to a ‘gold’ standard reference mitochondrial chromosome assembled using Illumina short-reads sequencing.

Results

Using a specialized bioinformatics tool, we first produced a short-reads mitochondrial genome assembly for the silky shark C. falciformis with an average base coverage of 9.8x. The complete mitochondrial genome of C. falciformis was 16,705 bp in length and 934 bp shorter than a previously assembled genome (17,639 bp in length) that used bioinformatics tools not specialized for the assembly of mitochondrial chromosomes. Next, low-pass whole genome sequencing using a MinION ONT pocket-sized platform plus customized de-novo and reference-based workflows assembled and circularized a highly accurate mitochondrial genome in the silky shark Carcharhinus falciformis. Indels at the flanks of homopolymer regions explained most of the dissimilarities observed between the ‘gold’ standard reference mitochondrial genome (assembled using Illumina short reads) and each of the long-reads mitochondrial genome assemblies. Although not completely accurate, mitophylogenomics and barcoding analyses (using entire mitogenomes and the D-Loop/Control Region, respectively) suggest that long-reads assembled mitochondrial genomes are reliable for identifying a sequenced individual, such as C. falciformis, and separating the same individual from others belonging to closely related congeneric species.

Conclusions

This study confirms that mitochondrial genomes can be sequenced from long-reads nanopore sequencing data exclusively. With further development, nanopore technology can be used to quickly test in situ mislabeling in the shark fin fishing industry and thus, improve surveillance protocols, law enforcement, and the regulation of this fishery. This study will also assist with the transferring of high-throughput sequencing technology to middle- and low-income countries so that international scientists can explore population genomics in sharks using inclusive research strategies. Lastly, we recommend assembling mitochondrial genomes using specialized assemblers instead of other assemblers developed for bacterial and/or nuclear genomes.

Genomic insights into the historical and contemporary demographics of the grey reef shark

Analyses of genetic diversity can shed light on both the origins of biodiversity hotspots, as well as the conservation status of species that are impacted by human activities. With these objectives, we assembled a genomic dataset of 14,935 single nucleotide polymorphisms from 513 grey reef sharks (Carcharhinus amblyrhynchos) sampled across 17 locations in the tropical Indo-Pacific. We analysed geographic variation in genetic diversity, estimated ancient and contemporary effective population size (N_e) across sampling locations (using coalescent and linkage disequilibrium methods) and modelled the history of gene flow between the Coral Triangle and the Coral Sea. Genetic diversity decreased with distance away from the Coral Triangle and north-western Australia, implying that C. amblyrhynchos may have originated in this region. Increases in N_e were detected across almost all sampling locations 40,000-90,000 generations ago (approximately 0.6-1.5 mya, given an estimated generation time of 16.4 years), suggesting a range expansion around this time. More recent, secondary increases in N_e were inferred for the Misool and North Great Barrier Reef sampling locations, but joint modelling did not clarify whether these were due to population growth, migration, or both. Despite the greater genetic diversity and ancient N_e observed at sites around Australia and the Coral Triangle, remote reefs around north-western New Caledonia had the highest contemporary N_e, demonstrating the importance of using multiple population size assessment methods. This study provides insight into both the past and present demographics of C. amblyrhynchos and contributes to our understanding of evolution in marine biodiversity hotspots.

A mitochondrial genome assembly of the opal chimaera, Chimaera opalescens Luchetti, Iglésias et Sellos 2011, using PacBio HiFi long reads

Chondrichthyans (sharks, rays and chimeras) are a fascinating and highly vulnerable group of early branching gnathostomes. However, they remain comparatively poorly sampled from the point of view of molecular resources, with deep water taxa being particularly data deficient. The development of long-read sequencing technologies enables the analysis of phylogenetic relationships through a precise and reliable assembly of complete mtDNA genomes. The sequencing and characterization of the complete mitogenome of the opal chimera Chimera opalescens Luchetti, Iglésias et Sellos 2011, using the long-read technique PacBio HiFi is presented. The entire mitogenome was 23,411 bp long and shows the same overall content, i.e. 13 protein-coding genes, 22 transfer RNA and 2 ribosomal RNA genes, as all other examined Chondrichthyan mitogenomes. Phylogenetic reconstructions using all available Chondrichthyan mitogenomes, including 11 Holocephali (chimeras and ratfishes), places C. opalescens within the Chimaeridae family. Furthermore, the results reinforce previous findings, showing the genus Chimera as paraphyletic and thus highlighting the need to expand molecular approaches in this group of cartilaginous fishes.

Genomic assessment of global population structure in a highly migratory and habitat versatile apex predator, the tiger shark (Galeocerdo cuvier)

Understanding the population dynamics of highly mobile, widely distributed, oceanic sharks, many of which are overexploited, is necessary to aid their conservation management. We investigated the global population genomics of tiger sharks (Galeocerdo cuvier), a circumglobally distributed, apex predator displaying remarkable behavioral versatility in its diet, habitat use (near coastal, coral reef, pelagic), and individual movement patterns (spatially resident to long-distance migrations). We genotyped 242 tiger sharks from 10 globally distributed locations at more than 2000 single nucleotide polymorphisms. Although this species often conducts massive distance migrations, the data show strong genetic differentiation at both neutral (FST=0.125-0.144) and candidate outlier loci (FST=0.570-0.761) between western Atlantic and Indo-Pacific sharks, suggesting the potential for adaptation to the environments specific to these oceanic regions. Within these regions, there was mixed support for population differentiation between northern and southern hemispheres in the western Atlantic, and none for structure within the Indian Ocean. Notably, the results demonstrate a low level of population differentiation of tiger sharks from the remote Hawaiian archipelago compared to sharks from the Indian Ocean (FST=0.003-0.005, P<0.01). Given concerns about biodiversity loss and marine ecosystem impacts caused by overfishing of oceanic sharks in the midst of rapid environmental change, our results suggest it imperative that international fishery management prioritize conservation of the evolutionary potential of the highly genetically differentiated Atlantic and Indo-Pacific populations of this unique apex predator. Furthermore, we suggest targeted management attention to tiger sharks in the Hawaiian archipelago based on a precautionary biodiversity conservation perspective.

Genomic divergence and differential gene expression between crustacean ecotypes across a marine thermal gradient

Environmental gradients between marine biogeographical provinces separate distinct faunal communities. However, the absence of absolute dispersal barriers allows numerous species to occur on both sides of such boundaries. While the regional populations of such widespread species are often morphologically indistinguishable from each other, genetic evidence suggests that they represent unique ecotypes, and likely even cryptic species, that may be uniquely adapted to their local environment. Here, we explored genomic divergence in four sympatric southern African decapod crustaceans whose ranges span the boundary between the cool-temperate west coast (south-eastern Atlantic) and the warm-temperate south coast (south-western Indian Ocean) near the southern tip of the African continent. Using genome-wide data, we found that all four species comprise distinct west coast and south coast ecotypes, with molecular dating suggesting divergence during the Pleistocene. Transcriptomic data from the hepatopancreas of twelve specimens of one of these species, the mudprawn Upogebia africana, which were exposed to either 10 °C or 20 °C, showed a clear difference in gene expression profiles between the west- and south coast ecotypes. This difference was particularly clear at 10 °C, where individuals from the south coast experienced a 'transcriptomic shock'. This low temperature is more typical of the west coast during upwelling events, and the physiological stress experienced by the south coast ecotype under such conditions may explain its absence from that coastline. Our results shed new light on the processes involved in driving genomic divergence and incipient speciation along coastlines with porous dispersal barriers.