Genome-wide comparisons reveal a clinal species pattern within a holobenthic octopod-the Australian Southern blue-ringed octopus, Hapalochlaena maculosa (Cephalopoda: Octopodidae)

SNP data reveals the complex and diverse evolutionary history of the blue-ringed octopus genus (Octopodidae: Hapalochlaena) in the Asia-Pacific

The blue-ringed octopus species complex (Hapalochlaena spp.), known to occur from Southern Australia to Japan, currently contains four formally described species (Hapalochlaena maculosa, Hapalochlaena fasciata, Hapalochlaena lunulata and Hapalochlaena nierstraszi). These species are distinguished based on morphological characters (iridescent blue rings and/or lines) along with reproductive strategies. However, the observation of greater morphological diversity than previously captured by the current taxonomic framework indicates that a revision is required. To examine species boundaries within the genus we used mitochondrial (12S rRNA, 16S rRNA, cytochrome c oxidase subunit 1 [COI], cytochrome c oxidase subunit 3 [COIII] and cytochrome b [Cytb]) and genome-wide SNP data (DaRT seq) from specimens collected across its geographic range including variations in depth from 3m to >100m. This investigation indicates substantially greater species diversity present within the genus Hapalochlaena than is currently described. We identified 10,346 SNPs across all locations, which when analysed support a minimum of 11 distinct clades. Bayesian phylogenetic analysis of the mitochondrial COI gene on a more limited sample set dates the diversification of the genus to ∼30mya and corroborates eight of the lineages indicated by the SNP analyses. Furthermore, we demonstrate that the diagnostic lined patterning of H. fasciata found in North Pacific waters and NSW, Australia is polyphyletic and therefore likely the result of convergent evolution. Several "deep water" (> 100m) lineages were also identified in this study with genetic convergence likely to be driven by external selective pressures. Examination of morphological traits, currently being undertaken in a parallel morphological study, is required to describe additional species within the complex.

The development of genome-wide single nucleotide polymorphisms in blue wildebeest using the DArTseq platform

Blue wildebeest (Connochaetes taurinus taurinus) are economically important antelope that are widely utilised in the South African wildlife industry. However, very few genomic resources are available for blue wildebeest that can assist in breeding management and facilitate research. This study aimed to develop a set of genome-wide single nucleotide polymorphism (SNP) markers for blue wildebeest. The DArTseq genotyping platform, commonly used in polyploid plant species, was selected for SNP discovery. A limited number of published articles have described the use of the DArTseq platform in animals and, therefore, this study also provided a unique opportunity to assess the performance of the DArTseq platform in an animal species. A total of 20,563 SNPs, each located within a 69 bp sequence, were generated. The developed SNP markers had a high average scoring reproducibility (>99%) and a low percentage missing data (~9.21%) compared to other reduced representation sequencing approaches that have been used in animal studies. Furthermore, the number of candidate SNPs per nucleotide position decreased towards the 3' end of sequence reads, and the ratio of transitions (Ts) to transversions (Tv) remained similar for each read position. These observations indicate that there was no read position bias, such as the identification of false SNPs due to low sequencing quality, towards the tail-end of sequencing reads. The DArTseq platform was also successful in identifying a large number of informative SNPs with desirable polymorphism parameters such as a high minor allele frequency (MAF). The Bos taurus genome was used for the in silico mapping of the marker sequences and a total of 6020 (29.28%) sequences were successfully mapped against the bovine genome. The marker sequences mapped to all of the bovine chromosomes establishing the genome-wide distribution of the SNPs. Moreover, the high observed Ts:Tv ratio (2.84:1) indicate that the DArTseq platform targeted gene-rich regions of the blue wildebeest genome. Finally, functional annotation of the marker sequences revealed a wide range of different putative functions indicating that these SNP markers can be useful in functional gene studies. The DArTseq platform, therefore, represents a high-throughput, robust and cost-effective genotyping platform, which may find adoption in several other African antelope and animal species.

Deciphering the Evolutionary History of Arowana Fishes (Teleostei, Osteoglossiformes, Osteoglossidae): Insight from Comparative Cytogenomics

Arowanas (Osteoglossinae) are charismatic freshwater fishes with six species and two genera (Osteoglossum and Scleropages) distributed in South America, Asia, and Australia. In an attempt to provide a better assessment of the processes shaping their evolution, we employed a set of cytogenetic and genomic approaches, including i) molecular cytogenetic analyses using C- and CMA₃/DAPI staining, repetitive DNA mapping, comparative genomic hybridization (CGH), and Zoo-FISH, along with ii) the genotypic analyses of single nucleotide polymorphisms (SNPs) generated by diversity array technology sequencing (DArTseq). We observed diploid chromosome numbers of 2n = 56 and 54 in O. bicirrhosum and O. ferreirai, respectively, and 2n = 50 in S. formosus, while S. jardinii and S. leichardti presented 2n = 48 and 44, respectively. A time-calibrated phylogenetic tree revealed that Osteoglossum and Scleropages divergence occurred approximately 50 million years ago (MYA), at the time of the final separation of Australia and South America (with Antarctica). Asian S. formosus and Australian Scleropages diverged about 35.5 MYA, substantially after the latest terrestrial connection between Australia and Southeast Asia through the Indian plate movement. Our combined data provided a comprehensive perspective of the cytogenomic diversity and evolution of arowana species on a timescale.

Tactical Tentacles: New Insights on the Processes of Sexual Selection Among the Cephalopoda

The cephalopods (Mollusca: Cephalopoda) are an exceptional class among the invertebrates, characterised by the advanced development of their conditional learning abilities, long-term memories, capacity for rapid colour change and extremely adaptable hydrostatic skeletons. These traits enable cephalopods to occupy diverse marine ecological niches, become successful predators, employ sophisticated predator avoidance behaviours and have complex intraspecific interactions. Where studied, observations of cephalopod mating systems have revealed detailed insights to the life histories and behavioural ecologies of these animals. The reproductive biology of cephalopods is typified by high levels of both male and female promiscuity, alternative mating tactics, long-term sperm storage prior to spawning, and the capacity for intricate visual displays and/or use of a distinct sensory ecology. This review summarises the current understanding of cephalopod reproductive biology, and where investigated, how both pre-copulatory behaviours and post-copulatory fertilisation patterns can influence the processes of sexual selection. Overall, it is concluded that sperm competition and possibly cryptic female choice are likely to be critical determinants of which individuals' alleles get transferred to subsequent generations in cephalopod mating systems. Additionally, it is emphasised that the optimisation of offspring quality and/or fertilisation bias to genetically compatible males are necessary drivers for the proliferation of polyandry observed among cephalopods, and potential methods for testing these hypotheses are proposed within the conclusion of this review. Further gaps within the current knowledge of how sexual selection operates in this group are also highlighted, in the hopes of prompting new directions for research of the distinctive mating systems in this unique lineage.

Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

BACKGROUND

The scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species.

RESULTS

After stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise FST estimates revealed low differentiation among populations (pairwise FST range = - 0.0008 - 0.0021). Analysis of genetic variation using putatively directional FST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range = 0.0288-0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus.

CONCLUSIONS

Findings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes.